Index

A

A() (PYME.localization.FitFactories.Gauss3DFitR.GaussFitResult method) (PYME.localization.FitFactories.LatPSFFitR.PSFFitResult method) A0 (PYME.DSView.modules.blobMeasure.DataBlock property) A1 (PYME.DSView.modules.blobMeasure.DataBlock property) A2 (PYME.DSView.modules.blobMeasure.DataBlock property) aberations (PYME.DSView.modules.psfGeneration.PupilGenerator attribute) abort() (PYME.IO.Spooler.Spooler method) abs_tolerance (PYME.recipes.base.IsClose attribute) acquire_focus_lock() (PYME.Acquire.stage_leveling.StageLeveler method) AcquireClient (class in PYME.Acquire.acquire_client) AcquireHTTPServer (class in PYME.Acquire.acquire_server) Action (class in PYME.Acquire.actions) action_from_dict() (in module PYME.Acquire.actions) ACTION_POSITION (PYME.DSView.displayOptions.DisplayOpts attribute) ACTION_SELECT_OBJECT (PYME.DSView.displayOptions.DisplayOpts attribute) ACTION_SELECTION (PYME.DSView.displayOptions.DisplayOpts attribute) action_server_url (PYME.recipes.acquisition.QueueAcquisitions attribute) ActionList (class in PYME.Acquire.ui.actionUI) ActionManager (class in PYME.Acquire.ActionManager) ActionManagerServer (class in PYME.Acquire.ActionManager) ActionManagerWebWrapper (class in PYME.Acquire.ActionManager) ActionPanel (class in PYME.Acquire.ui.actionUI) actions (PYME.Acquire.htsms.tweeter.LazyScopeTweeter property) activate() (PYME.DSView.eventLogViewer.eventLogPanel method) (PYME.DSView.eventLogViewer.eventLogTPanel method) active (PYME.ui.manualFoldPanel.CaptionButton property) activeRecipe (PYME.recipes.recipeGui.PipelineRecipeManager property) adapt_numarray() (in module PYME.IO.FileUtils.thumbnailDatabase) (in module PYME.misc.sqlitendarray) Add (class in PYME.recipes.base) add() (PYME.DSView.modules.annotation.AnnotationList method) add_96wp_positions() (PYME.Acquire.stage_leveling.StageLeveler method) add_common_menu_items() (PYME.ui.AUIFrame.AUIFrame method) add_curve() (PYME.DSView.modules.annotation.AnnotationList method) add_curved_line() (PYME.DSView.modules.annotation.AnnotateBase method) add_endpoints() (in module PYME.Acquire.webui) (PYME.util.webframework.APIHTTPServer method) add_filled_polygon() (PYME.DSView.modules.annotation.AnnotateBase method) add_grid() (PYME.Acquire.stage_leveling.StageLeveler method) add_ibidi8wellslide_positions() (PYME.Acquire.stage_leveling.StageLeveler method) add_integer_id_rule() (PYME.cluster.ruleserver.RuleServer method) add_layer() (PYME.LMVis.layer_panel.LayerPane method) (PYME.LMVis.visCore.VisGUICore method) add_line() (PYME.DSView.modules.annotation.AnnotationList method) add_menu_item() (PYME.LMVis.Extras.dockedPanel.DockedPanel static method) add_mesh_layer() (PYME.LMVis.visCore.VisGUICore method) add_module() (PYME.recipes.recipe.Recipe method) add_modules_and_execute() (PYME.recipes.recipe.Recipe method) add_octree_layer() (in module PYME.LMVis.Extras.extra_layers) add_overlay() (PYME.DSView.arrayViewPanel.ArrayViewPanel method) add_pointcloud_layer() (PYME.LMVis.visCore.VisGUICore method) add_polygon() (PYME.DSView.modules.annotation.AnnotationList method) add_position() (PYME.Acquire.stage_leveling.StageLeveler method) add_quiver_layer() (PYME.LMVis.visCore.VisGUICore method) add_rectangle() (PYME.DSView.modules.annotation.AnnotationList method) add_roi (PYME.tileviewer.tileviewer.TileServer attribute) add_service() (PYME.misc.pyme_zeroconf.ZCListener method) add_shader() (PYME.LMVis.shader_programs.shader_program.ShaderProgram method) add_shortcut() (PYME.LMVis.Extras.showShortcuts.ShowShortcuts method) add_snapshot() (PYME.LMVis.Extras.animation.VideoPanel method) add_snapshot_to_list() (PYME.LMVis.Extras.animation.VideoPanel method) add_static_handler() (PYME.util.webframework.APIHTTPServer method) add_tesselation() (in module PYME.LMVis.Extras.extra_layers) add_tesselation_layer() (in module PYME.LMVis.Extras.extra_layers) add_tile() (PYME.Acquire.htsms.rule_ui.ChainedAnalysisPage method) add_tweet_condition() (PYME.Acquire.htsms.tweeter.LazyScopeTweeter method) add_user() (in module PYME.util.authenticate) AddAqTool() (PYME.Acquire.acquiremainframe.PYMEMainFrame method) (PYME.Acquire.acquirewx.PYMEMainFrame method) AddCamTool() (PYME.Acquire.acquiremainframe.PYMEMainFrame method) (PYME.Acquire.acquirewx.PYMEMainFrame method) addChild() (PYME.cluster.webdav.Tag method) addColumn() (PYME.IO.tabular.DictSource method) (PYME.IO.tabular.MappingFilter method) (PYME.LMVis.pipeline.Pipeline method) addDataSource() (PYME.LMVis.pipeline.Pipeline method) addEdges() (in module PYME.Analysis.points.EdgeDB.edgeDB) AddElement() (PYME.ui.autoFoldPanel.foldingPane method) (PYME.ui.manualFoldPanel.foldingPane method) addEntries() (in module PYME.misc.tempDB) (PYME.ui.MetadataTree.MetadataPanel method) addEntry() (in module PYME.misc.tempDB) addEvents() (PYME.IO.h5rFile.H5RFile method) AddExtrasMenuItem() (PYME.DSView.modules.LMDisplay.LMDisplay method) (PYME.LMVis.VisGUI.VisGUIFrame method) addFrame() (PYME.IO.buffers.bgFrameBuffer method) (PYME.IO.buffers.bgFrameBufferC method) (PYME.IO.DataSources.BGSDataSource.bgFrameBuffer method) additionalDims (PYME.IO.DataSources.BaseDataSource.XYTCDataSource attribute) (PYME.IO.DataSources.BGSDataSource.XTZCBackgroundSource property) AddMeasurementsByLabel (class in PYME.recipes.localisations) AddMenuItem() (PYME.LMVis.visCore.VisGUICore method) (PYME.ui.AUIFrame.AUIFrame method) AddMetadataToMeasurements (class in PYME.recipes.measurement) AddNewElement() (PYME.ui.autoFoldPanel.foldingPane method) (PYME.ui.manualFoldPanel.foldingPane method) AddPage() (PYME.ui.AUIFrame.AUIFrame method) AddPane() (PYME.ui.autoFoldPanel.foldPanel method) (PYME.ui.manualFoldPanel.foldPanel method) AddRecord() (PYME.Analysis.processLogger.BackendBase method) (PYME.Analysis.processLogger.ContextLayer method) (PYME.Analysis.processLogger.ContextManager method) (PYME.Analysis.processLogger.TablesBackend method) address (PYME.misc.sqlite_ns.NSInfo property) AddSlice() (PYME.IO.FileUtils.saveTiffStack.TiffMP method) AddSphericalHarmonicShellMappedCoords (class in PYME.recipes.surface_fitting) AddTool() (PYME.Acquire.acquiremainframe.PYMEMainFrame method) (PYME.Acquire.acquirewx.PYMEMainFrame method) addVariable() (PYME.IO.tabular.MappingFilter method) AddVoxelSizeSetting() (PYME.Acquire.microscope.microscope method) advert (PYME.cluster.ruleserver.IntegerIDRule property) af() (PYME.Acquire.autofocus.AutoFocus method) afterPopupMenu() (PYME.contrib.listctrlMixins.ListCtrlSelectionManagerMix method) Afunc() (PYME.Analysis.PSFEst.dec.dec_psf method) (PYME.Deconv.dec.ClassicMappingFFTW method) (PYME.Deconv.dec.ClassicMappingNP method) (PYME.Deconv.dec.dec_4pi method) (PYME.Deconv.dec.dec_4pi_c method) (PYME.Deconv.dec.DeconvMappingBase method) (PYME.Deconv.dec.SpatialConvolutionMapping method) age (PYME.recipes.html_recipe_editor.Person attribute) aggregate_dirlisting() (in module PYME.IO.clusterListing) aggregateMean() (in module PYME.Analysis.points.DeClump.deClump) AggregateMeasurements (class in PYME.recipes.tablefilters) aggregateMin() (in module PYME.Analysis.points.DeClump.deClump) aggregateSum() (in module PYME.Analysis.points.DeClump.deClump) aggregateWeightedMean() (in module PYME.Analysis.points.DeClump.deClump) Ahfunc() (PYME.Analysis.PSFEst.dec.dec_psf method) (PYME.Deconv.dec.ClassicMappingFFTW method) (PYME.Deconv.dec.ClassicMappingNP method) (PYME.Deconv.dec.dec_4pi method) (PYME.Deconv.dec.dec_4pi_c method) (PYME.Deconv.dec.DeconvMappingBase method) (PYME.Deconv.dec.SpatialConvolutionMapping method) alignment_threshold (PYME.recipes.surface_fitting.FitSurfaceWithPatches attribute) all (PYME.Analysis.Tracking.trackUtils.ClumpManager property) (PYME.Analysis.Tracking.trackUtils.TrackManager property) all_props (PYME.cluster.webdav.DAVRequestHandler attribute) allmodules() (in module PYME.DSView.modules) alpha (PYME.LMVis.layers.image_layer.ImageRenderLayer attribute) (PYME.LMVis.layers.mesh.TriangleRenderLayer attribute) (PYME.LMVis.layers.pointcloud.PointCloudRenderLayer attribute) (PYME.LMVis.layers.tracks.TrackRenderLayer attribute) (PYME.LMVis.pointSettingsPanel.PointDisplaySettings attribute) (PYME.LMVis.view_clipping_pane.PointDisplaySettings attribute)

analysis_refresh_bruteforce() (PYME.DSView.modules.LMAnalysis.LMAnalyser2 method) AnalysisController (class in PYME.DSView.modules.LMAnalysis) AnalysisDetailsPanel (class in PYME.Acquire.ui.AnalysisSettingsUI) AnalysisSettings (class in PYME.Acquire.ui.AnalysisSettingsUI) AnalysisSettingsPanel (class in PYME.Acquire.ui.AnalysisSettingsUI) AnalysisSettingsView (class in PYME.DSView.modules.LMAnalysis) angHist() (in module PYME.Analysis.angleFilter) angHist2() (in module PYME.Analysis.angleFilter) angle_filter() (in module PYME.Analysis.angleFilter) angle_filter_m() (in module PYME.Analysis.angleFilter) angularDist() (PYME.DSView.modules.blobMeasure.BlobObject method) aniso() (in module PYME.misc.aniso) anisodiff() (in module PYME.contrib.aniso.aniso) anisodiff3() (in module PYME.contrib.aniso.aniso) AnndataSource (class in PYME.IO.tabular) annealThresh() (in module PYME.Analysis.annealThresh) annealThresh2() (in module PYME.Analysis.annealThresh) annealThresh2D() (in module PYME.Analysis.annealThresh) AnnotateBase (class in PYME.DSView.modules.annotation) AnnotatePoints (class in PYME.recipes.machine_learning) Annotater (class in PYME.DSView.modules.annotation) AnnotationList (class in PYME.DSView.modules.annotation) AnnotationOverlayLayer (class in PYME.LMVis.Extras.annotation) Annotator (class in PYME.LMVis.Extras.annotation) APIHTTPServer (class in PYME.util.webframework) apodization (PYME.DSView.modules.pupilTools.PupilTools attribute) (PYME.recipes.simulation.TheoreticalPSF attribute) append() (PYME.DSView.displayOptions.MyWeakSet method) Append() (PYME.DSView.modules.composite.ImageList method) append_original_locs (PYME.recipes.pointcloud.DelaunayCircumcentres attribute) appendToTable() (PYME.IO.h5rFile.H5RFile method) apply() (PYME.recipes.base.ModuleBase method) apply_filter() (PYME.recipes.base.Filter method) (PYME.recipes.filters.DespeckleFilter method) (PYME.recipes.filters.DoGFilter method) (PYME.recipes.filters.GaussianFilter method) (PYME.recipes.filters.MaskEdges method) (PYME.recipes.filters.MaxFilter method) (PYME.recipes.filters.MeanFilter method) (PYME.recipes.filters.MedianFilter method) (PYME.recipes.filters.MinFilter method) (PYME.recipes.filters.Subsample method) (PYME.recipes.filters.Zoom method) (PYME.recipes.machine_learning.CNNFilter method) (PYME.recipes.machine_learning.SVMSegment method) (PYME.recipes.processing.BinaryDilation method) (PYME.recipes.processing.BinaryErosion method) (PYME.recipes.processing.BinaryFillHoles method) (PYME.recipes.processing.Deconvolve method) (PYME.recipes.processing.DistanceTransform method) (PYME.recipes.processing.FractionalThreshold method) (PYME.recipes.processing.GreyDilation method) (PYME.recipes.processing.GreyErosion method) (PYME.recipes.processing.Label method) (PYME.recipes.processing.LocalMaxima method) (PYME.recipes.processing.Projection method) (PYME.recipes.processing.Rotate180 method) (PYME.recipes.processing.SelectLabel method) (PYME.recipes.processing.SelectLargestLabel method) (PYME.recipes.processing.SimpleThreshold method) (PYME.recipes.processing.SplineFitBackgroundEstimate method) (PYME.recipes.processing.Threshold method) (PYME.recipes.processing.WhiteTophat method) (PYME.recipes.skfilters.SKFilter method) apply_labels_to_points() (PYME.LMVis.Extras.annotation.Annotator method) apply_mask() (PYME.DSView.modules.annotation.Annotater method) apply_shifts_to_points() (in module PYME.Analysis.points.multiview) apply_simple() (PYME.recipes.base.ModuleBase method) applyByChannel() (in module PYME.Analysis.BleachProfile.kinModels) applyFilter() (PYME.recipes.base.Add method) (PYME.recipes.base.BinaryOr method) (PYME.recipes.base.Divide method) (PYME.recipes.base.Invert method) (PYME.recipes.base.IsClose method) (PYME.recipes.base.LogicalAnd method) (PYME.recipes.base.Multiply method) (PYME.recipes.base.Normalize method) (PYME.recipes.base.NormalizeMean method) (PYME.recipes.base.Pow method) (PYME.recipes.base.Scale method) (PYME.recipes.base.Subtract method) (PYME.recipes.processing.DeconvolveMotionCompensating method) (PYME.recipes.processing.Offset method) applyLUT() (in module PYME.DSView.LUT) applyLUTf() (in module PYME.DSView.LUT.lut) applyLUTu16() (in module PYME.DSView.LUT.lut) applyLUTu8() (in module PYME.DSView.LUT.lut) approximate_image_bounds() (PYME.Analysis.points.spherical_harmonics.ScaledShell method) approximate_normal() (PYME.Analysis.points.spherical_harmonics.ScaledShell method) arcmf() (in module PYME.Analysis.points.arcfit.arcmf) arcmft() (in module PYME.Analysis.points.arcfit.arcmf) ArithmaticFilter (class in PYME.recipes.base) arrangeNodes() (in module PYME.misc.depGraph) arrangeNodes_() (in module PYME.misc.depGraph) ArrayDataSource (class in PYME.IO.DataSources.ArrayDataSource) ArrayFrame (class in PYME.ui.recArrayView) ArrayPanel (class in PYME.ui.recArrayView) ArrayViewPanel (class in PYME.DSView.arrayViewPanel) as_html() (PYME.recipes.graphing.Plot method) as_pdf() (PYME.recipes.graphing.Plot method) as_png() (PYME.recipes.graphing.Plot method) as_svg() (PYME.recipes.graphing.Plot method) asarray() (PYME.contrib.gohlke.czifile.CziFile method) (PYME.contrib.gohlke.fcsfiles.ConfoCor2Raw method) (PYME.contrib.gohlke.fcsfiles.ConfoCor3Raw method) (PYME.contrib.gohlke.tifffile.TIFFfile method) ASF() (in module PYME.misc.snells) assert_name_ok() (in module PYME.IO.unifiedIO) assert_path_ok() (in module PYME.IO.unifiedIO) assert_uri_ok() (in module PYME.IO.unifiedIO) assert_uri_path_ok() (in module PYME.IO.unifiedIO) astig_lookup() (in module PYME.Analysis.points.astigmatism.astiglookup) astigmatic_gaussian() (in module PYME.localization.FitFactories.AstigGaussGPUFitFR) astigmatism_calibration_location (PYME.recipes.localisations.MapAstigZ attribute) (PYME.recipes.multiview.MapAstigZ attribute) atleast_nd() (in module PYME.IO.DataSources.ArrayDataSource) attachment_directory (PYME.contrib.gohlke.czifile.CziFile attribute) attachments() (PYME.contrib.gohlke.czifile.CziFile method) AUIFrame (class in PYME.ui.AUIFrame) Auserlist (PYME.cluster.webdav.DAVRequestHandler attribute) auth_enable (PYME.cluster.webdav.DAVRequestHandler attribute) auth_file (PYME.cluster.webdav.DAVRequestHandler attribute) authenticate() (in module PYME.util.authenticate) authenticate_hash() (in module PYME.util.authenticate) auto_promote() (PYME.IO.DataSources.BaseDataSource.XYZTCWrapper class method) auto_threshold (PYME.recipes.surface_fitting.DualMarchingCubes attribute) auto_threshold_offset (PYME.recipes.surface_fitting.DualMarchingCubes attribute) AutocorrelationDriftCorrection (class in PYME.recipes.localisations) AutoFocus (class in PYME.Acquire.autofocus) autostart_analysis (PYME.Acquire.SpoolController.SpoolController property) AutoWidthListCtrl (class in PYME.Acquire.sampleInformation) available_renderers (PYME.recipes.localisations.DensityMapping attribute) available_spool_methods (PYME.Acquire.SpoolController.SpoolController property) AverageFramesByZStep (class in PYME.recipes.processing) averageNormals() (in module PYME.Analysis.points.gen3DTriangs) averageNormalsF() (in module PYME.Analysis.points.gen3DTriangs) axes (PYME.contrib.gohlke.czifile.CziFile attribute) AxesOverlayLayer (class in PYME.LMVis.layers.AxesOverlayLayer) axis (PYME.recipes.processing.Projection attribute) axis_scaling (PYME.simulation.pointsets.SHNucleusSource attribute) axis_sigmas (PYME.simulation.pointsets.SHNucleusSource attribute)

B

Backend (class in PYME.Analysis.points.features.metal) (class in PYME.IO.acquisition_backends) BackendBase (class in PYME.Analysis.processLogger) background() (in module PYME.Analysis.PSFEst.psfQuality) (PYME.localization.FitFactories.Gauss3DFitR.GaussFitResult method) (PYME.localization.FitFactories.LatPSFFitR.PSFFitResult method) backgroundBuffer (class in PYME.IO.buffers) (class in PYME.IO.DataSources.BGSDataSource) backgroundBufferM (class in PYME.IO.buffers) (class in PYME.IO.DataSources.BGSDataSource) backgroundBufferMC (class in PYME.IO.buffers) backgroundCorrectPSFWF() (in module PYME.Analysis.PSFEst.extractImages) backgroundIntensity (PYME.LMVis.Extras.pointSetGeneration.Generator attribute) BackgroundSubtractionMovingAverage (class in PYME.recipes.processing) BackgroundSubtractionMovingPercentile (class in PYME.recipes.processing) BACKWARDS (PYME.Acquire.stackSettings.StackSettings attribute) bake() (in module PYME.recipes.batchProcess) bake_recipe() (in module PYME.recipes.batchProcess) bandwidthTesting (PYME.cluster.dataserver_wsgi.dataserver attribute) (PYME.cluster.HTTPDataServer.PYMEHTTPRequestHandler attribute) bareDNA() (in module PYME.simulation.wormlike) (in module PYME.simulation.wormlike2) (in module PYME.simulation.wormlike3) (in module PYME.simulation.wormlike_curled) base64_image() (in module PYME.IO.rgb_image) baseconvert() (in module PYME.IO.FileUtils.nameUtils) BaseDataSource (class in PYME.IO.DataSources.BaseDataSource) BaseEngine (class in PYME.LMVis.layers.base) BaseEnum (class in PYME.misc.mock_traits) BaseFloat (in module PYME.misc.mock_traits) BaseHDFSource (class in PYME.IO.tabular) BaseLayer (class in PYME.LMVis.layers.base) basePupil (PYME.DSView.modules.psfGeneration.PupilGenerator attribute) basic_props (PYME.cluster.webdav.DAVRequestHandler attribute) batch_size (PYME.recipes.surface_fitting.SHShellRadiusDensityEstimate attribute) BatchFrame (class in PYME.recipes.recipeGui) bbox (PYME.DSView.modules.blobMeasure.DataBlock property) (PYME.LMVis.layers.base.BaseLayer property) (PYME.LMVis.layers.image_layer.ImageRenderLayer property) (PYME.LMVis.layers.mesh.TriangleRenderLayer property) (PYME.LMVis.layers.pointcloud.PointCloudRenderLayer property) (PYME.LMVis.layers.quiver.QuiverRenderLayer property) (PYME.LMVis.layers.tracks.TrackRenderLayer property) bead() (in module PYME.localization.FitFactories.BeadConvolvedAstigGaussFit) beadDiameter (PYME.recipes.processing.Deconvolve attribute) between_post_throttle (PYME.recipes.acquisition.QueueAcquisitions attribute) bf_int() (in module PYME.Analysis.BleachProfile.intensProf) bgFrameBuffer (class in PYME.IO.buffers) (class in PYME.IO.DataSources.BGSDataSource) bgFrameBufferC (class in PYME.IO.buffers) BGInitTask (class in PYME.Acquire.ExecTools) Bid (class in PYME.cluster.ruleserver) bid() (PYME.cluster.ruleserver.IntegerIDRule method) bid_on_tasks() (PYME.cluster.ruleserver.RuleServer method) bidder_id (PYME.cluster.ruleserver.Bid property)

bin_spacing (PYME.recipes.processing.Threshold attribute) BinaryDilation (class in PYME.recipes.processing) BinaryErosion (class in PYME.recipes.processing) BinaryFillHoles (class in PYME.recipes.processing) BinaryOr (class in PYME.recipes.base) binAvg() (in module PYME.Analysis.binAvg) binBy (PYME.recipes.measurement.BinnedHistogram attribute) Bind() (PYME.DSView.modules.LMDisplay.LMDisplay method) bind_texture() (PYME.LMVis.shader_programs.PointSpriteShaderProgram.GaussTexture method) binMedian() (in module PYME.Analysis.binAvg) binned_average() (in module PYME.Analysis.binAvg) binned_median() (in module PYME.Analysis.binAvg) BinnedHistogram (class in PYME.recipes.measurement) binsize (PYME.recipes.localisations.AutocorrelationDriftCorrection attribute) binSize (PYME.recipes.measurement.PairwiseDistanceHistogram attribute) (PYME.recipes.pointcloud.Ripleys attribute) binSizeNM (PYME.recipes.processing.ColocalisationEDT attribute) binWidth (PYME.recipes.machine_learning.PointFeaturesPairwiseDist attribute) BitmapFromImage() (in module PYME.ui.wx_compat) BitPacker (class in PYME.contrib.lzw) bitstobytes() (in module PYME.contrib.lzw) BitUnpacker (class in PYME.contrib.lzw) BlankResult() (in module PYME.localization.FitFactories.MultiviewFitInterpNR) (in module PYME.localization.FitFactories.SplitterFitFNR) (in module PYME.localization.FitFactories.SplitterFitFusionR) (in module PYME.localization.FitFactories.SplitterFitInterpBNR) (in module PYME.localization.FitFactories.SplitterFitInterpNR) (in module PYME.localization.FitFactories.SplitterFitScavNR) blemish_variance (PYME.recipes.processing.DarkAndVarianceMap attribute) blob() (in module PYME.Analysis.tile_pyramid) blobColourKey (PYME.LMVis.triBlobs.BlobSettings attribute) BlobFinder (class in PYME.DSView.modules.blobFinding) (class in PYME.DSView.modules.shiftfield_estimation) blobify() (in module PYME.Analysis.points.gen3DTriangs) blobify2D() (in module PYME.Analysis.points.gen3DTriangs) BlobObject (class in PYME.DSView.modules.blobMeasure) BlobSettings (class in PYME.LMVis.triBlobs) BlobSettingsPanel (class in PYME.LMVis.triBlobs) blobSigma (PYME.recipes.measurement.MultifitBlobs attribute) block_size (PYME.recipes.localisations.TimeBlocks attribute) Blue() (in module PYME.misc.colormaps) blur_radius (PYME.recipes.measurement.DetectPoints2D attribute) Bool (in module PYME.misc.mock_traits) bool_map_between_events() (in module PYME.Analysis.piecewiseMapping) BoolFloatParam (class in PYME.localization.MetaDataEdit) BoolParam (class in PYME.localization.MetaDataEdit) bound_tolerance (PYME.recipes.surface_fitting.SphericalHarmonicShell attribute) bounds (PYME.IO.image.ImageBounds property) BufferManager (class in PYME.localization.remFitBuf) BufWriter (class in PYME.cluster.webdav) build_call_tree_threads() (in module PYME.util.fProfile.convertProfile) builddict() (in module PYME.cluster.webdav) (PYME.cluster.webdav.XMLDict_Parser method) ByteDecoder (class in PYME.contrib.lzw) ByteEncoder (class in PYME.contrib.lzw) bytestobits() (in module PYME.contrib.lzw)

C

C (in module PYME.Acquire.protocol) c_mul() (in module PYME.misc.hash32) CacheEntry (class in PYME.Analysis.tile_pyramid) CachingMDHandler (class in PYME.IO.MetaDataHandler) CachingResultsFilter (class in PYME.IO.tabular) cachingResultsFilter() (in module PYME.IO.tabular) calc_flow() (PYME.recipes.processing.OpticalFlow method) calc_flow_mp() (PYME.recipes.processing.OpticalFlow method) calc_gauss_weights() (in module PYME.localization.ofind) (in module PYME.localization.ofind_pri) (in module PYME.localization.ofind_split) calc_grad() (PYME.recipes.processing.DirectionToMask3D method) (PYME.recipes.processing.Gradient2D method) (PYME.recipes.processing.Gradient3D method) calc_proj() (PYME.recipes.processing.ProjectOnVector method) calc_shifts_for_points() (in module PYME.Analysis.points.multiview) calcCenteredMoments() (in module PYME.Analysis.points.moments) calcCoeffs() (in module PYME.misc.zernike) calcCoeffs_rays() (in module PYME.misc.zernike) calcCorrDrift() (PYME.recipes.localisations.AutocorrelationDriftCorrection method) calcCorrections() (in module PYME.Analysis.points.twoColour) calcCorrShift() (in module PYME.Analysis.deTile) CalcCramerRao() (in module PYME.Analysis.cramerRao) CalcCramerReoZ() (in module PYME.Analysis.cramerRao) calcDistances() (PYME.Analysis.points.EdgeDB.edges.EdgeDB method) calcDistCorr() (in module PYME.Analysis.Colocalisation.distColoc) calcEdgeDists() (in module PYME.Analysis.points.objectMeasure) calcEdgeLengths() (in module PYME.Analysis.points.EdgeDB.edgeDB) CalcFisherInfoModel() (in module PYME.Analysis.cramerRao) CalcFisherInform2D() (in module PYME.Analysis.cramerRao) CalcFisherInformZ() (in module PYME.Analysis.cramerRao) CalcFisherInformZn() (in module PYME.Analysis.cramerRao) CalcFisherInformZn2() (in module PYME.Analysis.cramerRao) calcLinkageMatrix() (PYME.Analysis.Tracking.tracking.Tracker method) calcLinkages() (PYME.Analysis.Tracking.tracking.Tracker method) calcMCCenteredMoments() (in module PYME.Analysis.points.moments) calcMeanEdge() (in module PYME.Analysis.points.gen3DTriangs) calcMEs() (PYME.localization.Test.fitTestJig.fitTestJig method) (PYME.localization.Test.fitTestJigSCMOS.fitTestJig method) (PYME.localization.Test.fitTestJigWC.fitTestJig method) calcNeighbourDistPart() (in module PYME.LMVis.visHelpers) calcNeighbourDists() (in module PYME.LMVis.visHelpers) (in module PYME.LMVis.visHelpersMin) calcProf() (in module PYME.Analysis.BleachProfile.intensProf) calcSigma() (PYME.localization.remFitBuf.fitTask class method) calcTetVolume() (in module PYME.Analysis.points.gen3DTriangs) calcThreshold() (PYME.localization.remFitBuf.fitTask method) calcTrackVelocity() (in module PYME.Analysis.Tracking.trackUtils) calcTs() (in module PYME.Analysis.BleachProfile.intensProf) calcTwist() (in module PYME.localization.twist) calculate_length_with_reversal() (in module PYME.Analysis.points.traveling_salesperson.sectioned_two_opt) calculate_path_length() (in module PYME.Analysis.points.traveling_salesperson.two_opt) CalcUnscrolledPosition() (PYME.DSView.scrolledImagePanel.ScrolledImagePanel method) calibrate() (in module PYME.localization.FitFactories.zEstimators.astigEstimator) (in module PYME.localization.FitFactories.zEstimators.biplaneEstimator) (in module PYME.localization.FitFactories.zEstimators.genericDualEstimator) (in module PYME.localization.FitFactories.zEstimators.genericEstimator) (in module PYME.localization.FitFactories.zEstimators.priEstimator) CalibrateShifts (class in PYME.recipes.multiview) call_in_main_thread() (in module PYME.ui.mytimer) (PYME.Acquire.event_loop.EventLoop method) CameraChooserPanel (class in PYME.Acquire.ui.selectCameraPanel) CameraInfoManager (class in PYME.localization.remFitBuf) can_fold (PYME.ui.manualFoldPanel.foldingPane property) candLineWidth (PYME.DSView.modules.particleTracking.ParticleTrackingView attribute) CaptionButton (class in PYME.ui.manualFoldPanel) cart2sph() (in module PYME.Analysis.points.coordinate_tools) cartesian_to_spherical() (in module PYME.Analysis.points.coordinate_tools) Cauchy() (in module PYME.misc.glassModel) CaWave (class in PYME.recipes.processing) CDLL (class in PYME.misc.mock_ctypes) center() (PYME.Acquire.zScanner.zScanner method) centre (PYME.simulation.pointsets.WiglyFibreSource attribute) CENTRE_AND_LENGTH (PYME.Acquire.stackSettings.StackSettings attribute) centre_roi_on() (PYME.Acquire.microscope.microscope method) CentreROIOn (class in PYME.Acquire.actions) centroid (PYME.DSView.modules.blobMeasure.DataBlock property) centroidNM (PYME.DSView.modules.blobMeasure.DataBlock property) cglob() (in module PYME.IO.clusterIO) (PYME.IO.cluster_directory.DirectoryInfoManager method) chain() (PYME.cluster.rules.RuleFactory method) ChainedAnalysisPage (class in PYME.Acquire.htsms.rule_ui) ChainedAnalysisPanel (class in PYME.Acquire.htsms.rule_ui) change_text_flavour() (PYME.LMVis.importTextDialog.ImportTextDialog method) channel (PYME.LMVis.layers.image_layer.ImageRenderLayer attribute) (PYME.recipes.localisations.ExtractTableChannel attribute) (PYME.recipes.measurement.FitPoints attribute) ChannelFoldingPane (class in PYME.ui.layerFoldPanel) channelToExtract (PYME.recipes.base.ExtractChannel attribute) check_for_updates() (in module PYME.misc.check_for_updates) check_inputs() (PYME.recipes.base.ModuleBase method) check_inside() (PYME.Analysis.points.spherical_harmonics.ScaledShell method) check_name() (in module PYME.IO.unifiedIO) check_path() (in module PYME.IO.unifiedIO) check_required_names() (in module PYME.IO.csv_flavours) check_uri() (in module PYME.IO.unifiedIO) CheckColNames() (PYME.LMVis.importTextDialog.ColumnMappingDialog method) checkHardware() (PYME.Acquire.frameWrangler.FrameWrangler method) CheckItem() (PYME.contrib.listctrlMixins.CheckListCtrlMixin method) CheckListCtrlMixin (class in PYME.contrib.listctrlMixins) ChecksumFitFactory (class in PYME.localization.FitFactories.ChecksumFR) (class in PYME.localization.FitFactories.ChecksumGPUFR) (class in PYME.localization.FitFactories.ChecksumMultifitSR) checkTQ() (PYME.DSView.modules.deconvolution.Deconvolver method) CheckWxPhoenix() (in module PYME.ui.wx_compat) cherrypy_server() (in module PYME.cluster.dataserver_wsgi) chi2_mse() (in module PYME.Analysis.BleachProfile.kinModels) ChoiceParam (class in PYME.localization.MetaDataEdit) choices (PYME.ui.custom_traits_editors.DictChoiceStrPanel property) chosenLineWidth (PYME.DSView.modules.particleTracking.ParticleTrackingView attribute) chromaticShifts (PYME.LMVis.pipeline.Pipeline property) ChunkedHuffmanCompress() (in module PYME.IO.PZFFormat) ChunkedHuffmanCompress_o() (in module PYME.IO.PZFFormat) ChunkedHuffmanDecompress() (in module PYME.IO.PZFFormat) ChunkedTravelingSalesperson (class in PYME.recipes.measurement) CInt (in module PYME.misc.mock_traits) circGeom (class in PYME.misc.coverslipGeometries) CircularPointScanner (class in PYME.Acquire.Utils.pointScanner) CircularTilePanel (class in PYME.Acquire.ui.tile_panel) CircularTiler (class in PYME.Acquire.Utils.tiler) circumcentres() (PYME.recipes.pointcloud.Tesselation method) ClassicMappingFFTW (class in PYME.Deconv.dec) ClassicMappingNP (class in PYME.Deconv.dec) classifier (PYME.recipes.machine_learning.SVMSegment attribute) classify() (PYME.Analysis.svmSegment.svmClassifier method) cleaned_dict_repr() (PYME.recipes.base.ModuleBase method) cleanup() (PYME.cluster.HTTPRulePusher.HTTPRulePusher method) (PYME.cluster.HTTPTaskPusher.HTTPTaskPusher method) (PYME.cluster.rules.Rule method) (PYME.Deconv.dec.dec_4pi_c method) (PYME.IO.HTTPSpooler.Spooler method) (PYME.IO.HTTPSpooler_v2.Spooler method) (PYME.IO.Spooler.Spooler method) clear() (PYME.Acquire.ui.intensity_trace.IntensityTracePanel method) (PYME.LMVis.Extras.animation.VideoPanel method) (PYME.recipes.recipe.Recipe method) Clear() (PYME.ui.autoFoldPanel.foldPanel method) (PYME.ui.manualFoldPanel.foldPanel method) clear_all() (PYME.DSView.modules.annotation.AnnotateBase method) clear_positions() (PYME.Acquire.stage_leveling.StageLeveler method) clear_rois (PYME.tileviewer.tileviewer.TileServer attribute) clear_selected() (PYME.DSView.modules.annotation.AnnotateBase method) clear_view() (PYME.LMVis.Extras.animation.VideoPanel method) ClearGenerated() (PYME.LMVis.pipeline.Pipeline method) ClearTrack() (PYME.Acquire.positionTracker.PositionTracker method) click_test() (PYME.ui.manualFoldPanel.CaptionButton method) client_disconnected() (PYME.Acquire.webui.ipy.IPYTermManager method) clim (PYME.LMVis.layers.image_layer.ImageRenderLayer attribute) (PYME.LMVis.layers.mesh.TriangleRenderLayer attribute) (PYME.LMVis.layers.pointcloud.PointCloudRenderLayer attribute) (PYME.LMVis.layers.tracks.TrackRenderLayer attribute) clipped_widefield_pupil_and_propagator() (in module PYME.Analysis.PSFGen.fourierHNA) (in module PYME.Analysis.PSFGen.fourierHNA2) ClippingPanel (class in PYME.LMVis.view_clipping_pane) CloneSource (class in PYME.IO.tabular) cloneSource() (in module PYME.IO.tabular) close() (PYME.contrib.gohlke.czifile.CziFile method) (PYME.contrib.gohlke.fcsfiles.ConfoCor2Raw method) (PYME.contrib.gohlke.fcsfiles.ConfoCor3Fcs method) (PYME.contrib.gohlke.fcsfiles.ConfoCor3Raw method) (PYME.contrib.gohlke.tifffile.TIFFfile method) (PYME.IO.cluster_streaming.Stream method) (PYME.IO.cluster_streaming.Streamer method) (PYME.IO.FileUtils.obf_support.File method) (PYME.IO.FileUtils.saveTiffStack.TiffMP method) (PYME.IO.tabular.BaseHDFSource method) CloseEditor() (PYME.contrib.listctrlMixins.TextEditMixin method) (PYME.ui.MetadataTree.TextEditMixin method) CloseFiles() (PYME.LMVis.pipeline.Pipeline method) Clump (class in PYME.Analysis.Tracking.trackUtils) clump_key (PYME.LMVis.layers.tracks.TrackRenderLayer attribute) clumpColumnName (PYME.recipes.localisations.DBSCANClustering attribute) ClumpManager (class in PYME.Analysis.Tracking.trackUtils) clumpRadiusMultiplier (PYME.recipes.localisations.FiducialCorrection attribute) clumpRadiusScale (PYME.recipes.tracking.FindClumps attribute) clumpRadiusVar (PYME.recipes.localisations.FiducialCorrection attribute) clumpRadiusVariable (PYME.recipes.tracking.FindClumps attribute) cluster() (in module PYME.Analysis.points.tCluster) ClusterAnalyser (class in PYME.LMVis.Extras.clusterAnalysis) ClusterBackend (class in PYME.IO.acquisition_backends) ClusterCountVsImagingTime (class in PYME.recipes.localisations) ClusterOfOne (class in PYME.cluster.cluster_of_one) ClusterPZFTileCache (class in PYME.Analysis.tile_pyramid) ClusterPZFTileIO (class in PYME.Analysis.tile_pyramid) cmap (PYME.LMVis.layers.image_layer.ImageRenderLayer attribute) (PYME.LMVis.layers.mesh.TriangleRenderLayer attribute) (PYME.LMVis.layers.pointcloud.PointCloudRenderLayer attribute) (PYME.LMVis.layers.tracks.TrackRenderLayer attribute) CMapDict (class in PYME.misc.colormaps) cmapnames (PYME.misc.colormaps.CMapDict property) cmp() (in module PYME.contrib.listctrlMixins) cnn_filter() (in module PYME.DSView.modules.convnet) CNNFilter (class in PYME.recipes.machine_learning) coalesce_dict_sorted() (in module PYME.Analysis.points.multiview) coalesceClumps() (in module PYME.Analysis.points.DeClump.pyDeClump) coalesceClumps_() (in module PYME.Analysis.points.DeClump.pyDeClump) code_size() (PYME.contrib.lzw.Decoder method) (PYME.contrib.lzw.Encoder method)

coeff (PYME.DSView.modules.psfGeneration.ZernikeMode attribute) COIFitFactory (class in PYME.localization.FitFactories.LatFitCOIR) (class in PYME.localization.FitFactories.SplitterFitCOIR) COIFitResultR() (in module PYME.localization.FitFactories.ConfocCOIR) (in module PYME.localization.FitFactories.LatFitCOIR) (in module PYME.localization.FitFactories.SplitterFitCOIR) collapsingPane (class in PYME.ui.autoFoldPanel) (class in PYME.ui.manualFoldPanel) collectConnected() (in module PYME.Analysis.points.EdgeDB.segment) (in module PYME.Analysis.points.gen3DTriangs) Collection (class in PYME.cluster.webdav) COLLECTION_MIME_TYPE (PYME.cluster.webdav.DirCollection attribute) Colocalisation (class in PYME.recipes.processing) ColocalisationEDT (class in PYME.recipes.processing) Colocaliser (class in PYME.DSView.modules.coloc) ColocSettingsDialog (class in PYME.DSView.modules.coloc) (class in PYME.DSView.modules.fourierRingCorrelation) colorblindFriendly (PYME.recipes.output.RGBImageOutput attribute) colorize_file() (in module PYME.util.mProfile.colorize_db_t) colour() (in module PYME.Analysis.PSFEst.psfQuality) colour_map (PYME.LMVis.layers.image_layer.ImageRenderLayer property) (PYME.LMVis.layers.mesh.TriangleRenderLayer property) (PYME.LMVis.layers.pointcloud.PointCloudRenderLayer property) (PYME.LMVis.layers.quiver.QuiverRenderLayer property) (PYME.LMVis.layers.tracks.TrackRenderLayer property) colour_mapper (PYME.LMVis.pipeline.Pipeline property) colourDataKey (PYME.LMVis.pointSettingsPanel.PointDisplaySettings attribute) (PYME.LMVis.view_clipping_pane.PointDisplaySettings attribute) ColourFilter (class in PYME.IO.tabular) colourFilter (PYME.LMVis.renderers.CurrentRenderer property) colourFilter() (in module PYME.IO.tabular) ColourFilterPane (class in PYME.LMVis.colourFilterGUI) ColourFromStyle() (in module PYME.ui.autoFoldPanel) (in module PYME.ui.manualFoldPanel) ColourImageViewPanel (class in PYME.LMVis.imageView) (class in PYME.LMVis.imageView2) colourPanel (class in PYME.LMVis.colourPanel) colourPlotPanel (class in PYME.LMVis.colourPanel) ColourRenderer (class in PYME.LMVis.renderers) colours (PYME.recipes.localisations.DensityMapping attribute) columnForEachFeature (PYME.recipes.machine_learning.PointFeatureBase attribute) ColumnMappingDialog (class in PYME.LMVis.importTextDialog) columns (PYME.recipes.localisations.DBSCANClustering attribute) (PYME.recipes.measurement.NearestNeighbourDistances attribute) ColumnSorterMixin (class in PYME.contrib.listctrlMixins) ColumnSource (class in PYME.IO.tabular) common_prefix() (in module PYME.Analysis.composite) complete (PYME.cluster.rules.LocalisationRule property) (PYME.cluster.rules.Rule property) completeMetadata() (PYME.recipes.base.ArithmaticFilter method) (PYME.recipes.base.Filter method) (PYME.recipes.filters.DespeckleFilter method) (PYME.recipes.filters.DoGFilter method) (PYME.recipes.filters.GaussianFilter method) (PYME.recipes.filters.MaxFilter method) (PYME.recipes.filters.MeanFilter method) (PYME.recipes.filters.MedianFilter method) (PYME.recipes.filters.MinFilter method) (PYME.recipes.filters.Subsample method) (PYME.recipes.filters.Zoom method) (PYME.recipes.machine_learning.CNNFilter method) (PYME.recipes.machine_learning.SVMSegment method) (PYME.recipes.processing.Label method) (PYME.recipes.skfilters.SKFilter method) complexMode (PYME.DSView.displayOptions.DisplayOpts property) Composite (class in PYME.recipes.processing) CompositeDialog (class in PYME.DSView.modules.composite) Compositor (class in PYME.DSView.modules.composite) compress() (in module PYME.contrib.lzw) ComputationInProgress (class in PYME.ui.progress) computeLoop() (PYME.cluster.taskWorkerHTTP.taskWorker method) ConcatenateFilter (class in PYME.IO.tabular) concatenateFilter() (in module PYME.IO.tabular) ConcatenateTables (class in PYME.recipes.tablefilters) configuration() (in module PYME.Acquire.setup) (in module PYME.Analysis.points.arcfit.setup) (in module PYME.Analysis.points.astigmatism.setup) (in module PYME.Analysis.points.DeClump.setup) (in module PYME.Analysis.points.DistHist.setup) (in module PYME.Analysis.points.EdgeDB.setup) (in module PYME.Analysis.points.setup) (in module PYME.Analysis.points.SoftRend.setup) (in module PYME.Analysis.points.traveling_salesperson.setup) (in module PYME.Analysis.PSFGen.setup) (in module PYME.Analysis.setup) (in module PYME.contrib.gohlke.setup) (in module PYME.contrib.setup) (in module PYME.DSView.LUT.setup) (in module PYME.DSView.setup) (in module PYME.IO.countdir.setup) (in module PYME.IO.FileUtils.setup) (in module PYME.IO.setup) (in module PYME.LMVis.setup) (in module PYME.localization.cInterp.setup) (in module PYME.localization.cModels.setup) (in module PYME.localization.lev_gfit.setup) (in module PYME.localization.setup) (in module PYME.recipes.setup) (in module PYME.resources.setup) (in module PYME.setup) (in module PYME.setup_exe) configureModule() (PYME.recipes.recipeGui.RecipeView method) confocal_parser (class in PYME.DSView.logparser) ConfocCOI() (in module PYME.localization.FitFactories.ConfocCOIR) ConfoCor2Raw (class in PYME.contrib.gohlke.fcsfiles) ConfoCor3Fcs (class in PYME.contrib.gohlke.fcsfiles) ConfoCor3Raw (class in PYME.contrib.gohlke.fcsfiles) congrid() (in module PYME.contrib.congrid) connect() (PYME.contrib.dispatch.dispatcher.Signal method) constrain_surface_to_point (PYME.recipes.surface_fitting.FitSurfaceWithPatches attribute) ContextLayer (class in PYME.Analysis.processLogger) ContextManager (class in PYME.Analysis.processLogger) Controller() (in module PYME.misc.mock_traitsui) convert() (in module PYME.util.fProfile.convertProfile) convert_numarray() (in module PYME.IO.FileUtils.thumbnailDatabase) (in module PYME.misc.sqlitendarray) convertFile() (in module PYME.IO.FileUtils.h5rToTxt) (in module PYME.IO.FileUtils.RawToHdf5) convertFiles() (in module PYME.IO.FileUtils.TiffSeqToHdf5) copy() (PYME.LMVis.views.View class method) copy_sample_metadata() (in module PYME.LMVis.renderers) copyEntriesFrom() (PYME.IO.MetaDataHandler.MDHandlerBase method) (PYME.IO.MetaDataHandler.QueueMDHandler method) CopyImage() (PYME.DSView.arrayViewPanel.ArrayViewPanel method) CopyOnWriteMDHandler (class in PYME.IO.MetaDataHandler) correct_target_positions() (in module PYME.Analysis.piezo_movement_correction) correctImage() (PYME.localization.remFitBuf.CameraInfoManager method) correlate() (PYME.localization.ofind_xcorr_fw.fftwWeiner method) correlative_shift() (in module PYME.Analysis.points.multiview) corrScale() (in module PYME.Analysis.Colocalisation.colocScaleDep) cost (PYME.cluster.ruleserver.Bid property) COST_THRESHOLD (PYME.cluster.ruleserver.IntegerIDRule attribute) covariance (PYME.recipes.pointcloud.GaussianMixtureModel attribute) crb3d() (in module PYME.Analysis.PSFEst.psfQuality) create() (in module PYME.Acquire.acquiremainframe) (in module PYME.Acquire.acquirewx) (in module PYME.Acquire.ui.seqdialog) (in module PYME.util.shmarray.shmarray) create_and_set_shader_program() (PYME.LMVis.shader_programs.GLProgram.GLProgram method) create_buttons() (PYME.LMVis.Extras.saved_views.ViewPanel method) create_copy() (in module PYME.util.shmarray.shmarray) create_ctrls() (PYME.DSView.OverlaysPanel.OverlayPanel method) create_distributed_pyramid_from_dataset() (in module PYME.Analysis.distributed_pyramid) create_editor() (PYME.simulation.pointsets.WRDictEnum method) create_gui() (PYME.LMVis.Extras.scaleBox.ScaleBoxPanel method) create_ipy_server() (in module PYME.Acquire.webui.ipy) create_overlay_panel() (PYME.DSView.dsviewer.DSViewFrame method) create_pyramid_from_dataset() (in module PYME.Analysis.tile_pyramid) create_remote_part() (PYME.Analysis.distributed_pyramid.DistributedImagePyramid method) create_tool_bar() (PYME.LMVis.visCore.VisGUICore method) CreateColourFilterPane() (in module PYME.LMVis.colourFilterGUI) CreateDisplayPane() (in module PYME.LMVis.displayPane) CreateFilterPane() (in module PYME.DSView.modules.measure.filterPan) (in module PYME.ui.filterPane) createFitTaskFromTaskDef() (in module PYME.localization.remFitBuf) CreateFoldPanel() (PYME.DSView.modules.LMDisplay.LMDisplay method) (PYME.ui.AUIFrame.AUIFrame method) createGUI() (PYME.localization.MetaDataEdit.BoolFloatParam method) (PYME.localization.MetaDataEdit.BoolParam method) (PYME.localization.MetaDataEdit.ChoiceParam method) (PYME.localization.MetaDataEdit.FilenameParam method) (PYME.localization.MetaDataEdit.FloatListParam method) (PYME.localization.MetaDataEdit.FloatParam method) (PYME.localization.MetaDataEdit.IntParam method) (PYME.localization.MetaDataEdit.ParamGroup method) (PYME.localization.MetaDataEdit.RangeParam method) (PYME.localization.MetaDataEdit.StringParam method) createImage() (in module PYME.Acquire.sampleInformation) CreateLayerPane() (in module PYME.LMVis.layer_panel) CreateLayerPanel() (in module PYME.LMVis.layer_panel) CreateMenuBar() (PYME.LMVis.visCore.VisGUICore method) CreateModuleMenu() (PYME.DSView.dsviewer.DSViewFrame method) CreatePens() (PYME.DSView.modules.flowView.FlowView method) (PYME.DSView.modules.particleTracking.ParticleTrackingView method) createQT() (in module PYME.Analysis.points.QuadTree.pointQT) (in module PYME.Analysis.points.QuadTree.pointQTF) CreateToolBar() (PYME.DSView.DisplayOptionsPanel.OptionsPanel method) CreateToolPanel() (PYME.Acquire.acquiremainframe.PYMEMainFrame method) (PYME.Acquire.acquirewx.PYMEMainFrame method) creation_time (PYME.misc.sqlite_ns.NSInfo property) Crop (class in PYME.recipes.base) crop_image() (in module PYME.IO.DataSources.CropDataSource) CropExportData() (in module PYME.ui.crop_dialog) Cropper (class in PYME.DSView.modules.cropping) CrosshairsOverlay (class in PYME.DSView.overlays) CSInterpolator (class in PYME.localization.FitFactories.Interpolators.CSInterpolator) (class in PYME.localization.FitFactories.Interpolators.CubeSInterpolatorP) CStr (class in PYME.misc.mock_traits) CSVOutput (class in PYME.recipes.output) CubicSplineInterpolator (class in PYME.localization.FitFactories.Interpolators.CubicSplineInterpolator) cull_inner_surfaces (PYME.recipes.surface_fitting.DualMarchingCubes attribute) (PYME.recipes.surface_fitting.NthPointIsosurface attribute) cull_triangles_2D() (in module PYME.Analysis.points.gen3DTriangs) cumuexpfit() (in module PYME.LMVis.Extras.QPobjectSegment) (in module PYME.LMVis.objectDarkMeasure) current_scan (PYME.Acquire.stage_leveling.StageLeveler property) CurrentRenderer (class in PYME.LMVis.renderers) Cyan() (in module PYME.misc.colormaps) CziFile (class in PYME.contrib.gohlke.czifile)

D

d_angles (PYME.recipes.surface_fitting.SphericalHarmonicShell attribute) dark() (in module PYME.DSView.modules.dark_and_flatfield) dark_threshold (PYME.recipes.processing.DarkAndVarianceMap attribute) DarkAndVarianceMap (class in PYME.recipes.processing) darkFilename (PYME.recipes.processing.FlatfiledAndDarkCorrect attribute) data (PYME.Analysis.tile_pyramid.CacheEntry property) (PYME.IO.image.ImageStack property) (PYME.misc.editgrid.EntryGrid property) data_complete (PYME.cluster.rules.LocalisationRule property) (PYME.cluster.rules.Rule property) (PYME.cluster.rules.SpoolLocalLocalizationRule property) data_limits (PYME.LMVis.view_clipping_pane.ClippingPanel property) data_type (PYME.Analysis.points.spherical_harmonics.ScaledShell attribute) data_xytc (PYME.IO.image.ImageStack property) data_xyztc (PYME.IO.image.ImageStack property) DataBlock (class in PYME.DSView.modules.blobMeasure) dataBuffer (class in PYME.IO.buffers) (class in PYME.IO.DataSources.BGSDataSource) DataChanged() (PYME.DSView.dsviewer.DSViewFrame method) dataserver (class in PYME.cluster.dataserver_wsgi) dataservers (PYME.IO.cluster_directory.DirectoryInfoManager property) DataSource (class in PYME.IO.DataSources.AlignDataSource) (class in PYME.IO.DataSources.BioformatsDataSource) (class in PYME.IO.DataSources.BufferedDataSource) (class in PYME.IO.DataSources.ClusterPZFDataSource) (class in PYME.IO.DataSources.ConcatenatedDataSource) (class in PYME.IO.DataSources.CropDataSource) (class in PYME.IO.DataSources.DcimgDataSource) (class in PYME.IO.DataSources.ElectronsPerSecondDataSource) (class in PYME.IO.DataSources.FlatFieldDataSource) (class in PYME.IO.DataSources.HDFDataSource) (class in PYME.IO.DataSources.HTTPDataSource) (class in PYME.IO.DataSources.ImageSeriesDataSource) (class in PYME.IO.DataSources.MultiviewDataSource) (class in PYME.IO.DataSources.OBFDataSource) (class in PYME.IO.DataSources.RandomDataSource) (class in PYME.IO.DataSources.TiffDataSource) (class in PYME.IO.DataSources.TQDataSource) (class in PYME.IO.DataSources.UnsplitDataSource) (in module PYME.IO.DataSources.BGSDataSource) datasource (PYME.LMVis.layers.image_layer.ImageRenderLayer property) (PYME.LMVis.layers.mesh.TriangleRenderLayer property) (PYME.LMVis.layers.pointcloud.PointCloudRenderLayer property) (PYME.LMVis.layers.quiver.QuiverRenderLayer property) (PYME.LMVis.layers.tracks.TrackRenderLayer property) dataSource (PYME.ui.filterPane.FilterPanel property) DataSource() (in module PYME.IO.DataSources.SupertileDatasource) dataSources (PYME.LMVis.pipeline.Pipeline property) DAVRequestHandler (class in PYME.cluster.webdav) DAVServer (class in PYME.cluster.webdav) dBdt() (in module PYME.Analysis.BleachProfile.deMod) DBSCANClustering (class in PYME.recipes.localisations) DCIMGFile (class in PYME.IO.dcimg) debounce_radius (PYME.recipes.measurement.DetectPoints2D attribute) debugPrint() (in module PYME.DSView.modules.LMAnalysis) (in module PYME.DSView.modules.LMDisplay) dec (class in PYME.Analysis.PSFEst.dec) dec_4pi (class in PYME.Deconv.dec) dec_4pi_c (class in PYME.Deconv.dec) dec_bead (class in PYME.Deconv.dec) dec_conv (class in PYME.Deconv.dec) (class in PYME.Deconv.richardsonLucy) (class in PYME.Deconv.richardsonLucyMV) (class in PYME.Deconv.richardsonLucyMVM) dec_conv_slow (class in PYME.Deconv.dec) (class in PYME.Deconv.richardsonLucy) (class in PYME.Deconv.richardsonLucyMV) (class in PYME.Deconv.richardsonLucyMVM) dec_psf (class in PYME.Analysis.PSFEst.dec) dec_test() (in module PYME.Analysis.PSFEst.psfQuality) dec_wiener (class in PYME.Deconv.wiener) DecayAnalyser (class in PYME.LMVis.Extras.photophysics) deClump() (in module PYME.Analysis.points.DeClump.pyDeClump) deClumpDialog (class in PYME.Analysis.points.DeClump.deClumpGUI) deClumpedDType() (in module PYME.Analysis.points.DeClump.pyDeClump) deClumpf() (in module PYME.Analysis.points.DeClump.pyDeClump) decmod_onestate() (in module PYME.Analysis.BleachProfile.intensProf) decode() (PYME.contrib.lzw.Decoder method) decode_json() (PYME.LMVis.views.View class method) decodefrombytes() (PYME.contrib.lzw.ByteDecoder method) decodepages() (PYME.contrib.lzw.PagingDecoder method) Decoder (class in PYME.contrib.lzw) decompress() (in module PYME.contrib.lzw) decompZar() (in module PYME.misc.zemax) deconv() (PYME.Analysis.PSFEst.dec.dec method) (PYME.Deconv.dec.ICTMDeconvolution method) (PYME.Deconv.richardsonLucy.RichardsonLucyDeconvolution method) (PYME.Deconv.richardsonLucyMV.MultiviewRichardsonLucy method) (PYME.Deconv.richardsonLucyMVM.MotionCompensatingRichardsonLucy method) (PYME.Deconv.wiener.dec_wiener method) DeconvMappingBase (class in PYME.Deconv.dec) Deconvolve (class in PYME.recipes.processing) DeconvolveMotionCompensating (class in PYME.recipes.processing) Deconvolver (class in PYME.DSView.modules.deconvolution) deconvp() (PYME.Deconv.dec.ICTMDeconvolution method) (PYME.Deconv.richardsonLucy.RichardsonLucyDeconvolution method) DeconvProgressDialog (class in PYME.Deconv.deconvDialogs) DeconvProgressPanel (class in PYME.Deconv.deconvDialogs) DeconvSettingsDialog (class in PYME.Deconv.deconvDialogs) decResult (class in PYME.Deconv.decTask) decTask (class in PYME.Deconv.decTask) decThread (class in PYME.Deconv.decThread) default_compression_settings (PYME.IO.acquisition_backends.ClusterBackend attribute) DEFAULT_PARAMS (PYME.Acquire.ui.AnalysisSettingsUI.AnalysisDetailsPanel attribute) (PYME.DSView.modules.LMAnalysis.AnalysisSettingsView attribute) default_recipe (PYME.recipes.processing.CaWave attribute) default_traits_view() (PYME.Acquire.htsms.rule_ui.RuleTile method) (PYME.DSView.modules.flowView.FlowView method) (PYME.DSView.modules.particleTracking.ParticleTrackingView method) (PYME.DSView.modules.psfGeneration.PupilGenerator method) (PYME.DSView.modules.pupilTools.PupilTools method) (PYME.LMVis.Extras.pointSetGeneration.Generator method) (PYME.LMVis.Extras.snapshot.SnapshotSettings method) (PYME.LMVis.layers.image_layer.ImageRenderLayer method) (PYME.LMVis.layers.mesh.TriangleRenderLayer method) (PYME.LMVis.layers.pointcloud.PointCloudRenderLayer method) (PYME.LMVis.layers.quiver.QuiverRenderLayer method) (PYME.LMVis.layers.tracks.TrackRenderLayer method) (PYME.recipes.base.ModuleBase method) (PYME.recipes.processing.Deconvolve method) (PYME.recipes.processing.DeconvolveMotionCompensating method) (PYME.simulation.pointsets.ImageSource method) default_view (PYME.Acquire.htsms.rule_ui.RuleTile property) (PYME.DSView.modules.particleTracking.ParticleTrackingView property) (PYME.LMVis.layers.image_layer.ImageRenderLayer property) (PYME.LMVis.layers.mesh.TriangleRenderLayer property) (PYME.LMVis.layers.octree.OctreeRenderLayer property) (PYME.LMVis.layers.pointcloud.PointCloudRenderLayer property) (PYME.LMVis.layers.quiver.QuiverRenderLayer property) (PYME.LMVis.layers.tracks.TrackRenderLayer property) (PYME.recipes.base.ModuleBase property) (PYME.recipes.output.HDFOutput property) DefaultGlass (class in PYME.misc.zemax) DefaultList (class in PYME.IO.DataSources.BaseDataSource) DEFAULTS (PYME.Acquire.stackSettings.StackSettings attribute) DefaultShaderProgram (class in PYME.LMVis.shader_programs.DefaultShaderProgram) defm() (in module PYME.Analysis.BleachProfile.rollins) DelaunayCircumcentres (class in PYME.recipes.pointcloud) DelaunayMarchingTetrahedra (class in PYME.recipes.surface_fitting) DelaunayTesselation (class in PYME.recipes.pointcloud) DelayPanel (class in PYME.Acquire.ui.mpd_picosecond_delay_panel) delete_rule_chains() (PYME.Acquire.htsms.rule_ui.ProtocolRuleFactoryListCtrl method) delete_snapshot() (PYME.LMVis.Extras.animation.VideoPanel method) delete_texture() (PYME.LMVis.shader_programs.PointSpriteShaderProgram.GaussTexture method) delete_tile() (PYME.Analysis.tile_pyramid.NumpyTileIO method) (PYME.Analysis.tile_pyramid.SqliteTileIO method) (PYME.Analysis.tile_pyramid.TileIO method) deleteFiles() (in module PYME.misc.diskCleanup) DeleteItem() (PYME.DSView.modules.composite.ImageList method) DeletePage() (PYME.ui.AUIFrame.AUIFrame method) denominator (PYME.IO.FileUtils.obf_support.Fraction property) density (PYME.LMVis.layers.octree.OctreeRenderLayer attribute) DensityFilter (class in PYME.Analysis.density_filter) DensityFitRenderer (class in PYME.LMVis.renderers) DensityMapping (class in PYME.recipes.localisations) dependancyGraph() (PYME.recipes.recipe.Recipe method) deprecated_name() (in module PYME.IO.tabular) depth (PYME.LMVis.layers.octree.OctreeRenderLayer attribute) depth_dec() (in module PYME.Analysis.PSFEst.psfQuality) depth_loc() (in module PYME.Analysis.PSFEst.psfQuality) descr (PYME.IO.dataExporter.H5Exporter attribute) (PYME.IO.dataExporter.NumpyExporter attribute) (PYME.IO.dataExporter.OMETiffExporter attribute) (PYME.IO.dataExporter.PSFExporter attribute) (PYME.IO.dataExporter.TiffSeriesExporter attribute) (PYME.IO.dataExporter.TiffStackExporter attribute) (PYME.IO.dataExporter.TxtExporter attribute) DespeckleFilter (class in PYME.recipes.filters) destroy() (PYME.Acquire.frameWrangler.FrameWrangler method) (PYME.Acquire.zScanner.zScanner method) detach() (PYME.Acquire.Utils.fastTiler.fastTiler method) Detach() (PYME.Acquire.Utils.vibrationAnalysis.VibrAnal method) detailed_version() (in module PYME.version) Detatch() (PYME.Acquire.positionTracker.PositionTracker method) DetectPoints2D (class in PYME.recipes.measurement) dfilter() (PYME.recipes.base.Filter method) Dict (in module PYME.misc.mock_traits) DictChoiceStrEditDialog (class in PYME.ui.custom_traits_editors) DictChoiceStrPanel (class in PYME.ui.custom_traits_editors) DictFloatEditList (class in PYME.ui.custom_traits_editors) DictMDHandler (class in PYME.IO.MetaDataHandler) DictSource (class in PYME.IO.tabular) DictStrAny (in module PYME.misc.mock_traits) DictStrBool (in module PYME.misc.mock_traits)

DictStrFloat (in module PYME.misc.mock_traits) DictStrList (in module PYME.misc.mock_traits) DictStrStr (in module PYME.misc.mock_traits) dictToRecarray() (in module PYME.Analysis.processLogger) dim_order (PYME.recipes.base.Redimension attribute) dimensionality (PYME.recipes.base.ImageModuleBase attribute) (PYME.recipes.filters.DoGFilter attribute) (PYME.recipes.filters.MaskEdges attribute) (PYME.recipes.filters.Subsample attribute) (PYME.recipes.filters.Zoom attribute) (PYME.recipes.processing.Deconvolve attribute) (PYME.recipes.processing.Offset attribute) (PYME.recipes.processing.Projection attribute) (PYME.recipes.processing.Rotate180 attribute) (PYME.recipes.processing.SplineFitBackgroundEstimate attribute) dir_lock() (PYME.IO.clusterListing.DirCache method) DirCache (class in PYME.IO.clusterListing) DirCollection (class in PYME.cluster.webdav) direction_data (PYME.recipes.processing.CaWave property) direction_plot (PYME.recipes.processing.CaWave property) direction_to_nearest_n_points() (in module PYME.Analysis.points.coordinate_tools) DirectionToMask3D (class in PYME.recipes.processing) DirectoryInfoManager (class in PYME.IO.cluster_directory) dirname (PYME.Acquire.SpoolController.SpoolController property) dirname() (in module PYME.IO.unifiedIO) dirsize() (in module PYME.IO.countdir.countdir) disable_texture_2d() (PYME.LMVis.shader_programs.PointSpriteShaderProgram.GaussTexture static method) discardTrivial (PYME.recipes.localisations.MergeClumps attribute) disconnect() (PYME.contrib.dispatch.dispatcher.Signal method) disk_usage() (in module PYME.IO.FileUtils.freeSpace) dispersion_data() (in module PYME.misc.read_agf) display_dirname (PYME.Acquire.SpoolController.SpoolController property) display_name (PYME.DSView.overlays.Overlay attribute) display_normals (PYME.LMVis.layers.mesh.TriangleRenderLayer attribute) (PYME.LMVis.layers.pointcloud.PointCloudRenderLayer attribute) DisplayOpts (class in PYME.DSView.displayOptions) DisplayPane (class in PYME.LMVis.displayPane) DisplayPaneHorizontal (class in PYME.LMVis.displayPane) DisplayPaneLight (class in PYME.LMVis.displayPane) dispRatio() (in module PYME.Analysis.points.twoColour) dispSettingsFrame (class in PYME.DSView.displaySettingsPanel) dispSettingsPanel (class in PYME.DSView.displaySettingsPanel) dispSettingsPanel2 (class in PYME.DSView.displaySettingsPanel) distance (PYME.Analysis.Tracking.trackUtils.Track property) distance_to_image_mask() (in module PYME.Analysis.points.coordinate_tools) distance_to_shell() (PYME.Analysis.points.spherical_harmonics.ScaledShell method) distance_to_shell_along_vector_from_point() (PYME.Analysis.points.spherical_harmonics.ScaledShell method) distance_to_surface() (in module PYME.LMVis.Extras.extra_layers) distanceHistogram() (in module PYME.Analysis.points.DistHist.distHist) distanceHistogram3D() (in module PYME.Analysis.points.DistHist.distHist) distanceHistogram3DThreaded() (in module PYME.Analysis.points.DistHist.distHistThreaded) distanceHistogramThreaded() (in module PYME.Analysis.points.DistHist.distHistThreaded) distanceProduct() (in module PYME.Analysis.points.DistHist.distHist) DistanceToMesh (class in PYME.recipes.surface_fitting) DistanceTransform (class in PYME.recipes.processing) distfcn_oidic() (in module PYME.IO.acquisition_backends) distributed_pyramid() (in module PYME.Analysis.distributed_pyramid) DistributedImagePyramid (class in PYME.Analysis.distributed_pyramid) distribution_function_round_robin() (in module PYME.IO.cluster_streaming) distributor_url (PYME.cluster.rulenodeserver.NodeServer property) distThreshold (PYME.LMVis.triBlobs.BlobSettings attribute) Divide (class in PYME.recipes.base) dlHd() (PYME.Deconv.richardsonLucyMVM.MotionCompensatingRichardsonLucy method) dlHd2() (PYME.Deconv.richardsonLucyMVM.MotionCompensatingRichardsonLucy method) dNdfcn() (in module PYME.Analysis.BleachProfile.intensProf) dNofcn() (in module PYME.Analysis.BleachProfile.intensProf) do (PYME.Acquire.ui.intensity_trace.IntensityTracePanel property) do_COPY() (PYME.cluster.webdav.DAVRequestHandler method) do_DELETE() (PYME.cluster.webdav.DAVRequestHandler method) do_GET() (PYME.cluster.dataserver_wsgi.dataserver method) (PYME.cluster.HTTPDataServer.PYMEHTTPRequestHandler method) (PYME.cluster.webdav.DAVRequestHandler method) (PYME.util.webframework.JSONAPIRequestHandler method) do_HEAD() (PYME.cluster.dataserver_wsgi.dataserver method) (PYME.cluster.webdav.DAVRequestHandler method) do_LOCK() (PYME.cluster.webdav.DAVRequestHandler method) do_login() (PYME.Acquire.acquire_server.AcquireHTTPServer method) do_MKCOL() (PYME.cluster.webdav.DAVRequestHandler method) do_MOVE() (PYME.cluster.webdav.DAVRequestHandler method) do_OPTIONS() (PYME.cluster.webdav.DAVRequestHandler method) do_POST() (PYME.util.webframework.JSONAPIRequestHandler method) do_proj() (PYME.recipes.processing.ProjectOnVector method) do_PROPFIND() (PYME.cluster.webdav.DAVRequestHandler method) do_PROPPATCH() (PYME.cluster.webdav.DAVRequestHandler method) do_PUT() (PYME.cluster.dataserver_wsgi.dataserver method) (PYME.cluster.HTTPDataServer.PYMEHTTPRequestHandler method) (PYME.cluster.webdav.DAVRequestHandler method) do_radial_anal() (in module PYME.Analysis.points.rings) do_summary_plots() (in module PYME.Analysis.points.rings) do_UNLOCK() (PYME.cluster.webdav.DAVRequestHandler method) DockedPanel (class in PYME.LMVis.Extras.dockedPanel) DoGetBestSize() (PYME.ui.MetadataTree.MyTreeListCtrl method) DoGFilter (class in PYME.recipes.filters) DoNix() (PYME.DSView.scrolledImagePanel.ImagePanel method) doNothing() (in module PYME.misc.mock_ctypes) DoPaint() (PYME.Acquire.ui.splashScreen.SplashPanel method) (PYME.DSView.eventLogViewer.eventLogPanel method) (PYME.DSView.eventLogViewer.eventLogTPanel method) (PYME.DSView.splashScreen.SplashPanel method) (PYME.LMVis.imageView.ColourImageViewPanel method) (PYME.LMVis.imageView.ImageViewPanel method) (PYME.LMVis.imageView2.ColourImageViewPanel method) (PYME.LMVis.imageView2.ImageViewPanel method) (PYME.LMVis.view_clipping_pane.ClippingPanel method) (PYME.ui.fastGraph.FastGraphPanel method) (PYME.ui.histLimits.HistLimitPanel method) doPostInit() (PYME.Acquire.acquiremainframe.PYMEMainFrame method) (PYME.Acquire.acquirewx.PYMEMainFrame method) doStartLog() (PYME.Acquire.stackSettings.StackSettings method) doStopLog() (PYME.Acquire.stackSettings.StackSettings method) doTraceDisp() (in module PYME.Analysis.BleachProfile.intensProf) doTraceDispdl() (in module PYME.Analysis.BleachProfile.intensProf) doTraceDispdl2() (in module PYME.Analysis.BleachProfile.intensProf) downstream_outputs() (PYME.recipes.recipe.Recipe method) draw() (PYME.Acquire.htsms.rule_ui.RulePlotPanel method) (PYME.Acquire.positionTracker.TrackerPanel method) (PYME.Acquire.positionTracker.TrackerPlotPanel method) (PYME.contrib.wxPlotPanel.PlotPanel method) (PYME.DSView.fitInfo.fitDispPanel method) (PYME.DSView.modules.fastGraphPanel.GraphViewPanel method) (PYME.LMVis.colourPanel.colourPlotPanel method) (PYME.LMVis.progGraph.progPanel method) (PYME.recipes.recipeGui.RecipePlotPanel method) draw_box_pixel_coords() (PYME.DSView.arrayViewPanel.ArrayViewPanel method) draw_cross_pixel_coords() (PYME.DSView.arrayViewPanel.ArrayViewPanel method) drawGraph() (in module PYME.misc.depGraph) drawNode() (PYME.Analysis.points.QuadTree.QTrend.QTRendererNode method) drawNodeDL() (PYME.Analysis.points.QuadTree.QTrend.QTRendererNode method) drawOverlay() (PYME.DSView.modules.blobMeasure.BlobObject method) DrawOverlays() (PYME.DSView.fitInfo.FitInfoPanel method) (PYME.DSView.modules.annotation.AnnotateBase method) (PYME.DSView.modules.blobMeasure.Measurements method) (PYME.DSView.modules.flowView.FlowView method) (PYME.DSView.modules.object_tagging.ObjectTagger method) (PYME.DSView.modules.particleTracking.ParticleTrackingView method) (PYME.DSView.modules.psfExtraction.PsfExtractor method) (PYME.LMVis.imageView.ImageViewPanel method) (PYME.LMVis.imageView2.ImageViewPanel method) DrawOverlays_() (PYME.DSView.modules.flowView.FlowView method) drawProgBar() (PYME.Acquire.ui.splashScreen.SplashPanel method) (PYME.DSView.splashScreen.SplashPanel method) drawProjection() (PYME.misc.VolProj.Isosurf method) drawTetrahedra() (in module PYME.Analysis.points.SoftRend.triRend) drawTree() (PYME.Analysis.points.QuadTree.pointQT.qtBranchNode method) (PYME.Analysis.points.QuadTree.pointQT.qtLeafNode method) (PYME.Analysis.points.QuadTree.pointQTF.qtBranchNode method) (PYME.Analysis.points.QuadTree.pointQTF.qtLeafNode method) drawTriang() (in module PYME.Analysis.points.SoftRend.triRend) drawTriangles() (in module PYME.Analysis.points.SoftRend.triRend) drift_auto_corr() (in module PYME.LMVis.Extras.fiducial) drift_correct() (in module PYME.LMVis.Extras.fiducial) dsa (PYME.Acquire.frameWrangler.FrameWrangler property) dsname (PYME.LMVis.layers.image_layer.ImageRenderLayer attribute) (PYME.LMVis.layers.mesh.TriangleRenderLayer attribute) (PYME.LMVis.layers.pointcloud.PointCloudRenderLayer attribute) (PYME.LMVis.layers.quiver.QuiverRenderLayer attribute) (PYME.LMVis.layers.tracks.TrackRenderLayer attribute) dsRefresh() (PYME.DSView.dsviewer.DSViewFrame method) dsviewer_plugin_callback() (PYME.recipes.base.Filter class method) DSViewFrame (class in PYME.DSView.dsviewer) dtype (PYME.contrib.gohlke.czifile.CziFile attribute) (PYME.IO.DataSources.ArrayDataSource.ArrayDataSource property) (PYME.IO.DataSources.ArrayDataSource.XYZTCArrayDataSource property) (PYME.IO.DataSources.BaseDataSource.BaseDataSource property) (PYME.IO.dataWrap.ListWrapper property) dtypes (PYME.Analysis.Tracking.trackUtils.Clump property) (PYME.LMVis.pipeline.Pipeline property) DualMarchingCubes (class in PYME.recipes.surface_fitting) Dumbell3DFitFactory (class in PYME.localization.FitFactories.Dumbell3DFitR) Dumbell3DFitResultR() (in module PYME.localization.FitFactories.Dumbell3DFitR) DumbellFitFactory (class in PYME.localization.FitFactories.DumbellFitR) dummy (class in PYME.localization.FitFactories.Interpolators.baseInterpolator) DummyFileMember (class in PYME.cluster.webdav) dumps() (in module PYME.IO.PZFFormat) duplicateFiles() (in module PYME.IO.clusterDuplication) duration (PYME.LMVis.Extras.animation.EditPanel property) (PYME.LMVis.views.VideoView property) dx_nm (PYME.recipes.simulation.TheoreticalPSF attribute) dyedyemod() (in module PYME.Analysis.BleachProfile.rawIntensity) dyedyemod2() (in module PYME.Analysis.BleachProfile.rawIntensity) dyedyemod3() (in module PYME.Analysis.BleachProfile.rawIntensity) dyedyemoda() (in module PYME.Analysis.BleachProfile.rawIntensity) dyedyemodt() (in module PYME.Analysis.BleachProfile.rawIntensity) dz_nm (PYME.recipes.simulation.TheoreticalPSF attribute)

E

e2mod() (in module PYME.Analysis.BleachProfile.kinModels) e3mod() (in module PYME.Analysis.BleachProfile.kinModels) e4mod() (in module PYME.Analysis.BleachProfile.kinModels) e_field() (PYME.Analysis.PSFGen.fourierHNA.FourierPSF method) E_field_from_pupil_and_propagator() (in module PYME.Analysis.PSFGen.fourierHNA) edge_cutoff (PYME.LMVis.Extras.objectMeasurements.OMDialog property) edge_mask_width (PYME.recipes.measurement.DetectPoints2D attribute) EdgeDB (class in PYME.Analysis.points.EdgeDB.edges) edgeRejectionPixels (PYME.recipes.tracking.LoadSpeckles attribute) edit_no_invalidate() (PYME.recipes.base.ModuleBase method) EditableTreeList (class in PYME.ui.MetadataTree) EditDialog (class in PYME.LMVis.Extras.animation) EditListCtrl (class in PYME.ui.editList) editorBgColour (PYME.contrib.listctrlMixins.TextEditMixin attribute) (PYME.ui.MetadataTree.TextEditMixin attribute) editorFgColour (PYME.contrib.listctrlMixins.TextEditMixin attribute) (PYME.ui.MetadataTree.TextEditMixin attribute) EditPanel (class in PYME.LMVis.Extras.animation) EField_from_pupil_and_propagator() (in module PYME.Analysis.PSFGen.fourierHNA) (in module PYME.Analysis.PSFGen.fourierHNA2) efunc() (in module PYME.misc.kdFit) ei2mod() (in module PYME.Analysis.BleachProfile.kinModels) ei3mod() (in module PYME.Analysis.BleachProfile.kinModels) eimod() (in module PYME.Analysis.BleachProfile.kinModels) emg() (in module PYME.localization.Test.fitTestJig) (in module PYME.localization.Test.fitTestJigSCMOS) (in module PYME.localization.Test.fitTestJigWC) eMod() (in module PYME.Analysis.BleachProfile.intensProf) emod() (in module PYME.Analysis.BleachProfile.kinModels) eMod2() (in module PYME.Analysis.BleachProfile.intensProf) eMod3() (in module PYME.Analysis.BleachProfile.intensProf) eMod4() (in module PYME.Analysis.BleachProfile.intensProf) eMod5() (in module PYME.Analysis.BleachProfile.intensProf) EmptyBitmap() (in module PYME.ui.wx_compat) EmptyImage() (in module PYME.ui.wx_compat) emptyListDict (class in PYME.Analysis.points.gen3DTriangs) enable_texture_2d() (PYME.LMVis.shader_programs.PointSpriteShaderProgram.GaussTexture static method) EnableJoystick() (PYME.Acquire.microscope.microscope method) encode() (PYME.contrib.lzw.Encoder method) encodepages() (PYME.contrib.lzw.PagingEncoder method) Encoder (class in PYME.contrib.lzw) encodetobytes() (PYME.contrib.lzw.ByteEncoder method) encoding (PYME.Acquire.webui.ipy.TTYDummy attribute) end (PYME.recipes.processing.DarkAndVarianceMap attribute) end_frame (PYME.recipes.processing.CaWave property) EndSelection() (PYME.DSView.displayOptions.DisplayOpts method) (PYME.LMVis.imageView.ImageViewPanel method) (PYME.LMVis.imageView2.ImageViewPanel method) engine (PYME.LMVis.layers.base.EngineLayer attribute) EngineLayer (class in PYME.LMVis.layers.base) ensure_VM() (in module PYME.IO.DataSources.BioformatsDataSource) EntryGrid (class in PYME.misc.editgrid) Enum (in module PYME.misc.mock_traits) EnumEditor() (in module PYME.misc.mock_traitsui) epsilon (PYME.recipes.measurement.ChunkedTravelingSalesperson attribute) (PYME.recipes.measurement.TravelingSalesperson attribute) errFunc() (PYME.misc.coverslipGeometries.circGeom method) error() (PYME.localization.Test.fitTestJig.fitTestJig method) (PYME.localization.Test.fitTestJigSCMOS.fitTestJig method) (PYME.localization.Test.fitTestJigWC.fitTestJig method) errorPlot() (in module PYME.Analysis.binAvg) errors (PYME.Acquire.webui.ipy.TTYDummy attribute) estimate_circumcentre_densities() (in module PYME.LMVis.Extras.extra_layers) estimate_density() (in module PYME.LMVis.Extras.extra_layers) EstimateFrameZFromStepMetadata (class in PYME.recipes.fudges) estimateFromSource() (PYME.IO.image.ImageBounds class method) (PYME.LMVis.visHelpersMin.ImageBounds class method) eth_mod2() (in module PYME.Analysis.BleachProfile.intensProf) eth_mod3() (in module PYME.Analysis.BleachProfile.intensProf) ethet3() (in module PYME.Analysis.BleachProfile.intensProf) ev() (PYME.Analysis.points.twoColour.lin2Model method) (PYME.Analysis.points.twoColour.lin3Model method) (PYME.Analysis.points.twoColour.lin3zModel method) (PYME.Analysis.points.twoColour.linModel method) (PYME.Analysis.points.twoColour.sffake method) (PYME.misc.sffake.sffake method) evalModel() (PYME.localization.FitFactories.AstigGaussFitFR.GaussianFitFactory class method) (PYME.localization.FitFactories.AstigGaussGPUFitFR.GaussianFitFactory class method) (PYME.localization.FitFactories.BeadConvolvedAstigGaussFit.GaussianFitFactory class method) (PYME.localization.FitFactories.Dumbell3DFitR.Dumbell3DFitFactory class method) (PYME.localization.FitFactories.DumbellFitR.DumbellFitFactory class method) (PYME.localization.FitFactories.GaussFitConstrR.GaussianFitFactory class method) (PYME.localization.FitFactories.GaussMultifitLinesR.GaussianFitFactory class method) (PYME.localization.FitFactories.GaussMultifitR.GaussianFitFactory class method) (PYME.localization.FitFactories.GaussMultifitSR.GaussianFitFactory class method) (PYME.localization.FitFactories.InterpFitR.PSFFitFactory class method) (PYME.localization.FitFactories.LatGaussFitFR.GaussianFitFactory class method) (PYME.localization.FitFactories.MultiviewFitInterpNR.InterpFitFactory class method) (PYME.localization.FitFactories.PRInterpFitQR.PSFFitFactory class method) (PYME.localization.FitFactories.PRInterpFitR.PSFFitFactory class method) (PYME.localization.FitFactories.SpecGaussFitFR.GaussianFitFactory class method) (PYME.localization.FitFactories.SplitterFitFNR.GaussianFitFactory class method) (PYME.localization.FitFactories.SplitterFitFusionR.GaussianFitFactory class method) (PYME.localization.FitFactories.SplitterFitInterpBNR.InterpFitFactory class method) (PYME.localization.FitFactories.SplitterFitInterpNR.InterpFitFactory class method) (PYME.localization.FitFactories.SplitterFitScavNR.GaussianFitFactory class method) (PYME.localization.FitFactories.SplitterMultifitSR.GaussianFitFactory class method) evalParams() (PYME.localization.Test.fitTestJigSCMOS.fitTestJig method) eventFileName (PYME.IO.DataSources.ClusterPZFDataSource.DataSource property) eventify() (in module PYME.simulation.locify) eventify2() (in module PYME.simulation.locify)

eventInfo (class in PYME.misc.eventSpy) EventLogger (class in PYME.IO.events) eventLogPanel (class in PYME.DSView.eventLogViewer) eventLogTPanel (class in PYME.DSView.eventLogViewer) EventLoop (class in PYME.Acquire.event_loop) events (PYME.IO.h5rFile.H5RFile property) Ex() (in module PYME.Acquire.protocol) excepthook() (in module PYME.misc.pyro_tracebacks) excitation_wavelength (PYME.recipes.simulation.TheoreticalPSF attribute) execBG() (in module PYME.Acquire.ExecTools) execFile() (in module PYME.Acquire.ExecTools) execFileBG() (in module PYME.Acquire.ExecTools) execute() (PYME.recipes.base.ModuleBase method) (PYME.recipes.base.OutputModule method) (PYME.recipes.fudges.EstimateFrameZFromStepMetadata method) (PYME.recipes.localisations.MapAstigZ method) (PYME.recipes.measurement.ChunkedTravelingSalesperson method) (PYME.recipes.measurement.Plot method) (PYME.recipes.measurement.TravelingSalesperson method) (PYME.recipes.multiview.CalibrateShifts method) (PYME.recipes.multiview.ExtractMultiviewChannel method) (PYME.recipes.multiview.FindClumps method) (PYME.recipes.multiview.Fold method) (PYME.recipes.multiview.MapAstigZ method) (PYME.recipes.multiview.MergeClumps method) (PYME.recipes.multiview.ShiftCorrect method) (PYME.recipes.pointcloud.DelaunayCircumcentres method) (PYME.recipes.pointcloud.DelaunayTesselation method) (PYME.recipes.pointcloud.GaussianMixtureModel method) (PYME.recipes.pointcloud.LocalPointDensity method) (PYME.recipes.pointcloud.Octree method) (PYME.recipes.pointcloud.Ripleys method) (PYME.recipes.processing.Composite method) (PYME.recipes.recipe.Recipe method) (PYME.recipes.surface_fitting.AddSphericalHarmonicShellMappedCoords method) (PYME.recipes.surface_fitting.DelaunayMarchingTetrahedra method) (PYME.recipes.surface_fitting.DistanceToMesh method) (PYME.recipes.surface_fitting.DualMarchingCubes method) (PYME.recipes.surface_fitting.FilterMeshComponentsByVolume method) (PYME.recipes.surface_fitting.FitSurfaceWithPatches method) (PYME.recipes.surface_fitting.ImageMaskFromSphericalHarmonicShell method) (PYME.recipes.surface_fitting.Isosurface method) (PYME.recipes.surface_fitting.SHShellRadiusDensityEstimate method) (PYME.recipes.surface_fitting.SphericalHarmonicShell method) (PYME.recipes.tracking.ExtractTracks method) (PYME.recipes.tracking.FindClumps method) (PYME.recipes.tracking.FitFusionTraces method) (PYME.recipes.tracking.LoadSpeckles method) (PYME.recipes.tracking.TrackFeatures method) execute_on_invalidation (PYME.recipes.recipe.Recipe attribute) exists() (in module PYME.IO.clusterIO) (in module PYME.IO.HTTPSpooler) (in module PYME.IO.HTTPSpooler_v2) (PYME.Analysis.tile_pyramid.TileCache method) (PYME.IO.cluster_directory.DirectoryInfoManager method) expired (PYME.cluster.ruleserver.IntegerIDRule property) Export() (PYME.IO.dataExporter.Exporter method) (PYME.IO.dataExporter.H5Exporter method) (PYME.IO.dataExporter.NumpyExporter method) (PYME.IO.dataExporter.OMETiffExporter method) (PYME.IO.dataExporter.PSFExporter method) (PYME.IO.dataExporter.TiffSeriesExporter method) (PYME.IO.dataExporter.TiffStackExporter method) (PYME.IO.dataExporter.TxtExporter method) ExportData() (in module PYME.IO.dataExporter) ExportDialog (class in PYME.ui.crop_dialog) Exporter (class in PYME.IO.dataExporter) exporter() (in module PYME.IO.dataExporter) ExportImageToCluster() (in module PYME.IO.clusterExport) ExportStackToPNG() (PYME.DSView.arrayViewPanel.ArrayViewPanel method) ExtendContext() (PYME.Analysis.processLogger.ContextManager method) extension (PYME.IO.dataExporter.H5Exporter attribute) (PYME.IO.dataExporter.NumpyExporter attribute) (PYME.IO.dataExporter.OMETiffExporter attribute) (PYME.IO.dataExporter.PSFExporter attribute) (PYME.IO.dataExporter.TiffSeriesExporter attribute) (PYME.IO.dataExporter.TiffStackExporter attribute) (PYME.IO.dataExporter.TxtExporter attribute) extensions_map (PYME.cluster.dataserver_wsgi.dataserver attribute) (PYME.util.webframework.StaticFileHandler attribute) extent (PYME.IO.image.ImageBounds property) extra_template_kwargs() (PYME.cluster.taskWorkerHTTP.RecipeTaskError method) (PYME.cluster.taskWorkerHTTP.TaskError method) extract_profile() (in module PYME.Analysis.profile_extraction) extractAverageTrajectory() (in module PYME.Analysis.points.fiducials) extractBlobs() (in module PYME.DSView.modules.extractBlobs) ExtractChannel (class in PYME.recipes.base) extractFeatures() (in module PYME.Analysis.svmSegment) extractFeatures2() (in module PYME.Analysis.svmSegment) extractFrames() (in module PYME.IO.FileUtils.h5ExFrames) extractFramesF() (in module PYME.IO.FileUtils.h5ExFrames) extractFromMetadata() (PYME.IO.image.ImageBounds class method) extractIms() (in module PYME.Analysis.PSFEst.extractImages) ExtractMultiviewChannel (class in PYME.recipes.multiview) ExtractPupil() (in module PYME.Analysis.PSFGen.fourierHNA) (in module PYME.Analysis.PSFGen.fourierHNA2) ExtractROIs (class in PYME.recipes.measurement) ExtractTableChannel (class in PYME.recipes.localisations) ExtractTracks (class in PYME.recipes.tracking) extraMetadata (PYME.recipes.output.HDFOutput attribute) (PYME.recipes.output.ImageOutput attribute)

F

f() (in module PYME.Analysis.points.surfit) f_dumbell() (in module PYME.localization.FitFactories.DumbellFitR) f_dumbell3d() (in module PYME.localization.FitFactories.Dumbell3DFitR) f_gauss1d() (in module PYME.localization.FitFactories.SpecGaussFitFR) f_gauss2d() (in module PYME.localization.FitFactories.GaussFitConstrR) (in module PYME.localization.FitFactories.GaussMultifitR) (in module PYME.localization.FitFactories.LatGaussFitFR) (in module PYME.localization.FitFactories.SplitterFitFusionR) (in module PYME.localization.FitFactories.SplitterMultifitSR) f_gauss2d2c() (in module PYME.localization.FitFactories.SplitterFitFNR) (in module PYME.localization.FitFactories.SplitterFitFusionR) (in module PYME.localization.FitFactories.SplitterFitScavNR) (in module PYME.localization.FitFactories.SplitterObjFindR) (in module PYME.localization.FitFactories.SplitterShiftEstFR) f_gauss2d2cA() (in module PYME.localization.FitFactories.SplitterFitFNR) (in module PYME.localization.FitFactories.SplitterFitFusionR) (in module PYME.localization.FitFactories.SplitterFitScavNR) f_gauss2d2ccb() (in module PYME.localization.FitFactories.SplitterFitFNR) (in module PYME.localization.FitFactories.SplitterFitFusionR) (in module PYME.localization.FitFactories.SplitterFitScavNR) f_gauss2d_no_bg() (in module PYME.localization.FitFactories.LatGaussFitFR) f_gauss2dF() (in module PYME.localization.FitFactories.GaussFitConstrR) (in module PYME.localization.FitFactories.GaussMultifitR) (in module PYME.localization.FitFactories.LatGaussFitFR) (in module PYME.localization.FitFactories.SplitterMultifitSR) f_gauss2dSlow() (in module PYME.localization.FitFactories.GaussFitConstrR) (in module PYME.localization.FitFactories.GaussMultifitR) (in module PYME.localization.FitFactories.LatGaussFitFR) (in module PYME.localization.FitFactories.SplitterMultifitSR) f_Gauss3d() (in module PYME.localization.FitFactories.Gauss3DFitR) f_gaussAstigBead() (in module PYME.localization.FitFactories.BeadConvolvedAstigGaussFit) f_gaussAstigSlow() (in module PYME.localization.FitFactories.AstigGaussFitFR) f_Interp3d() (in module PYME.localization.autopsf.roifit) (in module PYME.localization.FitFactories.InterpFitR) (in module PYME.localization.FitFactories.PRInterpFitQR) (in module PYME.localization.FitFactories.PRInterpFitR) f_Interp3d2c() (in module PYME.localization.FitFactories.SplitterFitInterpNR) f_Interp3d2cr() (in module PYME.localization.autopsf.roifit) (in module PYME.localization.FitFactories.SplitterFitInterpBNR) f_Interp3Dmultiview() (in module PYME.localization.FitFactories.MultiviewFitInterpNR) f_J_gauss2d() (in module PYME.localization.FitFactories.GaussFitConstrR) f_j_gauss2d() (in module PYME.localization.FitFactories.GaussFitConstrR) f_J_gauss2d() (in module PYME.localization.FitFactories.GaussMultifitR) f_j_gauss2d() (in module PYME.localization.FitFactories.GaussMultifitR) f_J_gauss2d() (in module PYME.localization.FitFactories.LatGaussFitFR) f_j_gauss2d() (in module PYME.localization.FitFactories.LatGaussFitFR) f_J_gauss2d() (in module PYME.localization.FitFactories.SplitterMultifitSR) f_j_gauss2d() (in module PYME.localization.FitFactories.SplitterMultifitSR) f_J_Interp3d2c() (in module PYME.localization.FitFactories.SplitterFitInterpBNR) (in module PYME.localization.FitFactories.SplitterFitInterpNR) f_J_Interp3Dmultiview() (in module PYME.localization.FitFactories.MultiviewFitInterpNR) f_multiGauss() (in module PYME.localization.FitFactories.GaussMultifitLinesR) (in module PYME.localization.FitFactories.GaussMultifitR) (in module PYME.localization.FitFactories.GaussMultifitSR) (in module PYME.localization.FitFactories.SplitterMultifitSR) f_multiGaussJ() (in module PYME.localization.FitFactories.GaussMultifitLinesR) (in module PYME.localization.FitFactories.GaussMultifitR) (in module PYME.localization.FitFactories.GaussMultifitSR) (in module PYME.localization.FitFactories.SplitterMultifitSR) f_multiGaussS() (in module PYME.localization.FitFactories.GaussMultifitLinesR) (in module PYME.localization.FitFactories.GaussMultifitR) (in module PYME.localization.FitFactories.GaussMultifitSR) (in module PYME.localization.FitFactories.SplitterMultifitSR) f_PSF3d() (in module PYME.localization.FitFactories.LatPSFFitR) f_rotGaussAstigBead() (in module PYME.localization.FitFactories.BeadConvolvedAstigGaussFit) face_normals (PYME.recipes.pointcloud.Tesselation property) faces (PYME.recipes.pointcloud.Tesselation property) facsPlotContour() (in module PYME.misc.facsPlot) facsPlotScatter() (in module PYME.misc.facsPlot) facsPlotScatter2() (in module PYME.misc.facsPlot) facsPlotScatterLog() (in module PYME.misc.facsPlot) Failsafe (class in PYME.Acquire.Utils.failsafe) FailsafeClient (class in PYME.Acquire.Utils.failsafe) FailsafeServer (class in PYME.Acquire.Utils.failsafe) FakeAPI (class in PYME.Acquire.htsms.tweeter) fast_grey() (in module PYME.DSView.displayOptions) fast_validate (PYME.recipes.traits.Input attribute) (PYME.recipes.traits.Output attribute) FastGraphPanel (class in PYME.ui.fastGraph) fastRectTiler (class in PYME.Acquire.Utils.fastTiler) fastTiler (class in PYME.Acquire.Utils.fastTiler) FeatureMean (class in PYME.Analysis.Tracking.trackUtils) FeaturePlot (class in PYME.Analysis.Tracking.trackUtils) features (PYME.recipes.tracking.TrackFeatures attribute) FeatureStd (class in PYME.Analysis.Tracking.trackUtils) FFBase (class in PYME.localization.FitFactories.FFBase) fftwWeiner (class in PYME.localization.ofind_xcorr_fw) fibre10nm() (in module PYME.simulation.wormlike2) (in module PYME.simulation.wormlike3) (in module PYME.simulation.wormlike_curled) fibre30nm() (in module PYME.simulation.wormlike) (in module PYME.simulation.wormlike2) (in module PYME.simulation.wormlike3) (in module PYME.simulation.wormlike_curled) fiducial_diagnosis() (in module PYME.LMVis.Extras.fiducial) fiducial_diagnosis_1() (in module PYME.LMVis.Extras.fiducial) FiducialCorrection (class in PYME.recipes.localisations) FIkz() (in module PYME.Analysis.cramerRao) File (class in PYME.IO.FileUtils.obf_support) (in module PYME.misc.mock_traits) file (PYME.simulation.pointsets.FileSource attribute) file_header_unpack() (in module PYME.IO.FileUtils.obf_support) file_info() (in module PYME.IO.countdir.countdir) file_inputs (PYME.recipes.base.ModuleBase property) (PYME.recipes.recipe.Recipe property) filebytes() (in module PYME.contrib.lzw) fileFitResult() (PYME.IO.h5rFile.H5RFile method) fileFormattedResults() (in module PYME.IO.clusterResults) FileInfo (class in PYME.IO.clusterListing) FileListPanel (class in PYME.recipes.recipeGui) FileMember (class in PYME.cluster.webdav) filename (PYME.LMVis.Extras.snapshot.SnapshotSettings attribute) filename() (PYME.contrib.gohlke.fcsfiles.ConfoCor3Raw method) FilenameParam (class in PYME.localization.MetaDataEdit) filenames (PYME.recipes.recipeGui.FileListPanel property) fileno() (PYME.Acquire.webui.ipy.TTYDummy method) FileOrURI (class in PYME.recipes.traits) filePattern (PYME.recipes.base.OutputModule attribute) (PYME.recipes.output.HDFOutput attribute) (PYME.recipes.output.ImageOutput attribute) (PYME.recipes.output.PlotOutput attribute) (PYME.recipes.output.ReportForEachOutput attribute) (PYME.recipes.output.ReportOutput attribute) (PYME.recipes.output.RGBImageOutput attribute) (PYME.recipes.output.STLOutput attribute) (PYME.recipes.output.XLSOutput attribute) (PYME.recipes.pyramid.TilePyramid attribute) fileResults() (in module PYME.IO.clusterResults) FileSelectionError FileSource (class in PYME.simulation.pointsets) fileTasksForFrames() (PYME.cluster.HTTPRulePusher.HTTPRulePusher method) (PYME.cluster.HTTPTaskPusher.HTTPTaskPusher method) fileTasksForInputs() (PYME.cluster.HTTPRulePusher.RecipePusher method) (PYME.cluster.HTTPTaskPusher.RecipePusher method) fileType (PYME.LMVis.importTextDialog.ColumnMappingDialog attribute) (PYME.LMVis.importTextDialog.ImportMatlabDialog attribute) (PYME.LMVis.importTextDialog.ImportTextDialog attribute) FILETYPE_SERIES_COMPLETE (in module PYME.IO.clusterListing) fillInBlanks() (in module PYME.Analysis.MetaData) Filter (class in PYME.recipes.base) filter() (PYME.Analysis.density_filter.DensityFilter method) (PYME.localization.ofind_xcorr_fw.fftwWeiner method) (PYME.recipes.base.ArithmaticFilter method) (PYME.recipes.base.Filter method) (PYME.recipes.processing.Watershed method) filter_quad_results() (in module PYME.Analysis.points.surfit) filter_radius_highpass (PYME.recipes.measurement.DetectPoints2D attribute) filter_radius_lowpass (PYME.recipes.measurement.DetectPoints2D attribute) filtered (PYME.Analysis.Tracking.trackUtils.TrackManager property) filtered_subblock_directory (PYME.contrib.gohlke.czifile.CziFile attribute) FilterEditDialog (class in PYME.ui.editFilterDialog) Filterer (class in PYME.DSView.modules.filtering) filterer (class in PYME.DSView.modules.sparkprepare) filterKeys (PYME.ui.filterPane.FilterPane property) FilterMeshComponentsByVolume (class in PYME.recipes.surface_fitting) FilterPane (class in PYME.DSView.modules.measure.filterPan) (class in PYME.ui.filterPane) FilterPanel (class in PYME.ui.filterPane) filterRadius (PYME.recipes.processing.OpticalFlow attribute) filters (PYME.recipes.tablefilters.FilterTable attribute) FilterTable (class in PYME.recipes.tablefilters) FilterTableByIDs (class in PYME.recipes.tablefilters) fImod() (in module PYME.Analysis.BleachProfile.kinModels) finalise() (PYME.Analysis.distributed_pyramid.PartialPyramid method) (PYME.IO.acquisition_backends.Backend method) (PYME.IO.acquisition_backends.ClusterBackend method) (PYME.IO.acquisition_backends.HDFBackend method) (PYME.IO.HDFSpooler.Spooler method) (PYME.IO.HTTPSpooler.Spooler method) (PYME.IO.HTTPSpooler_v2.Spooler method) (PYME.IO.Spooler.Spooler method) finalize() (PYME.IO.cluster_streaming.Stream method) find_and_add_zRange() (in module PYME.Analysis.points.astigmatism.astigTools) find_catalog() (in module PYME.misc.read_agf) find_clumps() (in module PYME.Analysis.points.multiview) find_clumps_within_channel() (in module PYME.Analysis.points.multiview) find_glassdict() (in module PYME.misc.read_agf) find_points_within_cone() (in module PYME.Analysis.points.coordinate_tools) find_points_within_cylinder() (in module PYME.Analysis.points.coordinate_tools) find_principle_axes() (in module PYME.Analysis.points.coordinate_tools) find_stack_by_name() (PYME.IO.FileUtils.obf_support.File method) FindAndFit() (PYME.localization.FitFactories.AstigGaussGPUFitFR.GaussianFitFactory method) (PYME.localization.FitFactories.ChecksumGPUFR.ChecksumFitFactory method) (PYME.localization.FitFactories.ChecksumMultifitSR.ChecksumFitFactory method) (PYME.localization.FitFactories.GaussMultifitLinesR.GaussianFitFactory method) (PYME.localization.FitFactories.GaussMultifitR.GaussianFitFactory method) (PYME.localization.FitFactories.GaussMultifitSR.GaussianFitFactory method) (PYME.localization.FitFactories.SplitterMultifitSR.GaussianFitFactory method) FindCaWaves (class in PYME.recipes.processing) FindClumps (class in PYME.recipes.multiview) (class in PYME.recipes.tracking) findClumps() (in module PYME.Analysis.points.DeClump) (in module PYME.Analysis.points.DeClump.deClump) findClumpsN() (in module PYME.Analysis.points.DeClump.deClump) findConnected() (in module PYME.Analysis.points.DeClump.pyDeClump) FINDING_PARAMS (PYME.DSView.modules.LMAnalysis.AnalysisSettingsView attribute) findMember() (PYME.cluster.webdav.DirCollection method) (PYME.cluster.webdav.TempDirCollection method) FindObjects() (PYME.localization.ofind.ObjectIdentifier method) (PYME.localization.ofind3d.ObjectIdentifier method) (PYME.localization.ofind_nofilt.ObjectIdentifier method) (PYME.localization.ofind_pri.ObjectIdentifier method) (PYME.localization.ofind_split.ObjectIdentifier method) (PYME.localization.ofind_xcorr.ObjectIdentifier method) (PYME.localization.ofind_xcorr_fw.ObjectIdentifier method) findRectangularROIs() (in module PYME.Analysis.deTile) findTracks() (in module PYME.Analysis.Tracking.trackUtils) findTracks2() (in module PYME.Analysis.Tracking.trackUtils) findWonkyVectors() (in module PYME.Analysis.points.twoColour) finish (PYME.ui.selection.Selection property) finish() (PYME.Acquire.xyztc.XYZTCAcquisition method) finish_base_tiles() (PYME.Analysis.distributed_pyramid.DistributedImagePyramid method) (PYME.Analysis.tile_pyramid.ImagePyramid method) finish_request() (PYME.cluster.webdav.DAVServer method) finished (PYME.cluster.ruleserver.IntegerIDRule property) finished() (PYME.IO.HTTPSpooler.Spooler method) (PYME.IO.HTTPSpooler_v2.Spooler method) (PYME.IO.Spooler.Spooler method) fit() (in module PYME.Analysis.points.qpaint) (PYME.Analysis.points.spherical_harmonics.SHShell method) (PYME.Analysis.points.twoColour.lin2Model method) (PYME.Analysis.points.twoColour.lin3Model method) (PYME.Analysis.points.twoColour.lin3zModel method) (PYME.Analysis.points.twoColour.linModel method) (PYME.Analysis.points.twoColour.sffake method) (PYME.localization.autopsf.autopsf.ZernikePSFModel method) Fit() (PYME.misc.coverslipGeometries.geom method) fit_influence_radius (PYME.recipes.surface_fitting.FitSurfaceWithPatches attribute) fit_model() (in module PYME.Analysis.autoencoder_classifier) fit_quad_surf() (in module PYME.Analysis.points.surfit) fit_quad_surf_to_neighbourbood() (in module PYME.Analysis.points.surfit) fit_quad_surfaces() (in module PYME.Analysis.points.surfit) fit_quad_surfaces_P() (in module PYME.Analysis.points.surfit) fit_quad_surfaces_Pr() (in module PYME.Analysis.points.surfit) fit_quad_surfaces_t() (in module PYME.Analysis.points.surfit) fit_quad_surfaces_tr() (in module PYME.Analysis.points.surfit) fit_shell() (PYME.Analysis.points.spherical_harmonics.ScaledShell method) fitallA() (in module PYME.localization.autopsf.roifit) fitDarktimes() (in module PYME.LMVis.objectDarkMeasure) fitDecay() (in module PYME.Analysis.BleachProfile.kinModels) FitDefaults (class in PYME.DSView.modules.LMAnalysis)

fitDispPanel (class in PYME.DSView.fitInfo) FitDumbells (class in PYME.recipes.measurement) FitFactory (in module PYME.localization.FitFactories.AstigGaussFitFR) (in module PYME.localization.FitFactories.AstigGaussGPUFitFR) (in module PYME.localization.FitFactories.BeadConvolvedAstigGaussFit) (in module PYME.localization.FitFactories.ChecksumFR) (in module PYME.localization.FitFactories.ChecksumGPUFR) (in module PYME.localization.FitFactories.ChecksumMultifitSR) (in module PYME.localization.FitFactories.Dumbell3DFitR) (in module PYME.localization.FitFactories.DumbellFitR) (in module PYME.localization.FitFactories.FFBase) (in module PYME.localization.FitFactories.Gauss3DFitR) (in module PYME.localization.FitFactories.GaussFitConstrR) (in module PYME.localization.FitFactories.GaussMultifitLinesR) (in module PYME.localization.FitFactories.GaussMultifitR) (in module PYME.localization.FitFactories.GaussMultifitSR) (in module PYME.localization.FitFactories.InterpFitR) (in module PYME.localization.FitFactories.InterpFitWFR) (in module PYME.localization.FitFactories.LatFitCOIR) (in module PYME.localization.FitFactories.LatGaussFitFR) (in module PYME.localization.FitFactories.LatObjFindFR) (in module PYME.localization.FitFactories.LatPSFFitR) (in module PYME.localization.FitFactories.MultiviewFitInterpNR) (in module PYME.localization.FitFactories.PRInterpFitQR) (in module PYME.localization.FitFactories.PRInterpFitR) (in module PYME.localization.FitFactories.ROIExtractNR) (in module PYME.localization.FitFactories.SpecGaussFitFR) (in module PYME.localization.FitFactories.SplitterFitCOIR) (in module PYME.localization.FitFactories.SplitterFitFNR) (in module PYME.localization.FitFactories.SplitterFitFusionR) (in module PYME.localization.FitFactories.SplitterFitInterpBNR) (in module PYME.localization.FitFactories.SplitterFitInterpNR) (in module PYME.localization.FitFactories.SplitterFitScavNR) (in module PYME.localization.FitFactories.SplitterMultifitSR) (in module PYME.localization.FitFactories.SplitterObjFindR) (in module PYME.localization.FitFactories.SplitterROIExtractNR) (in module PYME.localization.FitFactories.SplitterShiftEstFR) FitFactory() (in module PYME.localization.FitFactories.ConfocCOIR) fitFluorBrightness() (in module PYME.Analysis.BleachProfile.kinModels) fitFluorBrightnessT() (in module PYME.Analysis.BleachProfile.kinModels) FitFusionTraces (class in PYME.recipes.tracking) fitIndep() (in module PYME.Analysis.points.twoColour) FitInfoPanel (class in PYME.DSView.fitInfo) FitJumpSizeDist() (in module PYME.Analysis.Tracking.trackUtils) fitKD() (in module PYME.misc.kdFit) fitMod (PYME.localization.remFitBuf.fitTask property) fITmod() (in module PYME.Analysis.BleachProfile.kinModels) fITmod2() (in module PYME.Analysis.BleachProfile.kinModels) FitModel_N() (in module PYME.Analysis.BleachProfile.rollins) FitModel_NB() (in module PYME.Analysis.BleachProfile.rollins) FitModelG() (in module PYME.Analysis.BleachProfile.kinModels) fitModule (PYME.recipes.measurement.FitPoints attribute) fitOnTimes() (in module PYME.Analysis.BleachProfile.kinModels) FitPoints (class in PYME.recipes.measurement) fitPtA() (in module PYME.Analysis.points.surfit) fitPts() (in module PYME.Analysis.points.surfit) fitPtsA() (in module PYME.Analysis.points.surfit) fitPtsAP() (in module PYME.Analysis.points.surfit) fitPtsAt() (in module PYME.Analysis.points.surfit) fitResult (class in PYME.localization.remFitBuf) FitResult() (in module PYME.localization.FitFactories.ConfocCOIR) (in module PYME.localization.FitFactories.Dumbell3DFitR) (in module PYME.localization.FitFactories.DumbellFitR) (in module PYME.localization.FitFactories.Gauss3DFitR) (in module PYME.localization.FitFactories.GaussFitConstrR) (in module PYME.localization.FitFactories.GaussMultifitLinesR) (in module PYME.localization.FitFactories.GaussMultifitR) (in module PYME.localization.FitFactories.InterpFitR) (in module PYME.localization.FitFactories.LatFitCOIR) (in module PYME.localization.FitFactories.LatGaussFitFR) (in module PYME.localization.FitFactories.LatObjFindFR) (in module PYME.localization.FitFactories.LatPSFFitR) (in module PYME.localization.FitFactories.MultiviewFitInterpNR) (in module PYME.localization.FitFactories.PRInterpFitQR) (in module PYME.localization.FitFactories.PRInterpFitR) (in module PYME.localization.FitFactories.SpecGaussFitFR) (in module PYME.localization.FitFactories.SplitterFitCOIR) (in module PYME.localization.FitFactories.SplitterFitFNR) (in module PYME.localization.FitFactories.SplitterFitFusionR) (in module PYME.localization.FitFactories.SplitterFitInterpBNR) (in module PYME.localization.FitFactories.SplitterFitInterpNR) (in module PYME.localization.FitFactories.SplitterFitScavNR) (in module PYME.localization.FitFactories.SplitterMultifitSR) (in module PYME.localization.FitFactories.SplitterObjFindR) (in module PYME.localization.FitFactories.SplitterShiftEstFR) FitResultR() (in module PYME.localization.FitFactories.DumbellFitR) (in module PYME.simulation.locify) FitResultsDType() (in module PYME.localization.FitFactories.MultiviewFitInterpNR) FitResultsSource (class in PYME.IO.tabular) fitResultsSource() (in module PYME.IO.tabular) fitROI() (in module PYME.localization.autopsf.roifit) FitSurfaceWithPatches (class in PYME.recipes.surface_fitting) fitTask (class in PYME.localization.remFitBuf) Fitter (class in PYME.DSView.modules.profileFitting) fitTestJig (class in PYME.localization.Test.fitTestJig) (class in PYME.localization.Test.fitTestJigSCMOS) (class in PYME.localization.Test.fitTestJigWC) FitTrace() (in module PYME.Analysis.BleachProfile.fitRecover) fix_name() (in module PYME.IO.unifiedIO) fixEMGain() (in module PYME.Analysis.MetaData) flag_piezo_movement() (in module PYME.Analysis.piezo_movement_correction) flat() (in module PYME.DSView.modules.dark_and_flatfield) FlatFaceEngine (class in PYME.LMVis.layers.mesh) flatfieldFilename (PYME.recipes.processing.FlatfiledAndDarkCorrect attribute) FlatfiledAndDarkCorrect (class in PYME.recipes.processing) flatten (PYME.simulation.pointsets.WiglyFibreSource attribute) flF2() (in module PYME.Analysis.BleachProfile.deMod) flF2Mod() (in module PYME.Analysis.BleachProfile.deMod) flFpow() (in module PYME.Analysis.BleachProfile.deMod) flFsq() (in module PYME.Analysis.BleachProfile.deMod) flFsq1() (in module PYME.Analysis.BleachProfile.deMod) flip() (PYME.LMVis.Extras.scaleBox.ScaleBoxPanel method) flip_starts() (PYME.LMVis.layers.ScaleBoxOverlayLayer.ScaleBoxOverlayLayer method) flipSecondaryAxis() (PYME.DSView.modules.blobMeasure.DataBlock method) Float (class in PYME.misc.mock_traits) FloatListParam (class in PYME.localization.MetaDataEdit) FloatParam (class in PYME.localization.MetaDataEdit) flowImage (PYME.DSView.modules.flowView.FlowView property) flowImageName (PYME.DSView.modules.flowView.FlowView attribute) flowMaskName (PYME.DSView.modules.flowView.FlowView attribute) flowScale (PYME.recipes.processing.DeconvolveMotionCompensating attribute) flowVectArrowSize (PYME.DSView.modules.flowView.FlowView attribute) flowVectScale (PYME.DSView.modules.flowView.FlowView attribute) flowVectSpacing (PYME.DSView.modules.flowView.FlowView attribute) flowVectThresh (PYME.DSView.modules.flowView.FlowView attribute) flowVectType (PYME.DSView.modules.flowView.FlowView attribute) flowVectWidth (PYME.DSView.modules.flowView.FlowView attribute) FlowView (class in PYME.DSView.modules.flowView) fluorSpecies (PYME.LMVis.pipeline.Pipeline property) fluorSpeciesDyes (PYME.LMVis.pipeline.Pipeline property) flush() (PYME.Analysis.tile_pyramid.NumpyTileIO method) (PYME.Analysis.tile_pyramid.SqliteTileIO method) (PYME.Analysis.tile_pyramid.TileCache method) (PYME.Analysis.tile_pyramid.TileIO method) (PYME.cluster.webdav.BufWriter method) (PYME.contrib.lzw.Encoder method) (PYME.IO.h5rFile.H5RFile method) FLUSH_INTERVAL (PYME.IO.h5rFile.H5RFile attribute) FlushBuffer() (PYME.IO.HTTPSpooler.Spooler method) (PYME.IO.QueueSpooler.Spooler method) (PYME.IO.Spooler.Spooler method) fmfROI() (in module PYME.localization.autopsf.roifit) fmtSlicesUsed() (in module PYME.localization.FitFactories.fitCommon) FocusLockPanel (class in PYME.Acquire.ui.focus_lock_gui) FocusLogPanel (class in PYME.Acquire.ui.focus_lock_gui) Fold (class in PYME.recipes.multiview) fold() (in module PYME.Analysis.angleFilter) Fold() (PYME.ui.autoFoldPanel.foldingPane method) (PYME.ui.manualFoldPanel.foldingPane method) fold1() (PYME.ui.autoFoldPanel.foldPanel method) (PYME.ui.manualFoldPanel.foldingPane method) (PYME.ui.manualFoldPanel.foldPanel method) foldElement (class in PYME.ui.autoFoldPanel) (class in PYME.ui.manualFoldPanel) foldingPane (class in PYME.ui.autoFoldPanel) (class in PYME.ui.manualFoldPanel) foldPanel (class in PYME.ui.autoFoldPanel) (class in PYME.ui.manualFoldPanel) foldX() (in module PYME.Analysis.points.multiview) followFrames (PYME.recipes.tracking.LoadSpeckles attribute) foreshortening (PYME.recipes.localisations.Pipelineify attribute) format (PYME.recipes.output.PlotOutput attribute) format() (PYME.util.mProfile.colorize_db_t.Parser method) format_results() (in module PYME.IO.clusterResults) format_taskDesc() (PYME.cluster.taskWorkerHTTP.RecipeTaskError method) (PYME.cluster.taskWorkerHTTP.TaskError method) format_values() (in module PYME.recipes.acquisition) formField() (PYME.localization.MetaDataEdit.BoolFloatParam method) (PYME.localization.MetaDataEdit.BoolParam method) (PYME.localization.MetaDataEdit.ChoiceParam method) (PYME.localization.MetaDataEdit.FilenameParam method) (PYME.localization.MetaDataEdit.FloatListParam method) (PYME.localization.MetaDataEdit.FloatParam method) (PYME.localization.MetaDataEdit.IntParam method) (PYME.localization.MetaDataEdit.RangeParam method) (PYME.localization.MetaDataEdit.StringParam method) formFields() (PYME.localization.MetaDataEdit.MDParam method) (PYME.localization.MetaDataEdit.ParamGroup method) FORWARDS (PYME.Acquire.stackSettings.StackSettings attribute) fourier_ring_correlation() (in module PYME.Analysis.Colocalisation.correlationCoeffs) FourierPropagator (class in PYME.Analysis.PSFGen.fourier) (in module PYME.Analysis.PSFGen.fourierHNA) (in module PYME.Analysis.PSFGen.fourierHNA2) FourierPropagatorClipHNA (class in PYME.Analysis.PSFGen.fourierHNA) (class in PYME.Analysis.PSFGen.fourierHNA2) FourierPropagatorHNA (class in PYME.Analysis.PSFGen.fourierHNA) (class in PYME.Analysis.PSFGen.fourierHNA2) FourierPSF (class in PYME.Analysis.PSFGen.fourierHNA) Fraction (class in PYME.IO.FileUtils.obf_support) FractionalThreshold (class in PYME.recipes.processing) fractionThreshold (PYME.recipes.processing.FractionalThreshold attribute) frame_weights() (PYME.Analysis.tile_pyramid.ImagePyramid class method) frameCOI() (PYME.Acquire.Utils.vibrationAnalysis.VibrAnal method) frames_to_times() (in module PYME.Analysis.piecewiseMapping) framesPerStep (PYME.recipes.localisations.IDTransientFrames attribute) FrameWrangler (class in PYME.Acquire.frameWrangler) fresult_dtype() (in module PYME.localization.FitFactories.MultiviewFitInterpNR) from_filename() (PYME.IO.DataSources.SupertileDatasource.SupertileDataSource static method) from_json() (in module PYME.IO.MetaDataHandler) from_md_entry() (PYME.Analysis.points.twoColour.ShiftModel class method) from_raw_tile_series() (PYME.IO.DataSources.SupertileDatasource.SupertileDataSource static method) from_request() (PYME.Analysis.distributed_pyramid.PartialPyramid class method) from_tabular() (PYME.Analysis.points.spherical_harmonics.ScaledShell static method) fromJSON() (PYME.recipes.recipe.Recipe class method) fromMD() (PYME.recipes.recipe.Recipe class method) fromMDFile() (PYME.localization.Test.fitTestJig.fitTestJig class method) (PYME.localization.Test.fitTestJigSCMOS.fitTestJig class method) (PYME.localization.Test.fitTestJigWC.fitTestJig class method) FromPoint() (PYME.localization.FitFactories.AstigGaussFitFR.GaussianFitFactory method) (PYME.localization.FitFactories.AstigGaussGPUFitFR.GaussianFitFactory method) (PYME.localization.FitFactories.BeadConvolvedAstigGaussFit.GaussianFitFactory method) (PYME.localization.FitFactories.ChecksumFR.ChecksumFitFactory method) (PYME.localization.FitFactories.Dumbell3DFitR.Dumbell3DFitFactory method) (PYME.localization.FitFactories.DumbellFitR.DumbellFitFactory method) (PYME.localization.FitFactories.FFBase.FFBase method) (PYME.localization.FitFactories.Gauss3DFitR.Gauss3dFitFactory method) (PYME.localization.FitFactories.GaussFitConstrR.GaussianFitFactory method) (PYME.localization.FitFactories.InterpFitR.PSFFitFactory method) (PYME.localization.FitFactories.InterpFitWFR.WFPSFFitFactory method) (PYME.localization.FitFactories.LatFitCOIR.COIFitFactory method) (PYME.localization.FitFactories.LatGaussFitFR.GaussianFitFactory method) (PYME.localization.FitFactories.LatObjFindFR.GaussianFitFactory method) (PYME.localization.FitFactories.LatPSFFitR.PSFFitFactory method) (PYME.localization.FitFactories.MultiviewFitInterpNR.InterpFitFactory method) (PYME.localization.FitFactories.PRInterpFitQR.PSFFitFactory method) (PYME.localization.FitFactories.PRInterpFitR.PSFFitFactory method) (PYME.localization.FitFactories.ROIExtractNR.GaussianFitFactory method) (PYME.localization.FitFactories.SpecGaussFitFR.GaussianFitFactory method) (PYME.localization.FitFactories.SplitterFitCOIR.COIFitFactory method) (PYME.localization.FitFactories.SplitterFitFNR.GaussianFitFactory method) (PYME.localization.FitFactories.SplitterFitFusionR.GaussianFitFactory method) (PYME.localization.FitFactories.SplitterFitInterpBNR.InterpFitFactory method) (PYME.localization.FitFactories.SplitterFitInterpNR.InterpFitFactory method) (PYME.localization.FitFactories.SplitterFitScavNR.GaussianFitFactory method) (PYME.localization.FitFactories.SplitterObjFindR.GaussianFitFactory method) (PYME.localization.FitFactories.SplitterROIExtractNR.GaussianFitFactory method) (PYME.localization.FitFactories.SplitterShiftEstFR.GaussianFitFactory method) fromYAML() (PYME.recipes.recipe.Recipe class method) front() (PYME.LMVis.views.View method) fstat (PYME.contrib.gohlke.tifffile.TIFFfile attribute) FunctionAction (class in PYME.Acquire.actions) FunctionOverlay (class in PYME.DSView.overlays)

G

g_histfitting() (in module PYME.Analysis.BleachProfile.rollins) gather_outputs() (PYME.recipes.recipe.Recipe method) Gauss2D() (in module PYME.Analysis.points.segmentLL) (in module PYME.LMVis.rendGauss) (in module PYME.LMVis.visHelpers) Gauss3d() (in module PYME.LMVis.visHelpers) Gauss3dFitFactory (class in PYME.localization.FitFactories.Gauss3DFitR) Gauss3dFitResultR() (in module PYME.localization.FitFactories.Gauss3DFitR) GaussFitResult (class in PYME.localization.FitFactories.Gauss3DFitR) Gaussian3DRenderer (class in PYME.LMVis.renderers) gaussian_blob_paint() (in module PYME.Analysis.points.rings) GaussianFilter (class in PYME.recipes.filters) GaussianFitFactory (class in PYME.localization.FitFactories.AstigGaussFitFR) (class in PYME.localization.FitFactories.AstigGaussGPUFitFR) (class in PYME.localization.FitFactories.BeadConvolvedAstigGaussFit) (class in PYME.localization.FitFactories.GaussFitConstrR) (class in PYME.localization.FitFactories.GaussMultifitLinesR) (class in PYME.localization.FitFactories.GaussMultifitR) (class in PYME.localization.FitFactories.GaussMultifitSR) (class in PYME.localization.FitFactories.LatGaussFitFR) (class in PYME.localization.FitFactories.LatObjFindFR) (class in PYME.localization.FitFactories.ROIExtractNR) (class in PYME.localization.FitFactories.SpecGaussFitFR) (class in PYME.localization.FitFactories.SplitterFitFNR) (class in PYME.localization.FitFactories.SplitterFitFusionR) (class in PYME.localization.FitFactories.SplitterFitScavNR) (class in PYME.localization.FitFactories.SplitterMultifitSR) (class in PYME.localization.FitFactories.SplitterObjFindR) (class in PYME.localization.FitFactories.SplitterROIExtractNR) (class in PYME.localization.FitFactories.SplitterShiftEstFR) GaussianFitResultR() (in module PYME.localization.FitFactories.GaussFitConstrR) (in module PYME.localization.FitFactories.GaussMultifitLinesR) (in module PYME.localization.FitFactories.GaussMultifitR) (in module PYME.localization.FitFactories.LatGaussFitFR) (in module PYME.localization.FitFactories.LatObjFindFR) (in module PYME.localization.FitFactories.SpecGaussFitFR) (in module PYME.localization.FitFactories.SplitterFitFNR) (in module PYME.localization.FitFactories.SplitterFitFusionR) (in module PYME.localization.FitFactories.SplitterFitScavNR) (in module PYME.localization.FitFactories.SplitterMultifitSR) (in module PYME.localization.FitFactories.SplitterObjFindR) (in module PYME.localization.FitFactories.SplitterShiftEstFR) gaussianFWHM (PYME.recipes.processing.Deconvolve attribute) GaussianMixtureModel (class in PYME.recipes.pointcloud) GaussianRenderer (class in PYME.LMVis.renderers) gaussKernel() (in module PYME.LMVis.rendGauss) GaussTexture (class in PYME.LMVis.shader_programs.PointSpriteShaderProgram) gen2DMask() (in module PYME.Analysis.annealThresh) gen3DBlobs() (in module PYME.Analysis.points.gen3DTriangs) gen3DTriangs() (in module PYME.Analysis.points.gen3DTriangs) gen3DTriangsT() (in module PYME.Analysis.points.gen3DTriangs) gen3DTriangsTF() (in module PYME.Analysis.points.gen3DTriangs) gen3DTriangsTFC() (in module PYME.Analysis.points.gen3DTriangs) Gen4PiPSF() (in module PYME.Analysis.PSFGen.fourierHNA) (in module PYME.Analysis.PSFGen.fourierHNA2) gen_autoencoder() (in module PYME.Analysis.autoencoder_classifier) gen_features() (in module PYME.Analysis.fiducial_matching) gen_features2() (in module PYME.Analysis.fiducial_matching) gen_isosurface() (in module PYME.LMVis.Extras.extra_layers) gen_isosurface_from_tesselation() (in module PYME.LMVis.Extras.extra_layers) gen_mdh() (in module PYME.IO.csv_flavours) gen_nb_testdata() (in module PYME.Analysis.BleachProfile.rollins) gen_octree_from_points() (in module PYME.LMVis.Extras.extra_layers) gen_octree_isosurface() (in module PYME.LMVis.Extras.extra_layers) gen_pairwise_distance_features() (PYME.LMVis.Extras.objectMeasurements.ObjectMeasurer method) gen_point_dis_isosurface() (in module PYME.LMVis.Extras.extra_layers) gen_quad_rot_surf() (in module PYME.Analysis.points.surfit) gen_sequence_id() (PYME.IO.acquisition_backends.Backend class method) gen_text_image() (PYME.LMVis.layers.text.Text class method) gen_traces_from_speckles() (in module PYME.IO.FileUtils.readSpeckle) gen_training_data() (in module PYME.Analysis.autoencoder_classifier) GenAnalysisPanel() (PYME.DSView.modules.LMAnalysis.AnalysisSettingsView method) GenAstigPSF() (in module PYME.Analysis.PSFGen.fourier) (in module PYME.Analysis.PSFGen.fourierHNA) (in module PYME.Analysis.PSFGen.fourierHNA2) genBeadImage() (in module PYME.Deconv.beadGen) GenBesselPSF() (in module PYME.Analysis.PSFGen.fourierHNA) (in module PYME.Analysis.PSFGen.fourierHNA2) GenBiplanePSF() (in module PYME.Analysis.PSFGen.fourierHNA) (in module PYME.Analysis.PSFGen.fourierHNA2) GenBlobFindingPanel() (PYME.DSView.modules.blobFinding.BlobFinder method) (PYME.DSView.modules.shiftfield_estimation.BlobFinder method) GenBlobFitPanel() (PYME.DSView.modules.blobFinding.BlobFinder method) GenBlobPanel() (in module PYME.LMVis.triBlobs) GenClippedWidefieldPSF() (in module PYME.Analysis.PSFGen.fourierHNA) (in module PYME.Analysis.PSFGen.fourierHNA2) genClusterDataFilepath() (in module PYME.IO.FileUtils.nameUtils) genClusterResultFileName() (in module PYME.IO.FileUtils.nameUtils) GenColourPRIPSF() (in module PYME.Analysis.PSFGen.fourierHNA) (in module PYME.Analysis.PSFGen.fourierHNA2) genContents() (PYME.DSView.modules.playback.PlayPanel method) genCoords() (in module PYME.Analysis.angleFilter) (PYME.Acquire.Utils.pointScanner.CircularPointScanner method) (PYME.Acquire.Utils.pointScanner.PointScanner method) (PYME.Acquire.Utils.pointScanner.PointScanner3D method) GenCubicPhasePSF() (in module PYME.Analysis.PSFGen.fourierHNA) (in module PYME.Analysis.PSFGen.fourierHNA2) genCurves() (in module PYME.Analysis.PSFGen.genCRBcurves) genDark() (in module PYME.Analysis.deTile) genDataFileID() (in module PYME.IO.FileUtils.fileID) genDataSourceID() (in module PYME.IO.FileUtils.fileID) GenDataSourcePanel() (PYME.LMVis.visCore.VisGUICore method) genDefaultMask() (in module PYME.Analysis.annealThresh) GenDHPSF() (in module PYME.Analysis.PSFGen.fourierHNA) (in module PYME.Analysis.PSFGen.fourierHNA2) genEdgeDB() (in module PYME.LMVis.visHelpers) Generate() (PYME.LMVis.renderers.ColourRenderer method) (PYME.LMVis.renderers.CurrentRenderer method) generate() (PYME.recipes.base.OutputModule method) (PYME.recipes.output.ImageOutput method) (PYME.recipes.output.PlotOutput method) (PYME.recipes.output.ReportOutput method) (PYME.recipes.output.RGBImageOutput method) (PYME.recipes.output.STLOutput method) generate_a_pyrex_source() (in module PYME.misc.cython_numpy_monkey) generate_icosahedron() (in module PYME.Analysis.points.spherical_harmonics) generate_maps() (in module PYME.Analysis.gen_sCMOS_maps) generate_uniform_map() (in module PYME.Analysis.gen_sCMOS_maps) GenerateBacklashCorrPMFromEventList() (in module PYME.Analysis.piecewiseMapping) GenerateDataGrid() (PYME.LMVis.importTextDialog.ColumnMappingDialog method) GeneratedImage() (in module PYME.IO.image) GenerateGUI() (PYME.LMVis.renderers.ColourRenderer method) (PYME.LMVis.renderers.CurrentRenderer method) GeneratePMFromEventList() (in module PYME.Analysis.piecewiseMapping) GeneratePMFromProtocolEvents() (in module PYME.Analysis.piecewiseMapping) GeneratePupil() (PYME.DSView.modules.psfGeneration.MeasuredPupil method) (PYME.DSView.modules.psfGeneration.PhaseRampPupil method) (PYME.DSView.modules.psfGeneration.WidefieldPupil method) Generator (class in PYME.LMVis.Extras.pointSetGeneration) genFileID() (in module PYME.IO.FileUtils.fileID) genFitImage() (in module PYME.localization.FitFactories.InterpFitR) (in module PYME.localization.FitFactories.LatGaussFitFR) (in module PYME.localization.FitFactories.MultiviewFitInterpNR) (in module PYME.localization.FitFactories.PRInterpFitQR) (in module PYME.localization.FitFactories.PRInterpFitR) (in module PYME.localization.FitFactories.SplitterFitFNR) (in module PYME.localization.FitFactories.SplitterFitFusionR) (in module PYME.localization.FitFactories.SplitterFitInterpBNR) (in module PYME.localization.FitFactories.SplitterFitInterpNR) (in module PYME.localization.FitFactories.SplitterFitScavNR) GenFitStatusPanel() (PYME.DSView.modules.LMAnalysis.LMAnalyser2 method) GenFlowPanel() (PYME.DSView.modules.flowView.FlowView method) genFnl() (in module PYME.IO.FileUtils.fnlGen) genFrameID() (in module PYME.IO.FileUtils.fileID) genGauss() (in module PYME.localization.cModels.gauss_app) genGauss3D() (in module PYME.localization.cModels.gauss_app) genGaussA() (in module PYME.localization.cModels.gauss_app) genGaussInArray() (in module PYME.localization.cModels.gauss_app) genGaussJac() (in module PYME.localization.cModels.gauss_app) genGaussJacW() (in module PYME.localization.cModels.gauss_app) genGaussPhotonStats() (PYME.DSView.fitInfo.FitInfoPanel method) genHDFDataFilepath() (in module PYME.IO.FileUtils.nameUtils) GenHist() (PYME.ui.fastGraph.FastGraphPanel method) (PYME.ui.histLimits.HistLimitPanel method) GenICPRIPSF() (in module PYME.Analysis.PSFGen.fourierHNA) (in module PYME.Analysis.PSFGen.fourierHNA2) genIm() (in module PYME.Analysis.Colocalisation.colocScaleDep) (PYME.LMVis.renderers.CurrentRenderer method) (PYME.LMVis.renderers.DensityFitRenderer method) (PYME.LMVis.renderers.Gaussian3DRenderer method) (PYME.LMVis.renderers.GaussianRenderer method) (PYME.LMVis.renderers.Histogram3DRenderer method) (PYME.LMVis.renderers.HistogramRenderer method) (PYME.LMVis.renderers.LHoodRenderer method) (PYME.LMVis.renderers.QuadTreeRenderer method) (PYME.LMVis.renderers.Triangle3DRenderer method) (PYME.LMVis.renderers.TriangleRenderer method) (PYME.LMVis.renderers.TriangleRendererW method) (PYME.LMVis.renderers.VoronoiRenderer method) GenImageDialog (class in PYME.LMVis.genImageDialog) genImageID() (in module PYME.IO.FileUtils.fileID) genImageTime() (in module PYME.IO.FileUtils.fileID) genImR() (in module PYME.Analysis.Colocalisation.colocScaleDep) genImR2() (in module PYME.Analysis.Colocalisation.colocScaleDep) genIndexAndLabels() (in module PYME.Analysis.points.moments) genMetaData() (PYME.simulation.pointsets.FileSource method) (PYME.simulation.pointsets.ImageSource method) (PYME.simulation.pointsets.WormlikeSource method) genMetaDataFromSourceAndMDH() (in module PYME.Analysis.MetaData) GenMultiChanZernikeDPSF() (in module PYME.localization.autopsf.roifit) genMultiGauss() (in module PYME.localization.cModels.gauss_app) genMultiGaussJac() (in module PYME.localization.cModels.gauss_app) GenPanels() (PYME.LMVis.visCore.VisGUICore method) GenPlayPanel() (PYME.DSView.modules.playback.player method) genPlots() (in module PYME.Analysis.Colocalisation.colocScaleDep) GenPointFindingPanel() (PYME.DSView.modules.LMAnalysis.AnalysisSettingsView method) GenPointsPanel() (in module PYME.LMVis.pointSettingsPanel) GenPRIEField() (in module PYME.Analysis.PSFGen.fourierHNA) (in module PYME.Analysis.PSFGen.fourierHNA2) GenPRIPSF() (in module PYME.Analysis.PSFGen.fourier) (in module PYME.Analysis.PSFGen.fourierHNA) (in module PYME.Analysis.PSFGen.fourierHNA2) GenPSFPanel() (PYME.DSView.modules.object_tagging.ObjectTagger method) (PYME.DSView.modules.psfExtraction.PsfExtractor method) GenQuads() (PYME.LMVis.pipeline.Pipeline method) GenQuadTreePanel() (in module PYME.LMVis.quadTreeSettings) GenR3PSF() (in module PYME.Analysis.PSFGen.fourierHNA) (in module PYME.Analysis.PSFGen.fourierHNA2) genResultDirectoryPath() (in module PYME.IO.FileUtils.nameUtils) genResultFileName() (in module PYME.IO.FileUtils.nameUtils) genResultsFileID() (in module PYME.IO.FileUtils.fileID) genResultsText() (PYME.DSView.fitInfo.FitInfoPanel method) GenResultsView() (PYME.DSView.modules.LMDisplay.LMDisplay method) genRGBImage() (in module PYME.Analysis.points.twoColour) GenRunPositions() (PYME.Acquire.Utils.fastTiler.fastRectTiler method) GenSAAstigPSF() (in module PYME.Analysis.PSFGen.fourierHNA) (in module PYME.Analysis.PSFGen.fourierHNA2) GenSABesselPSF() (in module PYME.Analysis.PSFGen.fourierHNA) (in module PYME.Analysis.PSFGen.fourierHNA2) GenSAPRIPSF() (in module PYME.Analysis.PSFGen.fourierHNA) (in module PYME.Analysis.PSFGen.fourierHNA2) GenSAPSF() (in module PYME.Analysis.PSFGen.fourierHNA) (in module PYME.Analysis.PSFGen.fourierHNA2) genSequenceID() (in module PYME.IO.HTTPSpooler) GenShiftedPSF() (in module PYME.Analysis.PSFGen.fourier) (in module PYME.Analysis.PSFGen.fourierHNA) (in module PYME.Analysis.PSFGen.fourierHNA2) genShiftFieldDirectoryPath() (in module PYME.IO.FileUtils.nameUtils) GenShiftMapPanel() (PYME.DSView.modules.blobFinding.BlobFinder method) (PYME.DSView.modules.shiftfield_estimation.BlobFinder method) genShiftVectorField() (in module PYME.Analysis.points.twoColour) genShiftVectorFieldLinear() (in module PYME.Analysis.points.twoColour) genShiftVectorFieldMC() (in module PYME.Analysis.points.twoColour) genShiftVectorFieldQ() (in module PYME.Analysis.points.twoColour) genShiftVectorFieldQuad() (in module PYME.Analysis.points.twoColour) genShiftVectorFieldQuadz() (in module PYME.Analysis.points.twoColour) genShiftVectorFieldQz() (in module PYME.Analysis.points.twoColour) genShiftVectorFieldSpline() (in module PYME.Analysis.points.twoColour) genShiftVectors() (in module PYME.Analysis.points.twoColour) genSplitGaussInArray() (in module PYME.localization.cModels.gauss_app) genSplitGaussInArrayPVec() (in module PYME.localization.cModels.gauss_app) GenStartMetadata() (PYME.Acquire.microscope.microscope method) (PYME.Acquire.sampleInformation.SimpleSampleInfoPanel method) genStartMetadata() (PYME.Acquire.ui.AnalysisSettingsUI.AnalysisSettings method) genStartParams() (PYME.misc.coverslipGeometries.circGeom method) genStatus() (PYME.Acquire.microscope.microscope method) GenStatusText() (in module PYME.LMVis.statusLog) GenStripePRIPSF() (in module PYME.Analysis.PSFGen.fourier) (in module PYME.Analysis.PSFGen.fourierHNA) (in module PYME.Analysis.PSFGen.fourierHNA2) genTraces() (in module PYME.Analysis.BleachProfile.intensProf) genTracesDE() (in module PYME.Analysis.BleachProfile.intensProf) GenTrackingPanel() (PYME.DSView.modules.particleTracking.ParticleTrackingView method) GenViewClippingPanel() (in module PYME.LMVis.view_clipping_pane) GenWidefieldAP() (in module PYME.Analysis.PSFGen.fourier) GenWidefieldPSF() (in module PYME.Analysis.PSFGen.fourier) (in module PYME.Analysis.PSFGen.fourierHNA) (in module PYME.Analysis.PSFGen.fourierHNA2) genWidefieldPSF() (in module PYME.Analysis.PSFGen.ps_app) genWidefieldPSFW() (in module PYME.Analysis.PSFGen.ps_app) GenZernikeDAPSF() (in module PYME.Analysis.PSFGen.fourierHNA) (in module PYME.Analysis.PSFGen.fourierHNA2) GenZernikeDonutPSF() (in module PYME.Analysis.PSFGen.fourierHNA) (in module PYME.Analysis.PSFGen.fourierHNA2) GenZernikeDPSF() (in module PYME.Analysis.PSFGen.fourierHNA) (in module PYME.Analysis.PSFGen.fourierHNA2) GenZernikePSF() (in module PYME.Analysis.PSFGen.fourier) (in module PYME.Analysis.PSFGen.fourierHNA) (in module PYME.Analysis.PSFGen.fourierHNA2) geom (class in PYME.misc.coverslipGeometries) geom_depth (PYME.DSView.modules.blobMeasure.DataBlock property) geom_length (PYME.DSView.modules.blobMeasure.DataBlock property) geom_width (PYME.DSView.modules.blobMeasure.DataBlock property) get() (in module PYME.config) (PYME.Analysis.points.QuadTree.pointQT.qtBranchNode method) (PYME.Analysis.points.QuadTree.pointQT.qtLeafNode method) (PYME.Analysis.points.QuadTree.pointQTF.qtBranchNode method) (PYME.Analysis.points.QuadTree.pointQTF.qtLeafNode method) (PYME.misc.TiffImagePlugin.ImageFileDirectory method) get3DIsosurf() (PYME.DSView.modules.blobMeasure.BlobObject method) get3DROIAtPoint() (PYME.localization.FitFactories.FFBase.FFBase method) get_advertised_services() (PYME.misc.hybrid_ns.HybridNS method) (PYME.misc.pyme_zeroconf.ZCListener method) (PYME.misc.pyme_zeroconf.ZeroConfNS method) (PYME.misc.sqlite_ns.SQLiteNS method) get_all_glasses() (in module PYME.misc.read_agf) get_any() (PYME.cluster.rulenodeserver.Rater method) get_bead_pupil() (in module PYME.Analysis.PSFGen.fourierHNA) (in module PYME.Analysis.PSFGen.fourierHNA2) get_bounds() (PYME.simulation.pointsets.ImageSource method) get_cached_queue_info() (in module PYME.cluster.distribution) get_camera_physical_roi_origin() (in module PYME.IO.MetaDataHandler) get_camera_roi_origin() (in module PYME.IO.MetaDataHandler) get_canvas() (PYME.LMVis.Extras.dockedPanel.DockedPanel method) get_channel_column() (PYME.IO.tabular.ColourFilter method) get_channel_ds() (PYME.IO.tabular.ColourFilter method) get_cleaned_module_list() (PYME.recipes.recipe.Recipe method) get_cluster_dirname() (PYME.Acquire.SpoolController.SpoolController method) get_code() (PYME.LMVis.shader_programs.shader_loader.ShaderLoader method) get_color_limit() (PYME.LMVis.layers.image_layer.ImageRenderLayer method) (PYME.LMVis.layers.mesh.TriangleRenderLayer method) (PYME.LMVis.layers.pointcloud.PointCloudRenderLayer method) (PYME.LMVis.layers.tracks.TrackRenderLayer method) get_color_map() (PYME.LMVis.layers.image_layer.ImageRenderLayer method) (PYME.LMVis.layers.mesh.TriangleRenderLayer method) (PYME.LMVis.layers.pointcloud.PointCloudRenderLayer method) (PYME.LMVis.layers.tracks.TrackRenderLayer method) get_colors() (PYME.LMVis.layers.base.EngineLayer method) (PYME.LMVis.layers.mesh.TriangleRenderLayer method) (PYME.LMVis.layers.pointcloud.PointCloudRenderLayer method) (PYME.LMVis.layers.tracks.TrackRenderLayer method) get_colour_chans() (PYME.IO.tabular.ColourFilter class method) get_compression_settings() (PYME.Acquire.ui.HDFSpoolFrame.PanSpool method) get_custom_protocols() (in module PYME.config) get_custom_recipes() (in module PYME.config) get_datasource() (PYME.DSView.OpenSequenceDialog.OpenSequenceDialog method) get_dir_manager() (in module PYME.IO.clusterIO) get_dirname() (PYME.Acquire.SpoolController.SpoolController method) get_duration() (PYME.LMVis.Extras.animation.EditDialog method) get_file() (in module PYME.IO.clusterIO) (PYME.IO.h5File.H5File method) (PYME.util.webframework.StaticFileHandler method) get_fitted_shell() (PYME.Analysis.points.spherical_harmonics.ScaledShell method) get_frame() (PYME.IO.dcimg.DCIMGFile method) (PYME.IO.h5File.H5File method) get_frame_png() (PYME.Acquire.acquire_server.PYMEAcquireServer method) get_frame_png_b64() (PYME.Acquire.acquire_server.PYMEAcquireServer method) get_frame_pzf() (PYME.Acquire.acquire_server.PYMEAcquireServer method) get_frame_raw() (PYME.Acquire.acquire_server.PYMEAcquireServer method) get_free_space() (in module PYME.IO.FileUtils.freeSpace) (PYME.Acquire.SpoolController.SpoolController method) get_free_space_bytes() (in module PYME.IO.FileUtils.freeSpace) get_glob() (PYME.cluster.HTTPDataServer.PYMEHTTPRequestHandler method) get_h5_part() (PYME.cluster.HTTPDataServer.PYMEHTTPRequestHandler method) get_hist_data() (PYME.DSView.displayOptions.DisplayOpts method) get_index() (in module PYME.misc.read_agf) get_info() (PYME.Acquire.SpoolController.SpoolController method) (PYME.misc.pyme_zeroconf.ZCListener method) get_init_filename() (in module PYME.config) get_json_annotations() (PYME.DSView.modules.annotation.AnnotateBase method) get_k_for_exp_costheta() (in module PYME.simulation.wormlike3) get_label_image() (PYME.DSView.modules.annotation.Annotater method) get_labels() (PYME.DSView.modules.annotation.LabelPanel method) get_labels_from_image() (in module PYME.Analysis.points.cluster_morphology) get_layer_data() (PYME.LMVis.pipeline.Pipeline method) get_layer_tile_coords() (PYME.Analysis.tile_pyramid.ImagePyramid method) (PYME.Analysis.tile_pyramid.NumpyTileIO method) (PYME.Analysis.tile_pyramid.SqliteTileIO method) (PYME.Analysis.tile_pyramid.TileIO method) get_line_colour() (in module PYME.recipes.recipeGui) get_listing() (PYME.IO.h5File.H5File method) get_local() (PYME.cluster.rulenodeserver.Rater method) get_local_data_directory() (in module PYME.IO.FileUtils.nameUtils) get_local_path() (in module PYME.IO.clusterIO) get_localip() (in module PYME.cluster.webdav) get_mesh_vertices_faces() (PYME.Analysis.points.spherical_harmonics.ScaledShell method) get_n_frames() (PYME.IO.Spooler.Spooler method) get_name() (PYME.LMVis.Extras.animation.EditDialog method) (PYME.recipes.base.ModuleBase method) get_new_tasks() (PYME.cluster.rules.LocalisationRule method) (PYME.cluster.rules.Rule method) get_next_selected() (PYME.Acquire.htsms.rule_ui.ProtocolRuleFactoryListCtrl method) get_normals() (in module PYME.Analysis.points.surfit) (PYME.LMVis.layers.base.EngineLayer method) (PYME.LMVis.layers.mesh.TriangleRenderLayer method) (PYME.LMVis.layers.pointcloud.PointCloudRenderLayer method) (PYME.LMVis.layers.tracks.TrackRenderLayer method) get_ns() (in module PYME.IO.cluster_directory) get_num_slices() (PYME.IO.dcimg.DCIMGFile method) get_offset() (PYME.LMVis.layers.OverlayLayer.OverlayLayer method) get_offtime_cdf() (in module PYME.Analysis.points.qpaint) get_oversize_tile() (PYME.Analysis.tile_pyramid.ImagePyramid method) get_package_versions() (in module PYME.ui.progress) get_params() (PYME.Acquire.htsms.rule_ui.RuleTile method) (PYME.recipes.base.ModuleBase method) get_pct() (in module PYME.IO.buffer_helpers) get_plugin_report_filters() (in module PYME.config) get_plugin_template_dirs() (in module PYME.config) get_plugins() (in module PYME.config) get_polled_status() (in module PYME.cluster.status) get_position_from_events() (in module PYME.Analysis.tile_pyramid) get_profile_stats() (in module PYME.util.mProfile.tProfile) get_program() (PYME.LMVis.shader_programs.ShaderProgramFactory.ShaderProgramFactory static method) get_propagator() (PYME.Analysis.PSFGen.fourierHNA.FourierPropagatorHNA class method) (PYME.Analysis.PSFGen.fourierHNA2.FourierPropagatorHNA class method) get_protocol() (in module PYME.Acquire.protocol) get_protocol_list() (in module PYME.Acquire.htsms.rule_ui) (in module PYME.Acquire.protocol) get_queue_info() (PYME.cluster.ruleserver.RuleServer method) get_queues() (PYME.cluster.ruleserver.RuleServer method) get_ratios() (in module PYME.LMVis.dyeRatios) get_results() (PYME.localization.FitFactories.AstigGaussGPUFitFR.GaussianFitFactory method) get_roi_locations (PYME.tileviewer.tileviewer.TileServer attribute) get_roi_offset() (PYME.Acquire.microscope.microscope method) get_rule() (PYME.cluster.rules.RuleFactory method) get_rule_tile() (in module PYME.Acquire.htsms.rule_ui) get_salt() (in module PYME.util.authenticate) get_scale_box_layer() (PYME.LMVis.Extras.scaleBox.ScaleBoxPanel method) get_scope_state() (PYME.Acquire.acquire_server.PYMEAcquireServer method) get_selected_items() (PYME.Acquire.htsms.rule_ui.ProtocolRuleFactoryListCtrl method) get_sensor_size() (in module PYME.Analysis.gen_sCMOS_maps) get_service_name() (in module PYME.IO.FileUtils.nameUtils) get_settings() (PYME.LMVis.genImageDialog.GenImageDialog method) get_shader_program() (PYME.LMVis.layers.base.BaseEngine method) (PYME.LMVis.layers.base.SimpleLayer method) (PYME.LMVis.shader_programs.GLProgram.GLProgram method) get_shiftmap() (in module PYME.localization.FitFactories.FFBase) get_shifts() (in module PYME.localization.splitting) get_size_factor() (PYME.LMVis.shader_programs.PointSpriteShaderProgram.PointSpriteShaderProgram method) get_slice_shape() (PYME.IO.dcimg.DCIMGFile method) get_snap() (PYME.LMVis.gl_offScreenHandler.OffScreenHandler method) get_source() (PYME.reports.UnifiedLoader method) get_splitter_rois() (in module PYME.localization.splitting) get_spool_subdir() (in module PYME.IO.FileUtils.nameUtils) get_status() (in module PYME.IO.clusterIO) (PYME.cluster.dataserver_wsgi.dataserver method) (PYME.cluster.HTTPDataServer.PYMEHTTPRequestHandler method) get_status_msg() (PYME.Acquire.ExecTools.BGInitTask method) get_tabular_part() (PYME.cluster.HTTPDataServer.PYMEHTTPRequestHandler method) get_terminal() (PYME.Acquire.webui.ipy.IPYTermManager method) get_test_data_dir() (in module PYME.resources) get_tick_distance() (PYME.LMVis.layers.ScaleBoxOverlayLayer.ScaleBoxOverlayLayer method) get_tile (PYME.tileviewer.tileviewer.TileServer attribute) get_tile() (PYME.Analysis.tile_pyramid.ImagePyramid method) (PYME.Analysis.tile_pyramid.NumpyTileIO method) (PYME.Analysis.tile_pyramid.SqliteTileIO method) (PYME.Analysis.tile_pyramid.TileIO method) get_token() (in module PYME.util.authenticate) get_uniform_location() (PYME.LMVis.shader_programs.GLProgram.GLProgram method) (PYME.LMVis.shader_programs.shader_program.ShaderProgram method) get_vecs() (PYME.LMVis.layers.quiver.QuiverRenderLayer method)

get_vertices() (PYME.LMVis.layers.base.EngineLayer method) (PYME.LMVis.layers.mesh.TriangleRenderLayer method) (PYME.LMVis.layers.pointcloud.PointCloudRenderLayer method) (PYME.LMVis.layers.quiver.QuiverRenderLayer method) (PYME.LMVis.layers.tracks.TrackRenderLayer method) get_viewport_size() (PYME.LMVis.gl_offScreenHandler.OffScreenHandler method) get_voxelsize_nm() (in module PYME.IO.MetaDataHandler) get_web_dir() (in module PYME.resources) get_web_static_dir() (in module PYME.resources) GetActiveCameraName() (PYME.Acquire.microscope.microscope method) GetActiveChans() (PYME.DSView.displayOptions.DisplayOpts method) getAll() (PYME.Analysis.points.QuadTree.pointQT.qtNode method) (PYME.Analysis.points.QuadTree.pointQTF.qtNode method) GetBackground() (PYME.Deconv.deconvDialogs.DeconvSettingsDialog method) getBackground() (PYME.IO.buffers.backgroundBuffer method) (PYME.IO.buffers.backgroundBufferM method) (PYME.IO.DataSources.BGSDataSource.backgroundBuffer method) (PYME.IO.DataSources.BGSDataSource.backgroundBufferM method) GetBeadRadius() (PYME.Deconv.deconvDialogs.DeconvSettingsDialog method) getBestScanner() (in module PYME.Acquire.zScanner) GetBins() (PYME.DSView.modules.coloc.ColocSettingsDialog method) (PYME.DSView.modules.fourierRingCorrelation.ColocSettingsDialog method) getBlobs() (PYME.LMVis.pipeline.Pipeline method) GetBlocking() (PYME.Deconv.deconvDialogs.DeconvSettingsDialog method) GetBlockSize() (PYME.Deconv.deconvDialogs.DeconvSettingsDialog method) GetBoundingRect() (PYME.Acquire.Utils.fastTiler.fastRectTiler method) getCalibrationDir() (in module PYME.IO.FileUtils.nameUtils) getCentroid() (PYME.Acquire.zScanner.zScanner method) GetChanFilename() (PYME.DSView.modules.composite.ShiftmapSelectionDialog method) GetChannel() (PYME.Deconv.deconvDialogs.DeconvSettingsDialog method) GetChans() (PYME.DSView.modules.coloc.ColocSettingsDialog method) (PYME.DSView.modules.fourierRingCorrelation.ColocSettingsDialog method) GetClumpRadiusMultiplier() (PYME.Analysis.points.DeClump.deClumpGUI.deClumpDialog method) GetClumpRadiusVariable() (PYME.Analysis.points.DeClump.deClumpGUI.deClumpDialog method) GetClumpTimeWindow() (PYME.Analysis.points.DeClump.deClumpGUI.deClumpDialog method) GetCollapsedIconBitmap() (in module PYME.misc.fbpIcons) GetCollapsedIconData() (in module PYME.misc.fbpIcons) GetCollapsedIconImage() (in module PYME.misc.fbpIcons) getColour() (PYME.LMVis.genImageDialog.GenImageDialog method) getColourChans() (PYME.IO.tabular.ColourFilter method) GetColumnSorter() (PYME.contrib.listctrlMixins.ColumnSorterMixin method) GetColumnWidths() (PYME.contrib.listctrlMixins.ColumnSorterMixin method) GetComputerName() (in module PYME.misc.computerName) getConn() (in module PYME.misc.tempDB) getCoords() (PYME.localization.FitFactories.Interpolators.CSInterpolator.CSInterpolator method) (PYME.localization.FitFactories.Interpolators.CubeSInterpolatorP.CSInterpolator method) (PYME.localization.FitFactories.Interpolators.CubicSplineInterpolator.CubicSplineInterpolator method) (PYME.localization.FitFactories.Interpolators.LinearInterpolator.LinearInterpolator method) (PYME.localization.FitFactories.Interpolators.LinearPInterpolatorP.LinearInterpolator method) getCorrection() (in module PYME.Analysis.points.twoColour) getDarkMap() (PYME.localization.remFitBuf.CameraInfoManager method) getDataErrors() (in module PYME.localization.FitFactories.InterpFitR) (in module PYME.localization.FitFactories.MultiviewFitInterpNR) (in module PYME.localization.FitFactories.PRInterpFitQR) (in module PYME.localization.FitFactories.PRInterpFitR) (in module PYME.localization.FitFactories.SplitterFitInterpBNR) (in module PYME.localization.FitFactories.SplitterFitInterpNR) getDataSourceForFilename() (in module PYME.IO.DataSources) GetDec() (PYME.recipes.processing.Deconvolve method) (PYME.recipes.processing.DeconvolveMotionCompensating method) GetDelim() (PYME.LMVis.importTextDialog.ImportTextDialog method) GetDirection() (PYME.Acquire.stackSettings.StackSettings method) getDirectorySize() (in module PYME.misc.dirSize) getDistributorInfo() (in module PYME.cluster.distribution) getEdb() (PYME.LMVis.pipeline.Pipeline method) GetEndPos() (PYME.Acquire.stackSettings.StackSettings method) getEntries() (in module PYME.misc.tempDB) getEntry() (PYME.IO.MetaDataHandler.CachingMDHandler method) (PYME.IO.MetaDataHandler.CopyOnWriteMDHandler method) (PYME.IO.MetaDataHandler.DictMDHandler method) (PYME.IO.MetaDataHandler.HDFMDHandler method) (PYME.IO.MetaDataHandler.MDHandlerBase method) (PYME.IO.MetaDataHandler.NestedClassMDHandler method) (PYME.IO.MetaDataHandler.QueueMDHandler method) (PYME.IO.MetaDataHandler.XMLMDHandler method) getEntryNames() (PYME.IO.MetaDataHandler.CachingMDHandler method) (PYME.IO.MetaDataHandler.CopyOnWriteMDHandler method) (PYME.IO.MetaDataHandler.DictMDHandler method) (PYME.IO.MetaDataHandler.HDFMDHandler method) (PYME.IO.MetaDataHandler.MDHandlerBase method) (PYME.IO.MetaDataHandler.NestedClassMDHandler method) (PYME.IO.MetaDataHandler.QueueMDHandler method) (PYME.IO.MetaDataHandler.XMLMDHandler method) getEvents() (PYME.IO.DataSources.AlignDataSource.DataSource method) (PYME.IO.DataSources.BaseDataSource.BaseDataSource method) (PYME.IO.DataSources.BaseDataSource.XYTCWrapper method) (PYME.IO.DataSources.BaseDataSource.XYZTCWrapper method) (PYME.IO.DataSources.BGSDataSource.XTZCBackgroundSource method) (PYME.IO.DataSources.BGSDataSource.XYZTCBgsSource method) (PYME.IO.DataSources.BioformatsDataSource.DataSource method) (PYME.IO.DataSources.BufferedDataSource.DataSource method) (PYME.IO.DataSources.ClusterPZFDataSource.DataSource method) (PYME.IO.DataSources.ConcatenatedDataSource.DataSource method) (PYME.IO.DataSources.CropDataSource.DataSource method) (PYME.IO.DataSources.DcimgDataSource.DataSource method) (PYME.IO.DataSources.FlatFieldDataSource.DataSource method) (PYME.IO.DataSources.HDFDataSource.DataSource method) (PYME.IO.DataSources.HTTPDataSource.DataSource method) (PYME.IO.DataSources.ImageSeriesDataSource.DataSource method) (PYME.IO.DataSources.MultiviewDataSource.DataSource method) (PYME.IO.DataSources.OBFDataSource.DataSource method) (PYME.IO.DataSources.RandomDataSource.DataSource method) (PYME.IO.DataSources.SupertileDatasource.SupertileDataSource method) (PYME.IO.DataSources.TiffDataSource.DataSource method) (PYME.IO.DataSources.TQDataSource.DataSource method) (PYME.IO.DataSources.UnsplitDataSource.DataSource method) (PYME.IO.dataWrap.ListWrapper method) GetExpandedIconBitmap() (in module PYME.misc.fbpIcons) GetExpandedIconData() (in module PYME.misc.fbpIcons) GetExpandedIconImage() (in module PYME.misc.fbpIcons) getExternalEdges() (in module PYME.Analysis.points.gen3DTriangs) GetFieldNames() (PYME.LMVis.importTextDialog.ColumnMappingDialog method) (PYME.LMVis.importTextDialog.ImportMatDialog method) getFileMetadata() (in module PYME.IO.FileUtils.fileID) getFileTags() (in module PYME.IO.FileUtils.fileID) getFlatfieldMap() (PYME.localization.remFitBuf.CameraInfoManager method) GetFlavour() (PYME.LMVis.importTextDialog.ImportTextDialog method) GetFormat() (PYME.ui.crop_dialog.ExportDialog method) getFPS() (PYME.Acquire.frameWrangler.FrameWrangler method) getFrame() (PYME.Acquire.frameWrangler.FrameWrangler method) getFullExistingFilename() (in module PYME.IO.FileUtils.nameUtils) getFullFilename() (in module PYME.IO.FileUtils.nameUtils) getGeometricMean() (PYME.LMVis.genImageDialog.GenImageDialog method) GetGeometry() (in module PYME.misc.coverslipGeometries) getGraph() (PYME.DSView.modules.blobMeasure.BlobObject method) getIconPath() (in module PYME.resources) GetIgnoreZ() (PYME.DSView.modules.composite.CompositeDialog method) GetImage() (PYME.Acquire.positionTracker.PositionTracker method) getImage() (PYME.DSView.modules.blobMeasure.BlobObject method) getImageTags() (in module PYME.IO.FileUtils.fileID) getInfo() (PYME.IO.tabular.AnndataSource method) (PYME.IO.tabular.FitResultsSource method) (PYME.IO.tabular.H5RDSource method) (PYME.IO.tabular.H5RSource method) (PYME.IO.tabular.HDFSource method) (PYME.IO.tabular.MatfileColumnSource method) (PYME.IO.tabular.MatfileSource method) (PYME.IO.tabular.RandomSource method) (PYME.IO.tabular.RecArraySource method) (PYME.IO.tabular.TextfileSource method) getInRadius() (in module PYME.Analysis.points.QuadTree.pointQT) (in module PYME.Analysis.points.QuadTree.pointQTF) getIntCenter() (in module PYME.Analysis.PSFEst.extractImages) GetInterp() (PYME.DSView.modules.composite.CompositeDialog method) GetItemFullname() (PYME.ui.MetadataTree.MetadataPanel method) getJitterScale() (PYME.LMVis.genImageDialog.GenImageDialog method) getJitterScaleZ() (PYME.LMVis.genImageDialog.GenImageDialog method) getJitterVariable() (PYME.LMVis.genImageDialog.GenImageDialog method) getJitterVariableZ() (PYME.LMVis.genImageDialog.GenImageDialog method) getLeaves() (PYME.Analysis.points.QuadTree.pointQT.qtBranchNode method) (PYME.Analysis.points.QuadTree.pointQT.qtLeafNode method) (PYME.Analysis.points.QuadTree.pointQTF.qtBranchNode method) (PYME.Analysis.points.QuadTree.pointQTF.qtLeafNode method) GetLimits() (PYME.ui.histLimits.HistLimitDialog method) getLinkageCandidates() (PYME.Analysis.Tracking.tracking.Tracker method) getListCtrlSelection() (in module PYME.contrib.listctrlMixins) getLUT() (in module PYME.DSView.arrayViewPanel) getMappedResults() (PYME.IO.tabular.MappingFilter method) GetMaster() (PYME.DSView.modules.composite.CompositeDialog method) getMCProbability() (PYME.LMVis.genImageDialog.GenImageDialog method) getMembers() (PYME.cluster.webdav.Collection method) (PYME.cluster.webdav.DirCollection method) (PYME.cluster.webdav.TempDirCollection method) getMetadata() (PYME.IO.DataSources.ClusterPZFDataSource.DataSource method) (PYME.IO.DataSources.HTTPDataSource.DataSource method) GetMethod() (PYME.Deconv.deconvDialogs.DeconvSettingsDialog method) GetMixMatrix() (PYME.DSView.modules.unmixing.UnMixSettingsDlg method) getModuleNames() (in module PYME.recipes.modules) GetMultichannel() (PYME.LMVis.importTextDialog.ImportMatlabDialog method) getMultiviewROIAtPoint() (PYME.localization.FitFactories.FFBase.FFBase method) GetName() (PYME.DSView.modules.composite.ImageList method) getNeighbourDists() (PYME.Analysis.points.EdgeDB.edges.EdgeDB method) (PYME.LMVis.pipeline.Pipeline method) getNewID() (in module PYME.DSView.modules.blobMeasure) getnexttag() (PYME.cluster.webdav.XMLDict_Parser method) getNodeInfo() (in module PYME.cluster.distribution) getNS() (in module PYME.misc.hybrid_ns) (in module PYME.misc.pyme_zeroconf) (in module PYME.misc.sqlite_ns) GetNumberComments() (PYME.LMVis.importTextDialog.ColumnMappingDialog method) GetNumIterationss() (PYME.Deconv.deconvDialogs.DeconvSettingsDialog method) getNumSamples() (PYME.LMVis.genImageDialog.GenImageDialog method) getNumSlices() (PYME.IO.DataSources.AlignDataSource.DataSource method) (PYME.IO.DataSources.ArrayDataSource.ArrayDataSource method) (PYME.IO.DataSources.ArrayDataSource.XYZTCArrayDataSource method) (PYME.IO.DataSources.BaseDataSource.BaseDataSource method) (PYME.IO.DataSources.BaseDataSource.XYTCWrapper method) (PYME.IO.DataSources.BaseDataSource.XYZTCWrapper method) (PYME.IO.DataSources.BGSDataSource.XTZCBackgroundSource method) (PYME.IO.DataSources.BGSDataSource.XYZTCBgsSource method) (PYME.IO.DataSources.BioformatsDataSource.DataSource method) (PYME.IO.DataSources.BufferedDataSource.DataSource method) (PYME.IO.DataSources.ClusterPZFDataSource.DataSource method) (PYME.IO.DataSources.ConcatenatedDataSource.DataSource method) (PYME.IO.DataSources.CropDataSource.DataSource method) (PYME.IO.DataSources.DcimgDataSource.DataSource method) (PYME.IO.DataSources.FlatFieldDataSource.DataSource method) (PYME.IO.DataSources.HDFDataSource.DataSource method) (PYME.IO.DataSources.HTTPDataSource.DataSource method) (PYME.IO.DataSources.ImageSeriesDataSource.DataSource method) (PYME.IO.DataSources.MultiviewDataSource.DataSource method) (PYME.IO.DataSources.OBFDataSource.DataSource method) (PYME.IO.DataSources.RandomDataSource.DataSource method) (PYME.IO.DataSources.SupertileDatasource.SupertileDataSource method) (PYME.IO.DataSources.TiffDataSource.DataSource method) (PYME.IO.DataSources.TQDataSource.DataSource method) (PYME.IO.DataSources.UnsplitDataSource.DataSource method) (PYME.IO.dataWrap.ListWrapper method) GetOffset() (PYME.Deconv.deconvDialogs.DeconvSettingsDialog method) (PYME.DSView.modules.unmixing.UnMixSettingsDlg method) getOrDefault() (PYME.IO.MetaDataHandler.MDHandlerBase method) GetPadding() (PYME.Deconv.deconvDialogs.DeconvSettingsDialog method) GetPadSize() (PYME.Deconv.deconvDialogs.DeconvSettingsDialog method) getPercentile() (PYME.IO.buffers.bgFrameBuffer method) (PYME.IO.buffers.bgFrameBufferC method) (PYME.IO.DataSources.BGSDataSource.bgFrameBuffer method) getPerimeter() (in module PYME.Analysis.points.gen3DTriangs) getPhotonNums() (in module PYME.Analysis.BleachProfile.kinModels) GetPixelSize() (PYME.Acquire.microscope.microscope method) getPixelSize() (PYME.LMVis.genImageDialog.GenImageDialog method) GetPixelSize() (PYME.LMVis.importTextDialog.ColumnMappingDialog method) getPoints() (PYME.simulation.pointsets.FileSource method) (PYME.simulation.pointsets.ImageSource method) (PYME.simulation.pointsets.SHNucleusSource method) (PYME.simulation.pointsets.WiglyFibreSource method) (PYME.simulation.pointsets.WormlikeSource method) getPopupMenu() (PYME.contrib.listctrlMixins.ListCtrlSelectionManagerMix method) GetPos() (PYME.Acquire.microscope.microscope method) GetPosRange() (PYME.Acquire.microscope.microscope method) GetPrevPos() (PYME.Acquire.stackSettings.StackSettings method) getPrincipalAxis() (in module PYME.Analysis.points.objectMeasure) getProperties() (PYME.cluster.webdav.DirCollection method) (PYME.cluster.webdav.DummyFileMember method) (PYME.cluster.webdav.FileMember method) (PYME.cluster.webdav.Member method) (PYME.cluster.webdav.TempDirCollection method) getPSF() (in module PYME.Analysis.PSFEst.extractImages) GetPSF() (PYME.Deconv.deconvDialogs.DeconvSettingsDialog method) (PYME.recipes.processing.Deconvolve method) getPSF3D() (in module PYME.Analysis.PSFEst.extractImages) GetPSFFilename() (PYME.Deconv.deconvDialogs.DeconvSettingsDialog method) getPSFSlice() (in module PYME.Analysis.PSFEst.extractImages) GetPupil() (PYME.DSView.modules.psfGeneration.PupilGenerator method) getQTLeafSize() (PYME.LMVis.genImageDialog.GenImageDialog method) getQueueInfo() (in module PYME.cluster.distribution) getRatio() (in module PYME.LMVis.dyeRatios) getReducedFilename() (in module PYME.IO.HTTPSpooler) (in module PYME.IO.HTTPSpooler_v2) GetRegion() (PYME.DSView.modules.blobMeasure.Measurements method) GetRegularisationLambda() (PYME.Deconv.deconvDialogs.DeconvSettingsDialog method) getRelFilename() (in module PYME.IO.FileUtils.nameUtils) GetRemovePadding() (PYME.Deconv.deconvDialogs.DeconvSettingsDialog method) getReqMemChans() (PYME.Acquire.frameWrangler.FrameWrangler method) getROIAtPoint() (PYME.localization.FitFactories.FFBase.FFBase method) getSampleData() (in module PYME.Acquire.sampleInformation) getSampleDataFailsafe() (in module PYME.Acquire.sampleInformation) getscalar() (PYME.misc.TiffImagePlugin.ImageFileDirectory method) GetScanChannel() (PYME.Acquire.stackSettings.StackSettings method) getSchematic() (PYME.DSView.modules.blobMeasure.BlobObject method) getSchematic3D() (PYME.DSView.modules.blobMeasure.BlobObject method) GetScrollPixelsPerUnit() (PYME.DSView.scrolledImagePanel.ScrolledImagePanel method) GetSecondarySortValues() (PYME.contrib.listctrlMixins.ColumnSorterMixin method) GetSelectedModule() (PYME.recipes.recipeGui.ModuleSelectionDialog method) GetSelectedPage() (PYME.DSView.dsviewer.DSViewFrame method) getSelection() (PYME.contrib.listctrlMixins.ListCtrlSelectionManagerMix method) GetSelections() (PYME.DSView.modules.composite.CompositeDialog method) GetSeqLength() (PYME.Acquire.stackSettings.StackSettings method) GetShiftmap() (PYME.DSView.modules.composite.CompositeDialog method) GetSimpleString() (PYME.IO.MetaDataHandler.MDHandlerBase method) getSize() (PYME.cluster.webdav.BufWriter method) getSlice() (PYME.IO.buffers.dataBuffer method) (PYME.IO.buffers.SliceBuffer method) (PYME.IO.DataSources.AlignDataSource.DataSource method) (PYME.IO.DataSources.ArrayDataSource.ArrayDataSource method) (PYME.IO.DataSources.ArrayDataSource.XYZTCArrayDataSource method) (PYME.IO.DataSources.BaseDataSource.BaseDataSource method) (PYME.IO.DataSources.BaseDataSource.XYTCWrapper method) (PYME.IO.DataSources.BaseDataSource.XYZTCWrapper method) (PYME.IO.DataSources.BGSDataSource.dataBuffer method) (PYME.IO.DataSources.BGSDataSource.XTZCBackgroundSource method) (PYME.IO.DataSources.BGSDataSource.XYZTCBgsSource method) (PYME.IO.DataSources.BioformatsDataSource.DataSource method) (PYME.IO.DataSources.BufferedDataSource.DataSource method) (PYME.IO.DataSources.ClusterPZFDataSource.DataSource method) (PYME.IO.DataSources.ConcatenatedDataSource.DataSource method) (PYME.IO.DataSources.CropDataSource.DataSource method) (PYME.IO.DataSources.DcimgDataSource.DataSource method) (PYME.IO.DataSources.ElectronsPerSecondDataSource.DataSource method) (PYME.IO.DataSources.FlatFieldDataSource.DataSource method) (PYME.IO.DataSources.HDFDataSource.DataSource method) (PYME.IO.DataSources.HTTPDataSource.DataSource method) (PYME.IO.DataSources.ImageSeriesDataSource.DataSource method) (PYME.IO.DataSources.MultiviewDataSource.DataSource method) (PYME.IO.DataSources.OBFDataSource.DataSource method) (PYME.IO.DataSources.RandomDataSource.DataSource method) (PYME.IO.DataSources.SupertileDatasource.SupertileDataSource method) (PYME.IO.DataSources.TiffDataSource.DataSource method) (PYME.IO.DataSources.TQDataSource.DataSource method) (PYME.IO.DataSources.UnsplitDataSource.DataSource method) (PYME.IO.dataWrap.ListWrapper method) GetSliceSelection() (PYME.DSView.displayOptions.DisplayOpts method) getSliceShape() (PYME.IO.DataSources.AlignDataSource.DataSource method) (PYME.IO.DataSources.ArrayDataSource.ArrayDataSource method) (PYME.IO.DataSources.ArrayDataSource.XYZTCArrayDataSource method) (PYME.IO.DataSources.BaseDataSource.BaseDataSource method) (PYME.IO.DataSources.BaseDataSource.XYTCWrapper method) (PYME.IO.DataSources.BaseDataSource.XYZTCWrapper method) (PYME.IO.DataSources.BGSDataSource.XTZCBackgroundSource method) (PYME.IO.DataSources.BGSDataSource.XYZTCBgsSource method) (PYME.IO.DataSources.BioformatsDataSource.DataSource method) (PYME.IO.DataSources.BufferedDataSource.DataSource method) (PYME.IO.DataSources.ClusterPZFDataSource.DataSource method) (PYME.IO.DataSources.ConcatenatedDataSource.DataSource method) (PYME.IO.DataSources.CropDataSource.DataSource method) (PYME.IO.DataSources.DcimgDataSource.DataSource method) (PYME.IO.DataSources.FlatFieldDataSource.DataSource method) (PYME.IO.DataSources.HDFDataSource.DataSource method) (PYME.IO.DataSources.HTTPDataSource.DataSource method) (PYME.IO.DataSources.ImageSeriesDataSource.DataSource method) (PYME.IO.DataSources.MultiviewDataSource.DataSource method) (PYME.IO.DataSources.OBFDataSource.DataSource method) (PYME.IO.DataSources.RandomDataSource.DataSource method) (PYME.IO.DataSources.SupertileDatasource.SupertileDataSource method) (PYME.IO.DataSources.TiffDataSource.DataSource method) (PYME.IO.DataSources.TQDataSource.DataSource method) (PYME.IO.DataSources.UnsplitDataSource.DataSource method) (PYME.IO.dataWrap.ListWrapper method) getSoftRender() (PYME.LMVis.genImageDialog.GenImageDialog method) GetSortImages() (PYME.contrib.listctrlMixins.ColumnSorterMixin method) GetSortState() (PYME.contrib.listctrlMixins.ColumnSorterMixin method) GetSpeciesDescriptor() (PYME.LMVis.Extras.sequentialSpecies.SpeciesDialog method) getSplitROIAtPoint() (PYME.localization.FitFactories.FFBase.FFBase method) GetStartMode() (PYME.Acquire.stackSettings.StackSettings method) getStartParameters() (in module PYME.localization.FitFactories.zEstimators.astigEstimator) (in module PYME.localization.FitFactories.zEstimators.biplaneEstimator) (in module PYME.localization.FitFactories.zEstimators.genericDualEstimator) (in module PYME.localization.FitFactories.zEstimators.genericEstimator) (in module PYME.localization.FitFactories.zEstimators.priEstimator) GetStartPos() (PYME.Acquire.stackSettings.StackSettings method) GetStatusText() (PYME.DSView.modules.LMAnalysis.LMAnalyser2 method) (PYME.DSView.modules.LMDisplay.LMDisplay method) GetStepSize() (PYME.Acquire.stackSettings.StackSettings method) getTableData() (PYME.IO.h5rFile.H5RFile method) GetTags() (PYME.Acquire.positionTracker.PositionTracker method) getTextFileLock() (in module PYME.cluster.dataserver_wsgi) (in module PYME.cluster.HTTPDataServer) getThumbnail() (in module PYME.IO.FileUtils.thumbnailDatabase) GetTrack() (PYME.Acquire.positionTracker.PositionTracker method) getTriangles() (PYME.LMVis.pipeline.Pipeline method) GetTSlice() (PYME.ui.crop_dialog.ExportDialog method) getURL() (in module PYME.DSView.htmlServe) (PYME.IO.HTTPSpooler.Spooler method) (PYME.IO.HTTPSpooler_v2.Spooler method) GetUseMask() (PYME.DSView.modules.coloc.ColocSettingsDialog method) getUsername() (in module PYME.IO.FileUtils.nameUtils) GetValue() (PYME.ui.histLimits.HistLimitPanel method) getVarianceMap() (PYME.localization.remFitBuf.CameraInfoManager method) GetVarName() (PYME.LMVis.importTextDialog.ImportMatDialog method) getVertexEdgeLengths() (in module PYME.Analysis.points.EdgeDB.edgeDB) (PYME.Analysis.points.EdgeDB.edges.EdgeDB method) getVertexNeighbours() (in module PYME.Analysis.points.EdgeDB.edgeDB) (PYME.Analysis.points.EdgeDB.edges.EdgeDB method) GetVoxX() (PYME.DSView.voxSizeDialog.VoxSizeDialog method) GetVoxY() (PYME.DSView.voxSizeDialog.VoxSizeDialog method) GetVoxZ() (PYME.DSView.voxSizeDialog.VoxSizeDialog method) getXML() (PYME.IO.MetaDataHandler.OMEXMLMDHandler method) GetXSlice() (PYME.ui.crop_dialog.ExportDialog method) GetYSlice() (PYME.ui.crop_dialog.ExportDialog method) getZ() (in module PYME.localization.twist) getZBounds() (PYME.LMVis.genImageDialog.GenImageDialog method) GetZrange() (PYME.DSView.modules.coloc.ColocSettingsDialog method) GetZSlice() (PYME.ui.crop_dialog.ExportDialog method) getZSliceThickness() (PYME.LMVis.genImageDialog.GenImageDialog method) gfm() (in module PYME.Analysis.BleachProfile.rollins) Glass (class in PYME.misc.zemax) glob() (in module PYME.IO.clusterGlob) glob_test() (in module PYME.Analysis.PSFEst.psfQuality) globalLHood() (PYME.Analysis.points.segmentLL.segmenter method) GLProgram (class in PYME.LMVis.shader_programs.GLProgram) GLProgramException GLShaderLoadException goalfcn() (in module PYME.Analysis.BleachProfile.kinModels) GouraudShaderProgram (class in PYME.LMVis.shader_programs.GouraudShaderProgram) GouraudSphereShaderProgram (class in PYME.LMVis.shader_programs.GouraudShaderProgram) gp() (in module PYME.Analysis.points.surfit) gpn() (in module PYME.Analysis.points.surfit) gpnA() (in module PYME.Analysis.points.surfit) gpnA2() (in module PYME.Analysis.points.surfit) Grab() (PYME.misc.VolProj.Isosurf method) GrabComp() (PYME.misc.VolProj.Isosurf method) GrabImage() (in module PYME.misc.VolProj) (PYME.DSView.arrayViewPanel.ArrayViewPanel method) GrabPNG() (PYME.DSView.arrayViewPanel.ArrayViewPanel method) GrabPNGToBuffer() (PYME.DSView.arrayViewPanel.ArrayViewPanel method) graded_cmaps (PYME.misc.colormaps.CMapDict property) Gradient2D (class in PYME.recipes.processing) Gradient3D (class in PYME.recipes.processing) gradientThreshold (PYME.recipes.processing.WavefrontDetection attribute) graphs() (PYME.DSView.modules.blobMeasure.Measurements method) GraphViewPanel (class in PYME.DSView.modules.fastGraphPanel) greedy_sort() (in module PYME.Analysis.points.traveling_salesperson.sort) Green() (in module PYME.misc.colormaps) grey_overflow() (in module PYME.misc.colormaps) GreyDilation (class in PYME.recipes.processing) GreyErosion (class in PYME.recipes.processing) grff() (in module PYME.Analysis.BleachProfile.rollins) Group() (in module PYME.misc.mock_traitsui) gt() (in module PYME.Analysis.BleachProfile.intensProf) gt_mod() (in module PYME.Analysis.BleachProfile.intensProf) guess_flavour() (in module PYME.IO.csv_flavours) guess_install_type() (in module PYME.misc.check_for_updates) guess_text_options() (in module PYME.IO.csv_flavours) guess_type() (PYME.cluster.dataserver_wsgi.dataserver method) (PYME.util.webframework.StaticFileHandler method) guessFlat() (in module PYME.Analysis.deTile) guessH5RImageID() (in module PYME.IO.FileUtils.fileID) guessUserID() (in module PYME.IO.FileUtils.fileID) gui_prompt_once() (in module PYME.misc.check_for_updates) gui_prompt_update() (in module PYME.misc.check_for_updates) GuiGetDirList() (in module PYME.IO.FileUtils.fnlGen) GUIInitTask (class in PYME.Acquire.ExecTools)

H

H5Exporter (class in PYME.IO.dataExporter) H5File (class in PYME.IO.h5File) H5RDSource (class in PYME.IO.tabular) h5rDSource() (in module PYME.IO.tabular) H5RFile (class in PYME.IO.h5rFile) H5RSource (class in PYME.IO.tabular) h5rSource() (in module PYME.IO.tabular) handin() (PYME.cluster.ruleserver.RuleServer method) has_key() (PYME.misc.TiffImagePlugin.ImageFileDirectory method) has_listeners() (PYME.contrib.dispatch.dispatcher.Signal method) hash_password() (in module PYME.util.authenticate) hashString32() (in module PYME.misc.hash32) HasStrictTraits (in module PYME.misc.mock_traits) HasTraits (class in PYME.misc.mock_traits) HDFBackend (class in PYME.IO.acquisition_backends) HDFEventLogger (class in PYME.IO.events) HDFMDHandler (class in PYME.IO.MetaDataHandler) HDFOutput (class in PYME.recipes.output) HDFSource (class in PYME.IO.tabular) hdfSource() (in module PYME.IO.tabular) header_dtype_v3 (in module PYME.IO.PZFFormat) height() (PYME.IO.image.ImageBounds method) (PYME.LMVis.visHelpersMin.ImageBounds method) height_inches (PYME.LMVis.Extras.snapshot.SnapshotSettings attribute) height_pixels (PYME.LMVis.Extras.snapshot.SnapshotSettings attribute) help_url (PYME.misc.exceptions.UserError attribute) helpInfo (PYME.LMVis.Extras.pointSetGeneration.Generator attribute) (PYME.simulation.pointsets.ImageSource attribute)

helpStr() (PYME.LMVis.Extras.pointSetGeneration.Generator method) (PYME.simulation.pointsets.ImageSource method) hide() (PYME.DSView.modules.blobMeasure.Measurements method) hide_in_overview (PYME.recipes.base.ModuleBase property) (PYME.recipes.localisations.DBSCANClustering property) HideTextCtrl() (PYME.LMVis.view_clipping_pane.ClippingPanel method) higherMinPtsPerCluster (PYME.recipes.localisations.ClusterCountVsImagingTime attribute) hill() (in module PYME.misc.hillcurve) hist() (in module PYME.Analysis.graphing_filters) histfitting() (in module PYME.Analysis.BleachProfile.rollins) HistLimitDialog (class in PYME.ui.histLimits) HistLimitEditDialog (class in PYME.ui.histLimits) HistLimitPanel (class in PYME.ui.histLimits) Histogram (class in PYME.recipes.measurement) Histogram3DRenderer (class in PYME.LMVis.renderers) HistogramRenderer (class in PYME.LMVis.renderers) hls_to_rgb() (in module PYME.misc.colorsys) hmod() (in module PYME.Analysis.BleachProfile.kinModels) hook() (in module PYME.update_version) hsv_to_rgb() (in module PYME.misc.colorsys) html_error_template (PYME.cluster.taskWorkerHTTP.RecipeTaskError attribute) (PYME.cluster.taskWorkerHTTP.TaskError attribute) html_log_url (PYME.cluster.taskWorkerHTTP.TaskError property) HTTPRedirectResponse (class in PYME.util.webframework) HTTPResponse (class in PYME.util.webframework) HTTPRulePusher (class in PYME.cluster.HTTPRulePusher) HTTPTaskPusher (class in PYME.cluster.HTTPTaskPusher) HWNotPresent HybridNS (class in PYME.misc.hybrid_ns)

I

ib16() (in module PYME.misc.TiffImagePlugin) ib32() (in module PYME.misc.TiffImagePlugin) icosahedron_mesh() (in module PYME.Analysis.points.spherical_harmonics) ICTMDeconvolution (class in PYME.Deconv.dec) id (PYME.LMVis.Extras.animation.EditPanel property) idColumnName (PYME.recipes.tablefilters.FilterTableByIDs attribute) IdentifyOverlappingROIs (class in PYME.recipes.measurement) IdFilter (class in PYME.IO.tabular) idFilter() (in module PYME.IO.tabular) ids (PYME.recipes.tablefilters.FilterTableByIDs attribute) IDTransientFrames (class in PYME.recipes.localisations) iGen() (in module PYME.DSView.modules.blobMeasure) iglob() (in module PYME.IO.clusterGlob) ignoreZOrigin (PYME.recipes.processing.Composite attribute) il16() (in module PYME.misc.TiffImagePlugin) il32() (in module PYME.misc.TiffImagePlugin) image (PYME.DSView.modules.psfGeneration.MeasuredPupil attribute) (PYME.simulation.pointsets.ImageSource attribute) image_data (PYME.IO.h5File.H5File property) image_enrichment_and_fraction_at_distance() (in module PYME.Analysis.Colocalisation.edtColoc) image_to_cmy() (in module PYME.IO.rgb_image) image_to_rgb() (in module PYME.IO.rgb_image) ImageBounds (class in PYME.IO.image) (class in PYME.LMVis.visHelpersMin) ImageCumulativeHistogram (class in PYME.recipes.measurement) imageDensityAtDistance() (in module PYME.Analysis.Colocalisation.edtColoc) ImageEngine (class in PYME.LMVis.layers.image_layer) ImageFileDirectory (class in PYME.misc.TiffImagePlugin) ImageFrameSource (class in PYME.IO.clusterExport) ImageFromBitmap() (in module PYME.ui.wx_compat) ImageFromData() (in module PYME.ui.wx_compat) ImageHistogram (class in PYME.recipes.measurement) ImageList (class in PYME.DSView.modules.composite) ImageMaskFromSphericalHarmonicShell (class in PYME.recipes.surface_fitting) ImageModuleBase (class in PYME.recipes.base) ImageOutput (class in PYME.recipes.output) ImagePanel (class in PYME.DSView.scrolledImagePanel) ImagePyramid (class in PYME.Analysis.tile_pyramid) ImageRenderLayer (class in PYME.LMVis.layers.image_layer) images() (PYME.DSView.modules.blobMeasure.Measurements method) ImageShaderProgram (class in PYME.LMVis.shader_programs.DefaultShaderProgram) ImageSource (class in PYME.simulation.pointsets) ImageStack (class in PYME.IO.image) ImageViewPanel (class in PYME.LMVis.imageView) (class in PYME.LMVis.imageView2) imgBounds (PYME.IO.image.ImageStack property) impfilt() (in module PYME.Analysis.implicitFilter) impfilt2() (in module PYME.Analysis.implicitFilter) impfilt3() (in module PYME.Analysis.implicitFilter) import_fit_factory() (in module PYME.localization.FitFactories) ImportMatDialog (class in PYME.LMVis.importTextDialog) ImportMatlabDialog (class in PYME.LMVis.importTextDialog) ImportTextDialog (class in PYME.LMVis.importTextDialog) imread() (in module PYME.contrib.gohlke.czifile) (in module PYME.contrib.gohlke.tifffile) imsave() (in module PYME.contrib.gohlke.tifffile) imshow() (in module PYME.contrib.gohlke.tifffile) inactivate() (PYME.cluster.ruleserver.IntegerIDRule method) inactivate_rule() (PYME.cluster.ruleserver.RuleServer method) index (PYME.DSView.modules.particleTracking.ParticleTrackingView attribute) (PYME.IO.tabular.ColourFilter property) (PYME.tileviewer.tileviewer.TileServer attribute) index() (PYME.DSView.modules.blobMeasure.Measurements method) index_coeffs() (in module PYME.misc.read_agf) index_data() (in module PYME.misc.read_agf) infer_tileio_backend() (in module PYME.Analysis.tile_pyramid) info() (PYME.Acquire.SpoolController.SpoolControllerWrapper method) (PYME.cluster.ruleserver.IntegerIDRule method) info_longpoll() (PYME.Acquire.SpoolController.SpoolControllerWrapper method) info_text (PYME.recipes.processing.PSFFile attribute) (PYME.recipes.traits.FileOrURI attribute) Init() (PYME.Acquire.protocol.Protocol method) (PYME.Acquire.protocol.TaskListProtocol method) (PYME.Acquire.protocol.ZStackTaskListProtocol method) init_gui() (in module PYME.Acquire.ExecTools) init_hardware() (in module PYME.Acquire.ExecTools) init_pane() (PYME.LMVis.Extras.showShortcuts.ShowShortcuts method) init_params (PYME.recipes.pointcloud.GaussianMixtureModel attribute) init_renderers() (in module PYME.LMVis.renderers) init_tolerance (PYME.recipes.surface_fitting.SphericalHarmonicShell attribute) InitBG() (in module PYME.Acquire.ExecTools) InitGUI() (in module PYME.Acquire.ExecTools) initialise() (PYME.IO.acquisition_backends.Backend method) (PYME.IO.acquisition_backends.ClusterBackend method) initialize() (PYME.Acquire.microscope.microscope method) initialized (PYME.Acquire.microscope.microscope property) initializeWorkerTimeout() (PYME.misc.taskDef.Task method) InitPlugins() (in module PYME.LMVis.Extras) Input (class in PYME.recipes.traits) input (PYME.recipes.base.Crop attribute) (PYME.recipes.base.Redimension attribute) (PYME.recipes.localisations.ProcessColour attribute) (PYME.recipes.localisations.TimeBlocks attribute) (PYME.recipes.measurement.ChunkedTravelingSalesperson attribute) (PYME.recipes.measurement.IdentifyOverlappingROIs attribute) (PYME.recipes.measurement.TravelingSalesperson attribute) (PYME.recipes.pointcloud.DelaunayCircumcentres attribute) (PYME.recipes.pointcloud.DelaunayTesselation attribute) (PYME.recipes.pointcloud.LocalPointDensity attribute) (PYME.recipes.processing.DarkAndVarianceMap attribute) (PYME.recipes.processing.ResampleZ attribute) (PYME.recipes.surface_fitting.DelaunayMarchingTetrahedra attribute) (PYME.recipes.surface_fitting.DualMarchingCubes attribute) (PYME.recipes.surface_fitting.FitSurfaceWithPatches attribute) (PYME.recipes.surface_fitting.Isosurface attribute) (PYME.recipes.surface_fitting.NthPointIsosurface attribute) (PYME.recipes.tablefilters.RandomSubset attribute) input0 (PYME.recipes.measurement.Plot attribute) (PYME.recipes.processing.Composite attribute) input1 (PYME.recipes.measurement.Plot attribute) (PYME.recipes.processing.Composite attribute) input2 (PYME.recipes.measurement.Plot attribute) (PYME.recipes.processing.Composite attribute) input3 (PYME.recipes.measurement.Plot attribute) (PYME.recipes.processing.Composite attribute) input_image (PYME.recipes.processing.AverageFramesByZStep attribute) input_image_bound_source (PYME.recipes.surface_fitting.ImageMaskFromSphericalHarmonicShell attribute) INPUT_LIGHT (PYME.LMVis.shader_programs.GouraudShaderProgram.GouraudShaderProgram attribute) input_localizations (PYME.recipes.pointcloud.Octree attribute) (PYME.recipes.surface_fitting.AddSphericalHarmonicShellMappedCoords attribute) input_measurements (PYME.recipes.localisations.AddMeasurementsByLabel attribute) (PYME.recipes.pyramid.SupertilePhysicalCoords attribute) input_mesh (PYME.recipes.surface_fitting.DistanceToMesh attribute) (PYME.recipes.surface_fitting.FilterMeshComponentsByVolume attribute) input_name (PYME.recipes.localisations.MapAstigZ attribute) (PYME.recipes.measurement.DetectPoints2D attribute) (PYME.recipes.multiview.CalibrateShifts attribute) (PYME.recipes.multiview.ExtractMultiviewChannel attribute) (PYME.recipes.multiview.FindClumps attribute) (PYME.recipes.multiview.Fold attribute) (PYME.recipes.multiview.MapAstigZ attribute) (PYME.recipes.multiview.MergeClumps attribute) (PYME.recipes.multiview.ShiftCorrect attribute) (PYME.recipes.processing.BackgroundSubtractionMovingAverage attribute) (PYME.recipes.processing.RawADUToElectronsPerSecond attribute) (PYME.recipes.processing.StatisticsByFrame attribute) (PYME.recipes.surface_fitting.SphericalHarmonicShell attribute) input_points (PYME.recipes.localisations.AddMeasurementsByLabel attribute) (PYME.recipes.pointcloud.GaussianMixtureModel attribute) (PYME.recipes.surface_fitting.DistanceToMesh attribute) input_positions (PYME.recipes.acquisition.QueueAcquisitions attribute) (PYME.recipes.measurement.ExtractROIs attribute) input_sample_locations (PYME.recipes.pointcloud.LocalPointDensity attribute) input_series (PYME.recipes.measurement.ExtractROIs attribute) input_shell (PYME.recipes.surface_fitting.AddSphericalHarmonicShellMappedCoords attribute) (PYME.recipes.surface_fitting.ImageMaskFromSphericalHarmonicShell attribute) (PYME.recipes.surface_fitting.SHShellRadiusDensityEstimate attribute) input_supertile (PYME.recipes.pyramid.SupertilePhysicalCoords attribute) input_zvals (PYME.recipes.processing.AverageFramesByZStep attribute) inputAnnotations (PYME.recipes.machine_learning.AnnotatePoints attribute) inputChan0 (PYME.recipes.base.JoinChannels attribute) (PYME.recipes.measurement.NearestNeighbourDistances attribute) inputChan1 (PYME.recipes.base.JoinChannels attribute) (PYME.recipes.measurement.NearestNeighbourDistances attribute) inputChan2 (PYME.recipes.base.JoinChannels attribute) inputChan3 (PYME.recipes.base.JoinChannels attribute) inputDirX (PYME.recipes.processing.ProjectOnVector attribute) inputDirY (PYME.recipes.processing.ProjectOnVector attribute) inputEvents (PYME.recipes.localisations.IDTransientFrames attribute) (PYME.recipes.localisations.Pipelineify attribute) inputFiducials (PYME.recipes.localisations.FiducialCorrection attribute) inputFitResults (PYME.recipes.localisations.Pipelineify attribute) inputFlowX (PYME.recipes.processing.DeconvolveMotionCompensating attribute) (PYME.recipes.processing.WavefrontVelocity attribute) inputFlowY (PYME.recipes.processing.DeconvolveMotionCompensating attribute) (PYME.recipes.processing.WavefrontVelocity attribute) inputImage (PYME.recipes.fudges.EstimateFrameZFromStepMetadata attribute) (PYME.recipes.localisations.LabelsFromImage attribute) (PYME.recipes.measurement.AddMetadataToMeasurements attribute) (PYME.recipes.measurement.BinnedHistogram attribute) (PYME.recipes.measurement.FitDumbells attribute) (PYME.recipes.measurement.FitPoints attribute) (PYME.recipes.measurement.ImageCumulativeHistogram attribute) (PYME.recipes.measurement.ImageHistogram attribute) (PYME.recipes.measurement.IntensityAtPoints attribute) (PYME.recipes.measurement.MultifitBlobs attribute) (PYME.recipes.output.ReportForEachOutput attribute) (PYME.recipes.processing.ColocalisationEDT attribute) (PYME.recipes.processing.FlatfiledAndDarkCorrect attribute) (PYME.recipes.processing.Watershed attribute) (PYME.recipes.tracking.LoadSpeckles attribute) inputImageA (PYME.recipes.processing.Colocalisation attribute)

inputImageB (PYME.recipes.processing.Colocalisation attribute) (PYME.recipes.processing.ColocalisationEDT attribute) inputIntensity (PYME.recipes.measurement.Measure2D attribute) (PYME.recipes.processing.FindCaWaves attribute) inputLabels (PYME.recipes.machine_learning.LabelsToChannels attribute) (PYME.recipes.measurement.Measure2D attribute) inputLocalisations (PYME.recipes.machine_learning.AnnotatePoints attribute) (PYME.recipes.machine_learning.PointFeaturesPairwiseDist attribute) (PYME.recipes.machine_learning.PointFeaturesVectorial attribute) inputLocalizations (PYME.recipes.localisations.DensityMapping attribute) (PYME.recipes.localisations.FiducialCorrection attribute) inputMarkers (PYME.recipes.processing.Watershed attribute) inputMask (PYME.recipes.measurement.BinnedHistogram attribute) (PYME.recipes.measurement.ImageCumulativeHistogram attribute) (PYME.recipes.measurement.ImageHistogram attribute) (PYME.recipes.pointcloud.Ripleys attribute) (PYME.recipes.processing.ColocalisationEDT attribute) (PYME.recipes.processing.Watershed attribute) inputMaskA (PYME.recipes.processing.Colocalisation attribute) inputMaskB (PYME.recipes.processing.Colocalisation attribute) inputMeasurements (PYME.recipes.measurement.AddMetadataToMeasurements attribute) (PYME.recipes.measurement.Histogram attribute) (PYME.recipes.tablefilters.SelectTableColumns attribute) (PYME.recipes.tracking.ExtractTracks attribute) (PYME.recipes.tracking.TrackFeatures attribute) inputMeasurements1 (PYME.recipes.tablefilters.AggregateMeasurements attribute) inputMeasurements2 (PYME.recipes.tablefilters.AggregateMeasurements attribute) inputMeasurements3 (PYME.recipes.tablefilters.AggregateMeasurements attribute) inputMeasurements4 (PYME.recipes.tablefilters.AggregateMeasurements attribute) inputName (PYME.recipes.base.ExtractChannel attribute) (PYME.recipes.base.Filter attribute) (PYME.recipes.localisations.AutocorrelationDriftCorrection attribute) (PYME.recipes.localisations.ClusterCountVsImagingTime attribute) (PYME.recipes.localisations.DBSCANClustering attribute) (PYME.recipes.localisations.ExtractTableChannel attribute) (PYME.recipes.localisations.IDTransientFrames attribute) (PYME.recipes.localisations.LabelsFromImage attribute) (PYME.recipes.localisations.MeasureClusters3D attribute) (PYME.recipes.localisations.MergeClumps attribute) (PYME.recipes.output.CSVOutput attribute) (PYME.recipes.output.ImageOutput attribute) (PYME.recipes.output.PlotOutput attribute) (PYME.recipes.output.ReportForEachOutput attribute) (PYME.recipes.output.ReportOutput attribute) (PYME.recipes.output.RGBImageOutput attribute) (PYME.recipes.output.STLOutput attribute) (PYME.recipes.output.XLSOutput attribute) (PYME.recipes.processing.DirectionToMask3D attribute) (PYME.recipes.processing.Gradient2D attribute) (PYME.recipes.processing.Gradient3D attribute) (PYME.recipes.processing.OpticalFlow attribute) (PYME.recipes.processing.WavefrontDetection attribute) (PYME.recipes.pyramid.TilePyramid attribute) (PYME.recipes.tablefilters.FilterTable attribute) (PYME.recipes.tablefilters.FilterTableByIDs attribute) (PYME.recipes.tablefilters.Mapping attribute) (PYME.recipes.tracking.FindClumps attribute) inputName0 (PYME.recipes.base.ArithmaticFilter attribute) (PYME.recipes.tablefilters.ConcatenateTables attribute) inputName1 (PYME.recipes.base.ArithmaticFilter attribute) (PYME.recipes.tablefilters.ConcatenateTables attribute) inputPositions (PYME.recipes.measurement.FitDumbells attribute) (PYME.recipes.measurement.FitPoints attribute) (PYME.recipes.measurement.IntensityAtPoints attribute) (PYME.recipes.measurement.MeanNeighbourDistances attribute) (PYME.recipes.measurement.PairwiseDistanceHistogram attribute) (PYME.recipes.pointcloud.Ripleys attribute) inputPositions2 (PYME.recipes.measurement.PairwiseDistanceHistogram attribute) inputRoiMask (PYME.recipes.processing.Colocalisation attribute) (PYME.recipes.processing.ColocalisationEDT attribute) inputs (PYME.recipes.base.ModuleBase property) (PYME.recipes.output.HDFOutput property) (PYME.recipes.processing.Composite property) (PYME.recipes.recipe.Recipe property) inputTracks (PYME.recipes.tracking.FitFusionTraces attribute) inputVariables (PYME.recipes.output.HDFOutput attribute) inputWavefronts (PYME.recipes.processing.FindCaWaves attribute) (PYME.recipes.processing.WavefrontVelocity attribute) inputX (PYME.recipes.processing.ProjectOnVector attribute) (PYME.recipes.processing.VectorfieldAngle attribute) (PYME.recipes.processing.VectorfieldCurl attribute) (PYME.recipes.processing.VectorfieldNorm attribute) inputY (PYME.recipes.processing.ProjectOnVector attribute) (PYME.recipes.processing.VectorfieldAngle attribute) (PYME.recipes.processing.VectorfieldCurl attribute) (PYME.recipes.processing.VectorfieldNorm attribute) inputZ (PYME.recipes.processing.VectorfieldAngle attribute) (PYME.recipes.processing.VectorfieldCurl attribute) (PYME.recipes.processing.VectorfieldNorm attribute) insert() (PYME.Analysis.points.QuadTree.pointQT.qtBranchNode method) (PYME.Analysis.points.QuadTree.pointQT.qtLeafNode method) (PYME.Analysis.points.QuadTree.pointQT.qtNode method) (PYME.Analysis.points.QuadTree.pointQT.qtRoot method) (PYME.Analysis.points.QuadTree.pointQTF.qtBranchNode method) (PYME.Analysis.points.QuadTree.pointQTF.qtLeafNode method) (PYME.Analysis.points.QuadTree.pointQTF.qtNode method) (PYME.Analysis.points.QuadTree.pointQTF.qtRoot method) insert_dispersion_coeffs() (in module PYME.misc.read_agf) insert_into_full_map() (in module PYME.Analysis.gen_sCMOS_maps) insertRecords() (PYME.Analysis.points.QuadTree.pointQTF.qtBranchNode method) (PYME.Analysis.points.QuadTree.pointQTF.qtLeafNode method) install_map() (in module PYME.Analysis.gen_sCMOS_maps) InstallSpy() (in module PYME.misc.eventSpy) Instance (in module PYME.misc.mock_traits) InstanceEditor() (in module PYME.misc.mock_traitsui) instanceinlist() (in module PYME.IO.MetaDataHandler) Int (in module PYME.misc.mock_traits) IntegerIDRule (class in PYME.cluster.ruleserver) IntegrationSliders (class in PYME.Acquire.ui.intsliders) IntegrationSliders_ (class in PYME.Acquire.ui.intsliders) IntensityAtPoints (class in PYME.recipes.measurement) intensityThreshold (PYME.recipes.processing.WavefrontDetection attribute) IntensityTracePanel (class in PYME.Acquire.ui.intensity_trace) interp() (PYME.localization.FitFactories.Interpolators.CSInterpolator.CSInterpolator method) (PYME.localization.FitFactories.Interpolators.CubeSInterpolatorP.CSInterpolator method) (PYME.localization.FitFactories.Interpolators.CubicSplineInterpolator.CubicSplineInterpolator method) (PYME.localization.FitFactories.Interpolators.LinearInterpolator.LinearInterpolator method) (PYME.localization.FitFactories.Interpolators.LinearPInterpolatorP.LinearInterpolator method) InterpFitFactory (class in PYME.localization.FitFactories.MultiviewFitInterpNR) (class in PYME.localization.FitFactories.SplitterFitInterpBNR) (class in PYME.localization.FitFactories.SplitterFitInterpNR) interpG() (PYME.localization.FitFactories.Interpolators.CSInterpolator.CSInterpolator method) (PYME.localization.FitFactories.Interpolators.LinearInterpolator.LinearInterpolator method) interpolate (PYME.recipes.processing.Composite attribute) Interpolate() (in module PYME.localization.cInterp.cInterp) InterpolateCS() (in module PYME.localization.cInterp.cInterp) InterpolateInplace() (in module PYME.localization.cInterp.cInterp) InterpolateInplaceM() (in module PYME.localization.cInterp.cInterp) intfrombits() (in module PYME.contrib.lzw) IntParam (class in PYME.localization.MetaDataEdit) inttobits() (in module PYME.contrib.lzw) invalidate_data() (PYME.recipes.recipe.Recipe method) invalidate_directory() (PYME.IO.clusterListing.DirCache method) invalidate_layout() (PYME.recipes.vertical_recipe_display.RecipeDisplayPanel method) invalidate_parent() (PYME.recipes.base.ModuleBase method) Invert (class in PYME.recipes.base) IPY (class in PYME.Acquire.webui.ipy) IPYTermManager (class in PYME.Acquire.webui.ipy) ipython_pymevisualize() (in module PYME.LMVis.VisGUI) ipython_visgui() (in module PYME.LMVis.VisGUI) IPYWithClients (class in PYME.Acquire.webui.ipy) IQR() (in module PYME.localization.Test.fitTestJigSCMOS) (in module PYME.localization.Test.fitTestJigWC) is_bigtiff (PYME.contrib.gohlke.tifffile.TIFFfile attribute) is_cluster_uri() (in module PYME.IO.unifiedIO) is_complete (PYME.IO.DataSources.BaseDataSource.BaseDataSource property) (PYME.IO.DataSources.BaseDataSource.XYTCWrapper property) (PYME.IO.DataSources.BaseDataSource.XYZTCWrapper property) (PYME.IO.DataSources.BGSDataSource.XYZTCBgsSource property) (PYME.IO.DataSources.BufferedDataSource.DataSource property) (PYME.IO.DataSources.ClusterPZFDataSource.DataSource property) (PYME.IO.dataWrap.ListWrapper property) is_fluoview (PYME.contrib.gohlke.tifffile.TIFFfile attribute) is_local() (in module PYME.IO.clusterIO) is_lsm (PYME.contrib.gohlke.tifffile.TIFFfile attribute) is_nih (PYME.contrib.gohlke.tifffile.TIFFfile attribute) is_ome (PYME.contrib.gohlke.tifffile.TIFFfile attribute) is_palette (PYME.contrib.gohlke.tifffile.TIFFfile attribute) is_port_open() (in module PYME.misc.sqlite_ns) is_rgb (PYME.contrib.gohlke.tifffile.TIFFfile attribute) is_splitter_fit (PYME.localization.remFitBuf.fitTask property) is_stk (PYME.contrib.gohlke.tifffile.TIFFfile attribute) isatty() (PYME.Acquire.webui.ipy.TTYDummy method) IsChecked() (PYME.contrib.listctrlMixins.CheckListCtrlMixin method) IsClose (class in PYME.recipes.base) isdir() (in module PYME.IO.clusterIO) (PYME.IO.cluster_directory.DirectoryInfoManager method) isnumber() (in module PYME.IO.csv_flavours) (in module PYME.LMVis.importTextDialog) isodata() (in module PYME.Analysis.thresholding) isodata_f() (in module PYME.Analysis.thresholding) Isosurf (class in PYME.misc.VolProj) isosurf_builtin() (PYME.DSView.modules.vis3D.Visualiser method) isosurf_coloured() (PYME.DSView.modules.vis3D.Visualiser method) Isosurface (class in PYME.recipes.surface_fitting) isosurface3D() (PYME.DSView.modules.blobMeasure.Measurements method) isRunning() (PYME.Acquire.frameWrangler.FrameWrangler method) Item() (in module PYME.misc.mock_traitsui) items() (PYME.misc.TiffImagePlugin.ImageFileDirectory method) iterations (PYME.recipes.processing.BinaryDilation attribute) (PYME.recipes.processing.BinaryErosion attribute) (PYME.recipes.processing.Deconvolve attribute)

J

jitter_iterations (PYME.recipes.surface_fitting.SHShellRadiusDensityEstimate attribute) jittering (PYME.LMVis.triBlobs.BlobSettings attribute) jitterScale (PYME.recipes.localisations.DensityMapping attribute) jitterScaleZ (PYME.recipes.localisations.DensityMapping attribute) jitterVariable (PYME.recipes.localisations.DensityMapping attribute) jitterVariableZ (PYME.recipes.localisations.DensityMapping attribute) join() (PYME.Acquire.ExecTools.BGInitTask method) (PYME.cluster.rules.Rule method)

joinBGInit() (in module PYME.Acquire.ExecTools) JoinChannels (class in PYME.recipes.base) JSON_DURATION (PYME.LMVis.views.VideoView attribute) JSON_LIST_NAME (PYME.LMVis.Extras.animation.VideoPanel attribute) JSONAPIRequestHandler (class in PYME.util.webframework) jumpDistModel() (in module PYME.Analysis.Tracking.trackUtils) jumpDistProb() (in module PYME.Analysis.Tracking.trackUtils)

K

kbp (PYME.simulation.pointsets.WormlikeSource attribute) keep_alive() (in module PYME.IO.clusterDuplication) KEEP_ALIVE_TIMEOUT (PYME.IO.h5File.H5File attribute) keep_pairs() (in module PYME.Analysis.keep_pairs) kernelSize (PYME.recipes.processing.DirectionToMask3D attribute) key (PYME.recipes.measurement.Histogram attribute) (PYME.recipes.measurement.MeanNeighbourDistances attribute) (PYME.recipes.measurement.NearestNeighbourDistances attribute) keys (PYME.recipes.measurement.AddMetadataToMeasurements attribute) (PYME.recipes.tablefilters.SelectTableColumns attribute) keys() (PYME.Acquire.microscope.StateManager method) (PYME.Analysis.Tracking.trackUtils.Clump method) (PYME.IO.MetaDataHandler.MDHandlerBase method) (PYME.IO.tabular.AnndataSource method) (PYME.IO.tabular.CachingResultsFilter method) (PYME.IO.tabular.CloneSource method) (PYME.IO.tabular.ColourFilter method) (PYME.IO.tabular.ConcatenateFilter method) (PYME.IO.tabular.DictSource method) (PYME.IO.tabular.FitResultsSource method) (PYME.IO.tabular.HDFSource method) (PYME.IO.tabular.MappingFilter method) (PYME.IO.tabular.MatfileColumnSource method) (PYME.IO.tabular.MatfileSource method) (PYME.IO.tabular.RandomSource method) (PYME.IO.tabular.RecArraySource method) (PYME.IO.tabular.SelectionFilter method) (PYME.IO.tabular.TabularBase method) (PYME.IO.tabular.TextfileSource method) (PYME.LMVis.pipeline.Pipeline method) (PYME.misc.TiffImagePlugin.ImageFileDirectory method) (PYME.recipes.pointcloud.Tesselation method)

kill() (PYME.Acquire.Utils.failsafe.Failsafe method) (PYME.Acquire.Utils.failsafe.FailsafeClient method) (PYME.Acquire.webui.ipy.IPY method) (PYME.Acquire.webui.ipy.IPYWithClients method) (PYME.Deconv.decThread.decThread method) kill_all (PYME.Acquire.webui.ipy.IPYTermManager attribute) killpg() (PYME.Acquire.webui.ipy.IPYWithClients method) kind (PYME.recipes.processing.Projection attribute) kwargs() (PYME.recipes.skfilters.SKFilter method)

L

Label (class in PYME.recipes.processing) label (PYME.recipes.processing.SelectLabel attribute) label_count_key_name (PYME.recipes.localisations.LabelsFromImage attribute) label_key (PYME.LMVis.Extras.objectMeasurements.OMDialog property) (PYME.recipes.localisations.AddMeasurementsByLabel attribute) (PYME.recipes.pointcloud.GaussianMixtureModel attribute) label_key_name (PYME.recipes.localisations.LabelsFromImage attribute) label_points() (PYME.DSView.modules.annotation.AnnotationList method) labelColumnName (PYME.recipes.machine_learning.AnnotatePoints attribute) labeled() (in module PYME.DSView.displayOptions) (in module PYME.misc.colormaps) labelKey (PYME.recipes.localisations.MeasureClusters3D attribute) (PYME.recipes.localisations.MergeClumps attribute) (PYME.recipes.multiview.MergeClumps attribute) LabelPanel (class in PYME.DSView.modules.annotation) LabelsFromImage (class in PYME.recipes.localisations) labelsKey (PYME.recipes.localisations.ClusterCountVsImagingTime attribute) LabelsToChannels (class in PYME.recipes.machine_learning) LaserSliders (class in PYME.Acquire.ui.lasersliders) LaserSliders_ (class in PYME.Acquire.ui.lasersliders) LaserToggles (class in PYME.Acquire.ui.lasersliders) launch() (PYME.cluster.cluster_of_one.ClusterOfOne method) launch_browser() (in module PYME.util.fProfile.viewProfile) launch_cluster_analysis() (PYME.Acquire.SpoolController.SpoolController method) launch_ipy_server_thread() (in module PYME.Acquire.webui.ipy) launch_localize() (in module PYME.cluster.HTTPRulePusher) (in module PYME.cluster.HTTPTaskPusher) LaunchAnalysis() (PYME.Acquire.SpoolController.SpoolController method) layer_data_source_names (PYME.LMVis.pipeline.Pipeline property) layer_datasources (PYME.LMVis.pipeline.Pipeline property) LayerFoldingPane (class in PYME.ui.layerFoldPanel) LayerPane (class in PYME.LMVis.layer_panel) layers (PYME.LMVis.visCore.VisGUICore property) layout() (in module PYME.recipes.recipeLayout) (PYME.recipes.recipe.Recipe method) layout_vertical() (in module PYME.recipes.recipeLayout) LazyScopeTweeter (class in PYME.Acquire.htsms.tweeter) leadFrames (PYME.recipes.tracking.LoadSpeckles attribute) leafSize (PYME.LMVis.quadTreeSettings.QuadTreeSettings attribute) left (PYME.recipes.measurement.BinnedHistogram attribute) (PYME.recipes.measurement.Histogram attribute) (PYME.recipes.measurement.ImageHistogram attribute) length (PYME.simulation.pointsets.WiglyFibreSource attribute) length_nm (PYME.DSView.overlays.ScaleBarOverlay attribute) lengthPerKbp (PYME.simulation.pointsets.WormlikeSource attribute) Lfunc() (PYME.Analysis.PSFEst.dec.dec_psf method) (PYME.Deconv.dec.ClassicMappingFFTW method) (PYME.Deconv.dec.ClassicMappingNP method) (PYME.Deconv.dec.dec_4pi method) (PYME.Deconv.dec.dec_4pi_c method) (PYME.Deconv.dec.DeconvMappingBase method) (PYME.Deconv.dec.SpatialConvolutionMapping method) Lhfunc() (PYME.Analysis.PSFEst.dec.dec_psf method) (PYME.Deconv.dec.ClassicMappingFFTW method) (PYME.Deconv.dec.ClassicMappingNP method) (PYME.Deconv.dec.dec_4pi method) (PYME.Deconv.dec.dec_4pi_c method) (PYME.Deconv.dec.DeconvMappingBase method) (PYME.Deconv.dec.SpatialConvolutionMapping method) LHoodRenderer (class in PYME.LMVis.renderers) lifo (PYME.recipes.acquisition.QueueAcquisitions attribute) LIGHT_PROPS (PYME.LMVis.shader_programs.GouraudShaderProgram.GouraudShaderProgram attribute) lights_vector (PYME.LMVis.shader_programs.GouraudShaderProgram.GouraudShaderProgram attribute) limit_reconstruction_to_support_hull (PYME.recipes.surface_fitting.FitSurfaceWithPatches attribute) LimitedSizeDict (class in PYME.Acquire.sampleInformation) lin2Model (class in PYME.Analysis.points.twoColour) lin3Model (class in PYME.Analysis.points.twoColour) lin3zModel (class in PYME.Analysis.points.twoColour) line_width (PYME.LMVis.layers.tracks.TrackRenderLayer attribute) LinearInterpolator (class in PYME.localization.FitFactories.Interpolators.LinearInterpolator) (class in PYME.localization.FitFactories.Interpolators.LinearPInterpolatorP) link() (PYME.LMVis.shader_programs.shader_program.ShaderProgram method) link_route() (in module PYME.Analysis.points.traveling_salesperson.sectioned_two_opt) linMod() (in module PYME.Analysis.BleachProfile.rawIntensity) linModel (class in PYME.Analysis.points.twoColour) List (class in PYME.misc.mock_traits) list() (PYME.misc.hybrid_ns.HybridNS method) (PYME.misc.pyme_zeroconf.ZCListener method) (PYME.misc.pyme_zeroconf.ZeroConfNS method) (PYME.misc.sqlite_ns.SQLiteNS method) list_directory() (in module PYME.IO.clusterListing) (PYME.cluster.dataserver_wsgi.dataserver method) (PYME.cluster.HTTPDataServer.PYMEHTTPRequestHandler method) (PYME.IO.clusterListing.DirCache method) list_directory_p() (in module PYME.IO.clusterListing) list_h5() (in module PYME.IO.pyme_h5ls) (PYME.cluster.HTTPDataServer.PYMEHTTPRequestHandler method) list_single_node_dir() (PYME.IO.cluster_directory.DirectoryInfoManager method) list_to_array() (PYME.IO.events.EventLogger class method) listCalibrationDirs() (in module PYME.Analysis.gen_sCMOS_maps) ListCtrlAutoWidthMixin (class in PYME.contrib.listctrlMixins) ListCtrlSelectionManagerMix (class in PYME.contrib.listctrlMixins) listdir() (in module PYME.IO.clusterIO) (PYME.IO.cluster_directory.DirectoryInfoManager method) listdirectory() (in module PYME.IO.clusterIO) (PYME.IO.cluster_directory.DirectoryInfoManager method) ListFloat (in module PYME.misc.mock_traits) ListInt (in module PYME.misc.mock_traits) ListRowHighlighter (class in PYME.contrib.listctrlMixins) ListStr (in module PYME.misc.mock_traits)

ListWrapper (class in PYME.IO.dataWrap) LMAnalyser2 (class in PYME.DSView.modules.LMAnalysis) LMDisplay (class in PYME.DSView.modules.LMDisplay) lNdfcn() (in module PYME.Analysis.BleachProfile.intensProf) lNdfcnDE() (in module PYME.Analysis.BleachProfile.intensProf) lNofcn() (in module PYME.Analysis.BleachProfile.intensProf) lNofcnDE() (in module PYME.Analysis.BleachProfile.intensProf) load() (in module PYME.IO.FileUtils.SPAD) (PYME.Analysis.tile_pyramid.TileCache method) Load() (PYME.IO.image.ImageStack method) load() (PYME.LMVis.Extras.animation.VideoPanel method) (PYME.misc.TiffImagePlugin.ImageFileDirectory method) load_byte() (PYME.misc.TiffImagePlugin.ImageFileDirectory method) load_config() (in module PYME.config) load_dispatch (PYME.misc.TiffImagePlugin.ImageFileDirectory attribute) load_double() (PYME.misc.TiffImagePlugin.ImageFileDirectory method) load_existing() (PYME.Analysis.tile_pyramid.ImagePyramid class method) load_fiducial_info_from_second_file() (in module PYME.LMVis.Extras.fiducial) load_float() (PYME.misc.TiffImagePlugin.ImageFileDirectory method) load_header() (in module PYME.IO.PZFFormat) load_json() (in module PYME.IO.MetaDataHandler) load_long() (PYME.misc.TiffImagePlugin.ImageFileDirectory method) load_ply() (in module PYME.IO.FileUtils.ply) load_psf() (in module PYME.IO.load_psf) load_rational() (PYME.misc.TiffImagePlugin.ImageFileDirectory method) load_recipe_from_mdh() (PYME.recipes.recipeGui.PipelineRecipeManager method) load_shiftmap() (in module PYME.Analysis.points.multiview) load_short() (PYME.misc.TiffImagePlugin.ImageFileDirectory method) load_stl_binary() (in module PYME.IO.FileUtils.stl) load_string() (PYME.misc.TiffImagePlugin.ImageFileDirectory method) load_template() (in module PYME.Acquire.webui) load_texture() (PYME.LMVis.shader_programs.PointSpriteShaderProgram.GaussTexture method) load_undefined() (PYME.misc.TiffImagePlugin.ImageFileDirectory method) load_view() (PYME.LMVis.Extras.saved_views.ViewPanel method) load_wisdom() (in module PYME.Deconv.fftwWisdom) loadDark() (in module PYME.IO.FileUtils.SPAD) loadFile() (PYME.Analysis.svmSegment.svmClassifier method) loadInput() (PYME.recipes.recipe.Recipe method) loadMode() (in module PYME.DSView.modules) loadModule() (in module PYME.DSView.modules) LoadModule() (PYME.DSView.dsviewer.DSViewFrame method) LoadPerspective() (PYME.Acquire.acquiremainframe.PYMEMainFrame method) (PYME.Acquire.acquirewx.PYMEMainFrame method) loadRaw() (in module PYME.IO.FileUtils.SPAD) LoadRecipe() (PYME.recipes.recipeGui.RecipeManager method) LoadRecipeText() (PYME.recipes.recipeGui.PipelineRecipeManager method) (PYME.recipes.recipeGui.RecipeManager method) loads() (in module PYME.IO.PZFFormat) LoadShiftField() (in module PYME.Analysis.splitting) LoadSpeckles (class in PYME.recipes.tracking) loc_test() (in module PYME.Analysis.PSFEst.psfQuality) local_or_temp_filename() (in module PYME.IO.unifiedIO) localisation_origin_nm() (in module PYME.IO.MetaDataHandler) LocalisationRule (class in PYME.cluster.rules) LocalisationRuleFactory (class in PYME.cluster.rules) LocalizationSettingsPanel (class in PYME.Acquire.htsms.rule_ui) LocalMaxima (class in PYME.recipes.processing) LocalPointDensity (class in PYME.recipes.pointcloud) locate() (in module PYME.misc.locate) locate_file() (in module PYME.IO.clusterIO) (PYME.IO.cluster_directory.DirectoryInfoManager method) Location (class in PYME.tileviewer.tileviewer) locify() (in module PYME.simulation.locify) log_error() (PYME.cluster.HTTPDataServer.PYMEHTTPRequestHandler method) log_message() (PYME.cluster.HTTPDataServer.PYMEHTTPRequestHandler method) (PYME.cluster.webdav.DAVRequestHandler method) log_request() (PYME.cluster.HTTPDataServer.PYMEHTTPRequestHandler method) (PYME.util.webframework.JSONAPIRequestHandler method) log_stream() (in module PYME.cluster.PYMERuleServer) log_url (PYME.cluster.taskWorkerHTTP.TaskError property) logEvent() (in module PYME.Acquire.eventLog) (PYME.IO.events.EventLogger method) (PYME.IO.events.HDFEventLogger method) (PYME.IO.events.MemoryEventLogger method) (PYME.IO.events.QueueEventLogger method) logger (in module PYME.IO.dcimg) (in module PYME.recipes.skfilters) LogicalAnd (class in PYME.recipes.base) login() (PYME.Acquire.acquire_server.AcquireHTTPServer method) logout() (PYME.Acquire.acquire_server.AcquireHTTPServer method) logparser (class in PYME.DSView.logparser) logrequests (PYME.cluster.dataserver_wsgi.dataserver attribute) (PYME.cluster.HTTPDataServer.PYMEHTTPRequestHandler attribute) (PYME.util.webframework.JSONAPIRequestHandler attribute) logwriter (class in PYME.DSView.logparser) long_unpack() (in module PYME.IO.FileUtils.obf_support) longAxisDistN() (PYME.DSView.modules.blobMeasure.BlobObject method) longAxisOrthDist() (PYME.DSView.modules.blobMeasure.BlobObject method) lookup_astig_z() (in module PYME.Analysis.points.astigmatism.astigTools) lookup_astig_z_dsigma() (in module PYME.Analysis.points.astigmatism.astigTools) lookup_offset() (PYME.Acquire.stage_leveling.StageLeveler method) loop_forever() (in module PYME.ui.mytimer) (PYME.Acquire.event_loop.EventLoop method) (PYME.cluster.taskWorkerHTTP.taskWorker method) lorentzianFWHM (PYME.recipes.processing.Deconvolve attribute) lowerMinPtsPerCluster (PYME.recipes.localisations.ClusterCountVsImagingTime attribute) lp_poisson() (in module PYME.Analysis.cramerRao) lp_poisson_n() (in module PYME.Analysis.cramerRao) LUTBitmap (class in PYME.ui.layerFoldPanel) LUTOverlayLayer (class in PYME.LMVis.layers.LUTOverlayLayer)

M

M_COLLECTION (PYME.cluster.webdav.Member attribute) M_MEMBER (PYME.cluster.webdav.Member attribute) mad_0 (PYME.DSView.modules.blobMeasure.DataBlock property) mad_1 (PYME.DSView.modules.blobMeasure.DataBlock property) mad_2 (PYME.DSView.modules.blobMeasure.DataBlock property) Magenta() (in module PYME.misc.colormaps) main() (in module PYME.Acquire.acquire_server) (in module PYME.Acquire.PYMEAcquire) (in module PYME.Analysis.gen_sCMOS_maps) (in module PYME.cluster.cluster_of_one) (in module PYME.cluster.dataserver_wsgi) (in module PYME.cluster.HTTPDataServer) (in module PYME.cluster.PYMERuleNodeServer) (in module PYME.cluster.PYMERuleServer) (in module PYME.cluster.webdav) (in module PYME.DSView.dsviewer) (in module PYME.LMVis.VisGUI) (in module PYME.recipes.bakeshop) (in module PYME.recipes.batchProcess) (in module PYME.recipes.html_recipe_editor) (in module PYME.recipes.runRecipe) (in module PYME.util.authenticate) main_() (in module PYME.LMVis.VisGUI) main_loop() (PYME.Acquire.acquire_server.PYMEAcquireServer method) main_page() (PYME.Acquire.acquire_server.AcquireHTTPServer method) make() (PYME.LMVis.Extras.animation.VideoPanel method) make_composite() (in module PYME.Analysis.composite) make_editor() (PYME.contrib.listctrlMixins.TextEditMixin method) (PYME.ui.MetadataTree.TextEditMixin method) make_info() (in module PYME.misc.sqlite_ns) make_range_available() (PYME.cluster.ruleserver.IntegerIDRule method) makeColumnEditable() (PYME.contrib.listctrlMixins.TextEditMixin method) (PYME.ui.MetadataTree.TextEditMixin method) makedirs_safe() (in module PYME.cluster.HTTPDataServer) (in module PYME.cluster.webdav) makeFilter() (in module PYME.Analysis.points.fiducials) makeGraph() (in module PYME.misc.depGraph) makePathUnlessExists() (in module PYME.Analysis.gen_sCMOS_maps) managed() (in module PYME.ui.progress) manual_selection() (in module PYME.LMVis.Extras.fiducial) manualXYBounds (PYME.recipes.localisations.DensityMapping attribute) map_corrected_focus() (in module PYME.Analysis.piezo_movement_correction) map_filename() (in module PYME.Analysis.gen_sCMOS_maps) map_piezo_moving() (in module PYME.Analysis.piezo_movement_correction) map_splitter_coords() (in module PYME.localization.splitting) map_splitter_coords_() (in module PYME.localization.splitting) MapAstigZ (class in PYME.recipes.localisations) (class in PYME.recipes.multiview) Mapping (class in PYME.recipes.tablefilters) MappingFilter (class in PYME.IO.tabular) mappingFilter() (in module PYME.IO.tabular) mappings (PYME.recipes.tablefilters.Mapping attribute) mark_complete() (PYME.cluster.ruleserver.IntegerIDRule method) mark_release_complete() (PYME.cluster.ruleserver.IntegerIDRule method) (PYME.cluster.ruleserver.RuleServer method) mask (PYME.recipes.processing.StatisticsByFrame attribute) MaskEdges (class in PYME.recipes.filters) maskFractions() (in module PYME.Analysis.Colocalisation.correlationCoeffs) maskManders() (in module PYME.Analysis.Colocalisation.correlationCoeffs) match_points() (in module PYME.Analysis.fiducial_matching) MatfileColumnSource (class in PYME.IO.tabular) matfileColumnSource() (in module PYME.IO.tabular) MatfileMultiColumnSource (class in PYME.IO.tabular) MatfileSource (class in PYME.IO.tabular) matfileSource() (in module PYME.IO.tabular) MAX_ADVERTISEMENTS (PYME.cluster.ruleserver.RuleServer attribute) max_depth (PYME.recipes.pointcloud.Octree attribute) max_duration (PYME.recipes.acquisition.QueueAcquisitions attribute) max_iter (PYME.recipes.pointcloud.GaussianMixtureModel attribute) max_iterations (PYME.recipes.surface_fitting.SphericalHarmonicShell attribute) max_level_changed() (PYME.ui.histLimits.HistLimitDialog method) max_n_mode (PYME.recipes.surface_fitting.SphericalHarmonicShell attribute) max_size (PYME.recipes.surface_fitting.FilterMeshComponentsByVolume attribute) MaxFilter (class in PYME.recipes.filters) MAXIDX (PYME.IO.buffers.bgFrameBuffer attribute) (PYME.IO.DataSources.BGSDataSource.bgFrameBuffer attribute) maximumDistanceNM (PYME.recipes.processing.ColocalisationEDT attribute) maxParticleSize (PYME.recipes.tracking.TrackFeatures attribute) MAXSHORT (PYME.IO.buffers.bgFrameBuffer attribute) (PYME.IO.DataSources.BGSDataSource.bgFrameBuffer attribute) mc_points_from_mask() (in module PYME.Analysis.points.ripleys) mc_sampling_statistics() (in module PYME.Analysis.points.ripleys) MCProbability (PYME.recipes.localisations.DensityMapping attribute) mdh (PYME.Analysis.tile_pyramid.ImagePyramid property) (PYME.IO.DataSources.HDFDataSource.DataSource property) (PYME.IO.h5rFile.H5RFile property) (PYME.IO.tabular.CachingResultsFilter property) MDHandlerBase (class in PYME.IO.MetaDataHandler) MDParam (class in PYME.localization.MetaDataEdit) MDSource (class in PYME.IO.clusterExport) meanDuration (PYME.LMVis.Extras.pointSetGeneration.Generator attribute) meanEventNumber (PYME.LMVis.Extras.pointSetGeneration.Generator attribute) MeanFilter (class in PYME.recipes.filters) meanIntensity (PYME.LMVis.Extras.pointSetGeneration.Generator attribute) MeanNeighbourDistances (class in PYME.recipes.measurement) meanTime (PYME.LMVis.Extras.pointSetGeneration.Generator attribute) measure() (in module PYME.Analysis.points.objectMeasure) (in module PYME.LMVis.objectDarkMeasure) Measure2D (class in PYME.recipes.measurement) measure_3d() (in module PYME.Analysis.points.cluster_morphology) measure_offsets() (PYME.Acquire.stage_leveling.StageLeveler method) measureAligned() (in module PYME.Analysis.points.objectMeasure) MeasureClusters3D (class in PYME.recipes.localisations) measureContour (PYME.recipes.measurement.Measure2D attribute) MeasuredPupil (class in PYME.DSView.modules.psfGeneration) measurement_units (PYME.recipes.pyramid.SupertilePhysicalCoords attribute) Measurements (class in PYME.DSView.modules.blobMeasure) measureObjects() (in module PYME.Analysis.points.objectMeasure) (PYME.LMVis.pipeline.Pipeline method) measureObjectsByID() (in module PYME.Analysis.points.objectMeasure) (in module PYME.LMVis.objectDarkMeasure) MedianFilter (class in PYME.recipes.filters) Member (class in PYME.cluster.webdav) memmap() (in module PYME.misc.memmap) memory() (in module PYME.misc.memUsage) MemoryBackend (class in PYME.IO.acquisition_backends) MemoryEventLogger (class in PYME.IO.events) merge_clumps() (in module PYME.Analysis.points.multiview) MergeClumps (class in PYME.recipes.localisations) (class in PYME.recipes.multiview) mergeClumps() (in module PYME.Analysis.points.DeClump.pyDeClump) mergeEntriesFrom() (PYME.IO.MetaDataHandler.MDHandlerBase method) MeshViewFrame (class in PYME.DSView.modules.vis3D) metadata (PYME.contrib.gohlke.czifile.CziFile attribute) (PYME.IO.image.ImageStack property) metadataKeys (PYME.recipes.measurement.AddMetadataToMeasurements attribute) MetadataPanel (class in PYME.ui.MetadataTree) method (PYME.LMVis.layers.image_layer.ImageRenderLayer attribute) (PYME.LMVis.layers.mesh.TriangleRenderLayer attribute) (PYME.LMVis.layers.pointcloud.PointCloudRenderLayer attribute) (PYME.LMVis.layers.quiver.QuiverRenderLayer attribute) (PYME.LMVis.layers.tracks.TrackRenderLayer attribute) (PYME.recipes.processing.Deconvolve attribute) (PYME.recipes.processing.DeconvolveMotionCompensating attribute) (PYME.recipes.processing.Threshold attribute) mf() (in module PYME.Analysis.points.surfit) mf2() (in module PYME.Analysis.points.surfit) mfA() (in module PYME.Analysis.points.surfit) mfA1() (in module PYME.Analysis.points.surfit) microscope (class in PYME.Acquire.microscope) min_level_changed() (PYME.ui.histLimits.HistLimitDialog method) min_points (PYME.LMVis.layers.octree.OctreeRenderLayer attribute) min_size (PYME.recipes.surface_fitting.FilterMeshComponentsByVolume attribute) minActivePixels (PYME.recipes.processing.FindCaWaves attribute) minClumpSize (PYME.recipes.localisations.DBSCANClustering attribute) (PYME.recipes.tracking.FindClumps attribute) minDistance (PYME.recipes.processing.LocalMaxima attribute) MinFilter (class in PYME.recipes.filters) minimum_distance_to_poly() (in module PYME.DSView.modules.annotation) minimum_localizations (PYME.recipes.localisations.LabelsFromImage attribute) minimum_pixel_size (PYME.recipes.pointcloud.Octree attribute) minimumDistanceNM (PYME.recipes.processing.ColocalisationEDT attribute) minmax_u16() (in module PYME.DSView.LUT.lut) minRegionPixels (PYME.recipes.processing.Label attribute) minSize (PYME.LMVis.triBlobs.BlobSettings attribute) minTrackLength (PYME.recipes.tracking.TrackFeatures attribute) minWaveFrames (PYME.recipes.processing.FindCaWaves attribute) mirror (PYME.misc.zemax.DefaultGlass attribute) mirror_file() (in module PYME.IO.clusterIO) misfallA() (in module PYME.localization.autopsf.roifit) misfallB() (in module PYME.localization.autopsf.roifit) misfallB_MP() (in module PYME.localization.autopsf.roifit) misfitROI() (in module PYME.localization.autopsf.roifit) MissingInputError mkDefaultPath() (in module PYME.Analysis.gen_sCMOS_maps) mkDestPath() (in module PYME.Analysis.gen_sCMOS_maps) mock_decorator() (in module PYME.misc.mock_traits) mod1pk() (in module PYME.Analysis.BleachProfile.intensProf) mode (PYME.LMVis.Extras.pointSetGeneration.Generator attribute) (PYME.LMVis.renderers.CurrentRenderer attribute) (PYME.LMVis.renderers.DensityFitRenderer attribute) (PYME.LMVis.renderers.Gaussian3DRenderer attribute) (PYME.LMVis.renderers.GaussianRenderer attribute) (PYME.LMVis.renderers.Histogram3DRenderer attribute) (PYME.LMVis.renderers.HistogramRenderer attribute) (PYME.LMVis.renderers.LHoodRenderer attribute) (PYME.LMVis.renderers.QuadTreeRenderer attribute) (PYME.LMVis.renderers.Triangle3DRenderer attribute) (PYME.LMVis.renderers.TriangleRenderer attribute) (PYME.LMVis.renderers.TriangleRendererW attribute) (PYME.LMVis.renderers.VoronoiRenderer attribute) (PYME.recipes.measurement.IntensityAtPoints attribute) (PYME.recipes.pointcloud.GaussianMixtureModel attribute) model (PYME.recipes.machine_learning.CNNFilter attribute) module PYME PYME.Acquire PYME.Acquire.acquire_client PYME.Acquire.acquire_server PYME.Acquire.acquiremainframe PYME.Acquire.acquirewx PYME.Acquire.ActionManager PYME.Acquire.actions PYME.Acquire.autofocus PYME.Acquire.event_loop PYME.Acquire.eventLog PYME.Acquire.ExecTools PYME.Acquire.frameWrangler PYME.Acquire.htsms PYME.Acquire.htsms.rule_ui PYME.Acquire.htsms.tweeter PYME.Acquire.microscope PYME.Acquire.misc PYME.Acquire.misc.tempLogger PYME.Acquire.misc.tempLoggerDB PYME.Acquire.misc.tempMonitor PYME.Acquire.positionTracker PYME.Acquire.protocol PYME.Acquire.PYMEAcquire PYME.Acquire.sampleInformation PYME.Acquire.setup PYME.Acquire.SpoolController PYME.Acquire.stackSettings PYME.Acquire.stage_leveling PYME.Acquire.ui PYME.Acquire.ui.actionUI PYME.Acquire.ui.AnalysisSettingsUI PYME.Acquire.ui.focus_lock_gui PYME.Acquire.ui.HDFSpoolFrame PYME.Acquire.ui.intensity_trace PYME.Acquire.ui.intsliders PYME.Acquire.ui.lasersliders PYME.Acquire.ui.mpd_picosecond_delay_panel PYME.Acquire.ui.multiview_select PYME.Acquire.ui.positionUI PYME.Acquire.ui.preflight PYME.Acquire.ui.scanner_panel PYME.Acquire.ui.selectCameraPanel PYME.Acquire.ui.seqdialog PYME.Acquire.ui.splashScreen PYME.Acquire.ui.tile_panel PYME.Acquire.ui.voxelSizeDialog PYME.Acquire.Utils PYME.Acquire.Utils.failsafe PYME.Acquire.Utils.fastTiler PYME.Acquire.Utils.MultiPointScanner PYME.Acquire.Utils.pointScanner PYME.Acquire.Utils.sarcSpacing PYME.Acquire.Utils.strip_tiler PYME.Acquire.Utils.tiler PYME.Acquire.Utils.vibrationAnalysis PYME.Acquire.webui PYME.Acquire.webui.ipy PYME.Acquire.xyztc PYME.Acquire.zScanner PYME.Analysis PYME.Analysis.angleFilter PYME.Analysis.annealThresh PYME.Analysis.autoencoder_classifier PYME.Analysis.binAvg PYME.Analysis.BleachProfile PYME.Analysis.BleachProfile.deMod PYME.Analysis.BleachProfile.fitRecover PYME.Analysis.BleachProfile.intensProf PYME.Analysis.BleachProfile.kinModels PYME.Analysis.BleachProfile.rawIntensity PYME.Analysis.BleachProfile.rollins PYME.Analysis.Colocalisation PYME.Analysis.Colocalisation.colocScaleDep PYME.Analysis.Colocalisation.correlationCoeffs PYME.Analysis.Colocalisation.distColoc PYME.Analysis.Colocalisation.edtColoc PYME.Analysis.composite PYME.Analysis.cramerRao PYME.Analysis.density_filter PYME.Analysis.deTile PYME.Analysis.distributed_pyramid PYME.Analysis.fiducial_matching PYME.Analysis.gen_sCMOS_maps PYME.Analysis.graphing_filters PYME.Analysis.implicitFilter PYME.Analysis.keep_pairs PYME.Analysis.MetaData PYME.Analysis.optic_flow PYME.Analysis.piecewise PYME.Analysis.piecewiseMapping PYME.Analysis.piezo_movement_correction PYME.Analysis.points PYME.Analysis.points.arcfit PYME.Analysis.points.arcfit.arcmf PYME.Analysis.points.arcfit.setup PYME.Analysis.points.astigmatism PYME.Analysis.points.astigmatism.astiglookup PYME.Analysis.points.astigmatism.astigTools PYME.Analysis.points.astigmatism.setup PYME.Analysis.points.cluster_morphology PYME.Analysis.points.coordinate_tools PYME.Analysis.points.DeClump PYME.Analysis.points.DeClump.deClump PYME.Analysis.points.DeClump.deClumpGUI PYME.Analysis.points.DeClump.pyDeClump PYME.Analysis.points.DeClump.setup PYME.Analysis.points.DeClump.testClump PYME.Analysis.points.DistHist PYME.Analysis.points.DistHist.distHist PYME.Analysis.points.DistHist.distHistThreaded PYME.Analysis.points.DistHist.setup PYME.Analysis.points.EdgeDB PYME.Analysis.points.EdgeDB.edgeDB PYME.Analysis.points.EdgeDB.edges PYME.Analysis.points.EdgeDB.edgeTest PYME.Analysis.points.EdgeDB.segment PYME.Analysis.points.EdgeDB.setup PYME.Analysis.points.features PYME.Analysis.points.features.metal PYME.Analysis.points.fiducials PYME.Analysis.points.gen3DTriangs PYME.Analysis.points.moments PYME.Analysis.points.multiview PYME.Analysis.points.objectMeasure PYME.Analysis.points.qpaint PYME.Analysis.points.QuadTree PYME.Analysis.points.QuadTree.pointQT PYME.Analysis.points.QuadTree.pointQTF PYME.Analysis.points.QuadTree.QTrend PYME.Analysis.points.QuadTree.rendQT PYME.Analysis.points.rings PYME.Analysis.points.ripleys PYME.Analysis.points.segmentLL PYME.Analysis.points.setup PYME.Analysis.points.SoftRend PYME.Analysis.points.SoftRend.setup PYME.Analysis.points.SoftRend.testTetrahedra PYME.Analysis.points.SoftRend.triRend PYME.Analysis.points.spherical_harmonics PYME.Analysis.points.surfit PYME.Analysis.points.tCluster PYME.Analysis.points.traveling_salesperson PYME.Analysis.points.traveling_salesperson.queue_opt PYME.Analysis.points.traveling_salesperson.sectioned_two_opt PYME.Analysis.points.traveling_salesperson.setup PYME.Analysis.points.traveling_salesperson.sort PYME.Analysis.points.traveling_salesperson.two_opt PYME.Analysis.points.traveling_salesperson.two_opt_utils PYME.Analysis.points.twoColour PYME.Analysis.points.twoColourPlot PYME.Analysis.processLogger PYME.Analysis.profile_extraction PYME.Analysis.PSFEst PYME.Analysis.PSFEst.dec PYME.Analysis.PSFEst.extractImages PYME.Analysis.PSFEst.psfQuality PYME.Analysis.PSFGen PYME.Analysis.PSFGen.fourier PYME.Analysis.PSFGen.fourierHNA PYME.Analysis.PSFGen.fourierHNA2 PYME.Analysis.PSFGen.genCRBcurves PYME.Analysis.PSFGen.nijboer_zernike PYME.Analysis.PSFGen.ps_app PYME.Analysis.PSFGen.setup PYME.Analysis.PSFGen.test_ps_app PYME.Analysis.setup PYME.Analysis.splitting PYME.Analysis.svmSegment PYME.Analysis.thresholding PYME.Analysis.tile_pyramid PYME.Analysis.Tracking PYME.Analysis.Tracking.msd PYME.Analysis.Tracking.tracking PYME.Analysis.Tracking.trackUtils PYME.Analysis.widefieldify PYME.cluster PYME.cluster.cluster_of_one PYME.cluster.dataserver_wsgi PYME.cluster.distribution PYME.cluster.HTTPDataServer PYME.cluster.HTTPRulePusher PYME.cluster.HTTPTaskPusher PYME.cluster.PYMERuleNodeServer PYME.cluster.PYMERuleServer PYME.cluster.rulenodeserver PYME.cluster.rules PYME.cluster.ruleserver PYME.cluster.status PYME.cluster.taskWorkerHTTP PYME.cluster.webdav PYME.config PYME.contrib PYME.contrib.aniso PYME.contrib.aniso.aniso PYME.contrib.auiFloatBook PYME.contrib.congrid PYME.contrib.dispatch PYME.contrib.dispatch.dispatcher PYME.contrib.gohlke PYME.contrib.gohlke.czifile PYME.contrib.gohlke.fcsfiles PYME.contrib.gohlke.setup PYME.contrib.gohlke.tifffile PYME.contrib.listctrlMixins PYME.contrib.lzw PYME.contrib.pad PYME.contrib.pad.info_pad PYME.contrib.pad.pad PYME.contrib.setup PYME.contrib.TextCtrlAutoComplete PYME.contrib.wxPlotPanel PYME.Deconv PYME.Deconv.beadGen PYME.Deconv.dec PYME.Deconv.dec_test PYME.Deconv.deconvDialogs PYME.Deconv.decTask PYME.Deconv.decThread PYME.Deconv.fftwWisdom PYME.Deconv.richardsonLucy PYME.Deconv.richardsonLucyMV PYME.Deconv.richardsonLucyMVM PYME.Deconv.test_block_dec PYME.Deconv.wiener PYME.DSView PYME.DSView.arrayViewPanel PYME.DSView.displayOptions PYME.DSView.DisplayOptionsPanel PYME.DSView.displaySettingsPanel PYME.DSView.dsviewer PYME.DSView.eventLogViewer PYME.DSView.fitInfo PYME.DSView.htmlServe PYME.DSView.logparser PYME.DSView.LUT PYME.DSView.LUT.lut PYME.DSView.LUT.setup PYME.DSView.modules PYME.DSView.modules.annotation PYME.DSView.modules.arrayView PYME.DSView.modules.blobFinding PYME.DSView.modules.blobMeasure PYME.DSView.modules.camera_maps PYME.DSView.modules.coloc PYME.DSView.modules.composite PYME.DSView.modules.convnet PYME.DSView.modules.cropping PYME.DSView.modules.dark_and_flatfield PYME.DSView.modules.deconvolution PYME.DSView.modules.eventView PYME.DSView.modules.extractBlobs PYME.DSView.modules.fastGraphPanel PYME.DSView.modules.filtering PYME.DSView.modules.flowView PYME.DSView.modules.fourierRingCorrelation PYME.DSView.modules.gl_image_view PYME.DSView.modules.LMAnalysis PYME.DSView.modules.LMDisplay PYME.DSView.modules.measure PYME.DSView.modules.measure.filterPan PYME.DSView.modules.metadataView PYME.DSView.modules.multithreshold PYME.DSView.modules.neuroglancer PYME.DSView.modules.object_tagging PYME.DSView.modules.particleTracking PYME.DSView.modules.playback PYME.DSView.modules.prebleachExtraction PYME.DSView.modules.profileFitting PYME.DSView.modules.profilePlotting PYME.DSView.modules.projections PYME.DSView.modules.psfExtraction PYME.DSView.modules.psfGeneration PYME.DSView.modules.pupilTools PYME.DSView.modules.recipes PYME.DSView.modules.redimension PYME.DSView.modules.segmentation PYME.DSView.modules.sheetView PYME.DSView.modules.shell PYME.DSView.modules.shiftfield_estimation PYME.DSView.modules.sparkprepare PYME.DSView.modules.splitter PYME.DSView.modules.synchronise PYME.DSView.modules.tiling PYME.DSView.modules.unmixing PYME.DSView.modules.vis3D PYME.DSView.modules.visgui PYME.DSView.modules.webview PYME.DSView.OpenSequenceDialog PYME.DSView.overlays PYME.DSView.OverlaysPanel PYME.DSView.scrolledImagePanel PYME.DSView.setup PYME.DSView.splashScreen PYME.DSView.voxSizeDialog PYME.IO PYME.IO.acquisition_backends PYME.IO.buffer_helpers PYME.IO.buffers PYME.IO.cluster_directory PYME.IO.cluster_streaming PYME.IO.clusterDuplication PYME.IO.clusterExport PYME.IO.clusterGlob PYME.IO.clusterIO PYME.IO.clusterListing PYME.IO.clusterResults PYME.IO.clusterUpload PYME.IO.compatibility PYME.IO.countdir PYME.IO.countdir.countdir PYME.IO.countdir.setup PYME.IO.csv_flavours PYME.IO.dataExporter PYME.IO.DataSources PYME.IO.DataSources.AlignDataSource PYME.IO.DataSources.ArrayDataSource PYME.IO.DataSources.BaseDataSource PYME.IO.DataSources.BGSDataSource PYME.IO.DataSources.BioformatsDataSource PYME.IO.DataSources.BufferedDataSource PYME.IO.DataSources.ClusterPZFDataSource PYME.IO.DataSources.ConcatenatedDataSource PYME.IO.DataSources.CropDataSource PYME.IO.DataSources.DcimgDataSource PYME.IO.DataSources.ElectronsPerSecondDataSource PYME.IO.DataSources.FlatFieldDataSource PYME.IO.DataSources.HDFDataSource PYME.IO.DataSources.HTTPDataSource PYME.IO.DataSources.ImageSeriesDataSource PYME.IO.DataSources.MultiviewDataSource PYME.IO.DataSources.OBFDataSource PYME.IO.DataSources.RandomDataSource PYME.IO.DataSources.SupertileDatasource PYME.IO.DataSources.TiffDataSource PYME.IO.DataSources.TQDataSource PYME.IO.DataSources.UnsplitDataSource PYME.IO.dataWrap PYME.IO.dcimg PYME.IO.events PYME.IO.FileUtils PYME.IO.FileUtils.compHdf PYME.IO.FileUtils.fileID PYME.IO.FileUtils.fnlGen PYME.IO.FileUtils.freeSpace PYME.IO.FileUtils.h5ExFrames PYME.IO.FileUtils.h5rFormatDef PYME.IO.FileUtils.h5rToTxt PYME.IO.FileUtils.h5ToTiffSeries PYME.IO.FileUtils.IJLut PYME.IO.FileUtils.nameUtils PYME.IO.FileUtils.obf_support PYME.IO.FileUtils.ply PYME.IO.FileUtils.RawToHdf5 PYME.IO.FileUtils.readSpeckle PYME.IO.FileUtils.readTiff PYME.IO.FileUtils.saveTiffStack PYME.IO.FileUtils.setup PYME.IO.FileUtils.SPAD PYME.IO.FileUtils.stl PYME.IO.FileUtils.thumbnailDatabase PYME.IO.FileUtils.TiffSeqToHdf5 PYME.IO.h5File PYME.IO.h5rFile PYME.IO.HDFSpooler PYME.IO.HTTPSpooler PYME.IO.HTTPSpooler_v2 PYME.IO.image PYME.IO.load_psf PYME.IO.MetaDataHandler PYME.IO.pyme_h5ls PYME.IO.PZFFormat PYME.IO.QueueSpooler PYME.IO.ragged PYME.IO.rgb_image PYME.IO.setup PYME.IO.Spooler PYME.IO.tabular PYME.IO.testClusterSpooling PYME.IO.unifiedIO PYME.LMVis PYME.LMVis.colourFilterGUI PYME.LMVis.colourPanel PYME.LMVis.displayPane PYME.LMVis.dyeRatios PYME.LMVis.Extras PYME.LMVis.Extras.animation PYME.LMVis.Extras.annotation PYME.LMVis.Extras.clusterAnalysis PYME.LMVis.Extras.dockedPanel PYME.LMVis.Extras.extra_layers PYME.LMVis.Extras.fiducial PYME.LMVis.Extras.flagZMotionArtifacts PYME.LMVis.Extras.fusionUtils PYME.LMVis.Extras.multiColourAnalysis PYME.LMVis.Extras.multiviewMapping PYME.LMVis.Extras.objectMeasurements PYME.LMVis.Extras.particleTracking PYME.LMVis.Extras.perFrameVariable PYME.LMVis.Extras.photophysics PYME.LMVis.Extras.pointSetGeneration PYME.LMVis.Extras.pointwiseColoc PYME.LMVis.Extras.QPobjectSegment PYME.LMVis.Extras.saved_views PYME.LMVis.Extras.scaleBox PYME.LMVis.Extras.sequentialSpecies PYME.LMVis.Extras.setBGImage PYME.LMVis.Extras.shiftmapGenerator PYME.LMVis.Extras.showShortcuts PYME.LMVis.Extras.snapshot PYME.LMVis.Extras.spherical_harmonics PYME.LMVis.Extras.subsets PYME.LMVis.Extras.surface_fitting PYME.LMVis.Extras.temperaturePlot PYME.LMVis.Extras.vibration PYME.LMVis.genImageDialog PYME.LMVis.gl_offScreenHandler PYME.LMVis.gl_render3D_shaders PYME.LMVis.imageView PYME.LMVis.imageView2 PYME.LMVis.importTextDialog PYME.LMVis.layer_panel PYME.LMVis.layers PYME.LMVis.layers.AxesOverlayLayer PYME.LMVis.layers.base PYME.LMVis.layers.image_layer PYME.LMVis.layers.layer_defaults PYME.LMVis.layers.LUTOverlayLayer PYME.LMVis.layers.mesh PYME.LMVis.layers.octree PYME.LMVis.layers.OverlayLayer PYME.LMVis.layers.pointcloud PYME.LMVis.layers.quiver PYME.LMVis.layers.ScaleBarOverlayLayer PYME.LMVis.layers.ScaleBoxOverlayLayer PYME.LMVis.layers.SelectionOverlayLayer PYME.LMVis.layers.text PYME.LMVis.layers.tracks PYME.LMVis.objectDarkMeasure PYME.LMVis.pipeline PYME.LMVis.pipelineView PYME.LMVis.pointSettingsPanel PYME.LMVis.progGraph PYME.LMVis.quadTreeSettings PYME.LMVis.renderers PYME.LMVis.rendGauss PYME.LMVis.setup PYME.LMVis.setup_exe PYME.LMVis.shader_programs PYME.LMVis.shader_programs.DefaultShaderProgram PYME.LMVis.shader_programs.GLProgram PYME.LMVis.shader_programs.GouraudShaderProgram PYME.LMVis.shader_programs.oit_compositor PYME.LMVis.shader_programs.PointSpriteShaderProgram PYME.LMVis.shader_programs.shader_loader PYME.LMVis.shader_programs.shader_program PYME.LMVis.shader_programs.ShaderProgramFactory PYME.LMVis.shader_programs.TesselShaderProgram PYME.LMVis.shader_programs.WireFrameShaderProgram PYME.LMVis.statusLog PYME.LMVis.tests PYME.LMVis.triBlobs PYME.LMVis.view_clipping_pane PYME.LMVis.views PYME.LMVis.visCore PYME.LMVis.VisGUI PYME.LMVis.visHelpers PYME.LMVis.visHelpersMin PYME.localization PYME.localization.autopsf PYME.localization.autopsf.autopsf PYME.localization.autopsf.roifit PYME.localization.cInterp PYME.localization.cInterp.cInterp PYME.localization.cInterp.setup PYME.localization.cModels PYME.localization.cModels.gauss_app PYME.localization.cModels.setup PYME.localization.FitFactories PYME.localization.FitFactories.AstigGaussFitFR PYME.localization.FitFactories.AstigGaussGPUFitFR PYME.localization.FitFactories.BeadConvolvedAstigGaussFit PYME.localization.FitFactories.ChecksumFR PYME.localization.FitFactories.ChecksumGPUFR PYME.localization.FitFactories.ChecksumMultifitSR PYME.localization.FitFactories.ConfocCOIR PYME.localization.FitFactories.Dumbell3DFitR PYME.localization.FitFactories.DumbellFitR PYME.localization.FitFactories.FFBase PYME.localization.FitFactories.fitCommon PYME.localization.FitFactories.Gauss3DFitR PYME.localization.FitFactories.GaussFitConstrR PYME.localization.FitFactories.GaussMultifitLinesR PYME.localization.FitFactories.GaussMultifitR PYME.localization.FitFactories.GaussMultifitSR PYME.localization.FitFactories.InterpFitR PYME.localization.FitFactories.InterpFitWFR PYME.localization.FitFactories.Interpolators PYME.localization.FitFactories.Interpolators.baseInterpolator PYME.localization.FitFactories.Interpolators.CSInterpolator PYME.localization.FitFactories.Interpolators.CubeSInterpolatorP PYME.localization.FitFactories.Interpolators.CubicSplineInterpolator PYME.localization.FitFactories.Interpolators.LinearInterpolator PYME.localization.FitFactories.Interpolators.LinearPInterpolatorP PYME.localization.FitFactories.LatFitCOIR PYME.localization.FitFactories.LatGaussFitFR PYME.localization.FitFactories.LatObjFindFR PYME.localization.FitFactories.LatPSFFitR PYME.localization.FitFactories.MultiviewFitInterpNR PYME.localization.FitFactories.PRInterpFitQR PYME.localization.FitFactories.PRInterpFitR PYME.localization.FitFactories.ROIExtractNR PYME.localization.FitFactories.SpecGaussFitFR PYME.localization.FitFactories.SplitterFitCOIR PYME.localization.FitFactories.SplitterFitFNR PYME.localization.FitFactories.SplitterFitFusionR PYME.localization.FitFactories.SplitterFitInterpBNR PYME.localization.FitFactories.SplitterFitInterpNR PYME.localization.FitFactories.SplitterFitScavNR PYME.localization.FitFactories.SplitterMultifitSR PYME.localization.FitFactories.SplitterObjFindR PYME.localization.FitFactories.SplitterROIExtractNR PYME.localization.FitFactories.SplitterShiftEstFR PYME.localization.FitFactories.zEstimators PYME.localization.FitFactories.zEstimators.astigEstimator PYME.localization.FitFactories.zEstimators.biplaneEstimator PYME.localization.FitFactories.zEstimators.genericDualEstimator PYME.localization.FitFactories.zEstimators.genericEstimator PYME.localization.FitFactories.zEstimators.priEstimator PYME.localization.lev_gfit PYME.localization.lev_gfit.setup PYME.localization.MetaDataEdit PYME.localization.ofind PYME.localization.ofind3d PYME.localization.ofind_nofilt PYME.localization.ofind_pri PYME.localization.ofind_split PYME.localization.ofind_xcorr PYME.localization.ofind_xcorr_fw PYME.localization.remFitBuf PYME.localization.setup PYME.localization.splitting PYME.localization.Test PYME.localization.Test.fitTestJig PYME.localization.Test.fitTestJigSCMOS PYME.localization.Test.fitTestJigWC PYME.localization.twist PYME.misc PYME.misc.aligned_array PYME.misc.aniso PYME.misc.big_sur_fix PYME.misc.check_for_updates PYME.misc.colormaps PYME.misc.colorsys PYME.misc.computerName PYME.misc.coverslipGeometries PYME.misc.cython_numpy_monkey PYME.misc.depGraph PYME.misc.dirSize PYME.misc.diskCleanup PYME.misc.django_widgets PYME.misc.djangoRecarray PYME.misc.editgrid PYME.misc.eventSpy PYME.misc.exceptions PYME.misc.facsPlot PYME.misc.fbpIcons PYME.misc.fftw_compat PYME.misc.findCycles PYME.misc.fortran_interrupt_defeat PYME.misc.glassModel PYME.misc.hash32 PYME.misc.hillcurve PYME.misc.hybrid_ns PYME.misc.kdFit PYME.misc.locate PYME.misc.memmap PYME.misc.memUsage PYME.misc.mock_ctypes PYME.misc.mock_traits PYME.misc.mock_traitsui PYME.misc.pyme_zeroconf PYME.misc.pyro_tracebacks PYME.misc.read_agf PYME.misc.sffake PYME.misc.snells PYME.misc.sqlite_ns PYME.misc.sqlitendarray PYME.misc.taskDef PYME.misc.tempDB PYME.misc.TiffImagePlugin PYME.misc.TiSettings PYME.misc.VolProj PYME.misc.wxThread PYME.misc.zemax PYME.misc.zernike PYME.recipes PYME.recipes.acquisition PYME.recipes.bakeshop PYME.recipes.base PYME.recipes.batchProcess PYME.recipes.filters PYME.recipes.fudges PYME.recipes.graphing PYME.recipes.html_recipe_editor PYME.recipes.localisations PYME.recipes.machine_learning PYME.recipes.measurement PYME.recipes.modules PYME.recipes.multiview PYME.recipes.output PYME.recipes.pointcloud PYME.recipes.processing PYME.recipes.pyramid PYME.recipes.recipe PYME.recipes.recipeGui PYME.recipes.recipeLayout PYME.recipes.runRecipe PYME.recipes.setup PYME.recipes.simulation PYME.recipes.skfilters PYME.recipes.surface_fitting PYME.recipes.tablefilters PYME.recipes.tracking PYME.recipes.traits PYME.recipes.vertical_recipe_display PYME.reports PYME.reports.filters PYME.resources PYME.resources.setup PYME.setup PYME.setup_exe PYME.simulation PYME.simulation.locify PYME.simulation.pointsets PYME.simulation.wormlike PYME.simulation.wormlike2 PYME.simulation.wormlike3 PYME.simulation.wormlike_curled PYME.tileviewer PYME.tileviewer.tileviewer PYME.ui PYME.ui.about_dlg PYME.ui.AUIFrame PYME.ui.autoFoldPanel PYME.ui.crop_dialog PYME.ui.custom_traits_editors PYME.ui.editFilterDialog PYME.ui.editList PYME.ui.fastGraph PYME.ui.filterPane PYME.ui.histLimits PYME.ui.layerFoldPanel PYME.ui.manualFoldPanel PYME.ui.MetadataTree PYME.ui.mytimer PYME.ui.progress PYME.ui.recArrayView PYME.ui.selection PYME.ui.wx_compat PYME.update_version PYME.util PYME.util.authenticate PYME.util.execfile PYME.util.fProfile PYME.util.fProfile.convertProfile PYME.util.fProfile.fProfile PYME.util.fProfile.viewProfile PYME.util.install_dependencies PYME.util.log_verbosity PYME.util.mProfile PYME.util.mProfile.colorize_db_t PYME.util.mProfile.mProfile PYME.util.mProfile.p PYME.util.mProfile.tProfile PYME.util.pymelauncher PYME.util.shmarray PYME.util.shmarray.shmarray PYME.util.shmarray.shmTest PYME.util.webframework PYME.version PYME.warnings

module_outputs (PYME.recipes.recipe.Recipe property) ModuleBase (class in PYME.recipes.base) ModuleCollection() (in module PYME.recipes.base) moduleName (PYME.IO.DataSources.AlignDataSource.DataSource attribute) (PYME.IO.DataSources.BGSDataSource.XTZCBackgroundSource attribute) (PYME.IO.DataSources.BGSDataSource.XYZTCBgsSource attribute) (PYME.IO.DataSources.BioformatsDataSource.DataSource attribute) (PYME.IO.DataSources.BufferedDataSource.DataSource attribute) (PYME.IO.DataSources.ClusterPZFDataSource.DataSource attribute) (PYME.IO.DataSources.CropDataSource.DataSource attribute) (PYME.IO.DataSources.DcimgDataSource.DataSource attribute) (PYME.IO.DataSources.ElectronsPerSecondDataSource.DataSource attribute) (PYME.IO.DataSources.FlatFieldDataSource.DataSource attribute) (PYME.IO.DataSources.HDFDataSource.DataSource attribute) (PYME.IO.DataSources.HTTPDataSource.DataSource attribute) (PYME.IO.DataSources.ImageSeriesDataSource.DataSource attribute) (PYME.IO.DataSources.MultiviewDataSource.DataSource attribute) (PYME.IO.DataSources.OBFDataSource.DataSource attribute) (PYME.IO.DataSources.RandomDataSource.DataSource attribute) (PYME.IO.DataSources.SupertileDatasource.SupertileDataSource attribute) (PYME.IO.DataSources.TiffDataSource.DataSource attribute) (PYME.IO.DataSources.TQDataSource.DataSource attribute) (PYME.IO.DataSources.UnsplitDataSource.DataSource attribute) modules (PYME.recipes.recipe.Recipe attribute) ModuleSelectionDialog (class in PYME.recipes.recipeGui) MotionCompensatingRichardsonLucy (class in PYME.Deconv.richardsonLucyMVM) motionFlagger (class in PYME.LMVis.Extras.flagZMotionArtifacts) mount() (in module PYME.DSView.htmlServe) MouseEvent() (in module PYME.misc.eventSpy) movieplot (PYME.Analysis.Tracking.trackUtils.Track property) movieplot() (in module PYME.Analysis.graphing_filters) movieplot2() (in module PYME.Analysis.graphing_filters) msd() (in module PYME.Analysis.Tracking.msd) msdHistogram() (in module PYME.Analysis.points.DistHist.distHist) msdinfo (PYME.Analysis.Tracking.trackUtils.Track property) msdplot (PYME.Analysis.Tracking.trackUtils.Track property) muiltithreshold (PYME.recipes.measurement.DetectPoints2D attribute) multichannel (PYME.LMVis.importTextDialog.ImportMatlabDialog attribute) MultiColAnalyzer (class in PYME.LMVis.Extras.multiColourAnalysis) multicolcheck() (in module PYME.LMVis.Extras.multiColourAnalysis) MultifitBlobs (class in PYME.recipes.measurement) Multiply (class in PYME.recipes.base) multiprocessing (PYME.recipes.localisations.DBSCANClustering attribute) MultiTargetTimer() (PYME.Acquire.event_loop.EventLoop method) multithreaded (PYME.recipes.localisations.DBSCANClustering attribute) MultiThreshold (class in PYME.DSView.modules.multithreshold) MultiviewMapper (class in PYME.LMVis.Extras.multiviewMapping) MultiviewRichardsonLucy (class in PYME.Deconv.richardsonLucyMV) MultiviewSelect (class in PYME.Acquire.ui.multiview_select) MultiwellCircularTiler (class in PYME.Acquire.Utils.tiler) MultiwellProtocolQueuePanel (class in PYME.Acquire.ui.tile_panel) MultiwellTilePanel (class in PYME.Acquire.ui.tile_panel) munge_res() (in module PYME.Analysis.BleachProfile.kinModels) mutual_information() (in module PYME.Analysis.Colocalisation.correlationCoeffs) mydict (class in PYME.util.mProfile.mProfile) (class in PYME.util.mProfile.p) mydictn (class in PYME.util.mProfile.mProfile) (class in PYME.util.mProfile.p) myListCtrl (class in PYME.DSView.modules.annotation) myTask (class in PYME.misc.taskDef) MyTreeListCtrl (class in PYME.ui.MetadataTree) MyWeakSet (class in PYME.DSView.displayOptions)

N

n (PYME.DSView.modules.psfGeneration.PupilGenerator attribute) (PYME.recipes.pointcloud.GaussianMixtureModel attribute) (PYME.recipes.simulation.TheoreticalPSF attribute) n() (PYME.misc.zemax.DefaultGlass method) (PYME.misc.zemax.Glass method) n_cluster_servers() (in module PYME.IO.cluster_streaming) n_frames (PYME.IO.h5File.H5File property) n_histogram_bins (PYME.recipes.processing.Threshold attribute) n_nearest_neighbours (PYME.recipes.pointcloud.LocalPointDensity attribute) n_points_min (PYME.recipes.surface_fitting.DualMarchingCubes attribute) n_processes (PYME.recipes.measurement.ChunkedTravelingSalesperson attribute) NA (PYME.DSView.modules.psfGeneration.PupilGenerator attribute) (PYME.DSView.modules.pupilTools.PupilTools attribute) (PYME.recipes.simulation.TheoreticalPSF attribute) name (PYME.DSView.modules.psfGeneration.ZernikeMode attribute) (PYME.LMVis.renderers.CurrentRenderer attribute) (PYME.LMVis.renderers.DensityFitRenderer attribute) (PYME.LMVis.renderers.Gaussian3DRenderer attribute) (PYME.LMVis.renderers.GaussianRenderer attribute) (PYME.LMVis.renderers.Histogram3DRenderer attribute) (PYME.LMVis.renderers.HistogramRenderer attribute) (PYME.LMVis.renderers.LHoodRenderer attribute) (PYME.LMVis.renderers.QuadTreeRenderer attribute) (PYME.LMVis.renderers.Triangle3DRenderer attribute) (PYME.LMVis.renderers.TriangleRenderer attribute) (PYME.LMVis.renderers.TriangleRendererW attribute) (PYME.LMVis.renderers.VoronoiRenderer attribute) (PYME.misc.sqlite_ns.NSInfo property) (PYME.recipes.html_recipe_editor.Person attribute) name_distance_to_shell (PYME.recipes.surface_fitting.SphericalHarmonicShell attribute) name_inside_shell (PYME.recipes.surface_fitting.SphericalHarmonicShell attribute) name_normalized_radius (PYME.recipes.surface_fitting.AddSphericalHarmonicShellMappedCoords attribute) name_scaled_azimuth (PYME.recipes.surface_fitting.AddSphericalHarmonicShellMappedCoords attribute) name_scaled_radius (PYME.recipes.surface_fitting.AddSphericalHarmonicShellMappedCoords attribute) name_scaled_zenith (PYME.recipes.surface_fitting.AddSphericalHarmonicShellMappedCoords attribute) names (PYME.IO.image.ImageStack property) nbins (PYME.recipes.measurement.BinnedHistogram attribute) (PYME.recipes.measurement.Histogram attribute) (PYME.recipes.measurement.ImageHistogram attribute) (PYME.recipes.measurement.PairwiseDistanceHistogram attribute) (PYME.recipes.pointcloud.Ripleys attribute) nbmf() (in module PYME.Analysis.BleachProfile.rollins) nbrff() (in module PYME.Analysis.BleachProfile.rollins) nbytes (PYME.IO.DataSources.BaseDataSource.BaseDataSource property) ndim (PYME.IO.DataSources.ArrayDataSource.ArrayDataSource property) (PYME.IO.DataSources.ArrayDataSource.XYZTCArrayDataSource property) (PYME.IO.DataSources.BaseDataSource.BaseDataSource property) (PYME.IO.DataSources.BaseDataSource.XYTCDataSource property) (PYME.IO.DataSources.BaseDataSource.XYZTCDataSource property) (PYME.IO.dataWrap.ListWrapper property) NearestNeighbourDistances (class in PYME.recipes.measurement) neg_binom_histfitting() (in module PYME.Analysis.BleachProfile.rollins) NestedClassMDHandler (class in PYME.IO.MetaDataHandler) Neuroglancer (class in PYME.DSView.modules.neuroglancer) new_ds_name() (PYME.LMVis.pipeline.Pipeline method)

new_layer_settings() (in module PYME.LMVis.layers.layer_defaults) new_mesh_viewer() (in module PYME.DSView.modules.vis3D) new_output_name() (PYME.recipes.recipe.Recipe method) new_terminal() (PYME.Acquire.webui.ipy.IPYTermManager method) next() (PYME.cluster.rulenodeserver.Rater method) next_page() (PYME.contrib.lzw.PagingDecoder method) ng_viewer (PYME.DSView.modules.neuroglancer.Neuroglancer property) nice (PYME.recipes.acquisition.QueueAcquisitions attribute) niceVariables (PYME.LMVis.importTextDialog.ColumnMappingDialog attribute) NodeServer (class in PYME.cluster.rulenodeserver) noise() (in module PYME.Analysis.PSFEst.psfQuality) NoNewTasks NoninteractiveContext (class in PYME.warnings) normal_mode (PYME.LMVis.layers.mesh.TriangleRenderLayer attribute) normal_scaling (PYME.LMVis.layers.mesh.TriangleRenderLayer attribute) (PYME.LMVis.layers.pointcloud.PointCloudRenderLayer attribute) normalise (PYME.recipes.machine_learning.PointFeatureBase attribute) normaliseRelativeDensity (PYME.recipes.machine_learning.PointFeaturesPairwiseDist attribute) (PYME.recipes.machine_learning.PointFeaturesVectorial attribute) normalization (PYME.recipes.pointcloud.Ripleys attribute) Normalize (class in PYME.recipes.base) normalize (PYME.recipes.measurement.Histogram attribute) (PYME.recipes.measurement.ImageHistogram attribute) normalize() (PYME.LMVis.views.View static method) normalize_view() (PYME.LMVis.views.View method) normalizeFeatures() (in module PYME.Analysis.svmSegment) NormalizeMean (class in PYME.recipes.base) NOT_PRESENT (PYME.Acquire.ExecTools.BGInitTask attribute) notebook (PYME.LMVis.VisGUI.VisGUIFrame property) Notify() (PYME.Acquire.frameWrangler.FrameWrangler method) notify() (PYME.ui.filterPane.FilterPanel method) notimes() (in module PYME.LMVis.objectDarkMeasure) np_load_legacy() (in module PYME.IO.compatibility) nPix (PYME.recipes.filters.DespeckleFilter attribute) NRFilter() (in module PYME.localization.cModels.gauss_app) ns (PYME.recipes.simulation.TheoreticalPSF attribute) nsim (PYME.recipes.pointcloud.Ripleys attribute) NSInfo (class in PYME.misc.sqlite_ns) NthPointIsosurface (class in PYME.recipes.surface_fitting) nTrueDims (PYME.IO.DataSources.BaseDataSource.XYTCDataSource property) nudge() (PYME.Acquire.ui.positionUI.PositionPanel method) num (PYME.DSView.modules.psfGeneration.ZernikeMode attribute) num_tasks_to_request (PYME.cluster.rulenodeserver.NodeServer property) num_to_select (PYME.recipes.tablefilters.RandomSubset attribute) numAngleBins (PYME.recipes.machine_learning.PointFeaturesVectorial attribute) numberOfJobs (PYME.recipes.localisations.DBSCANClustering attribute) numBins (PYME.recipes.machine_learning.PointFeaturesPairwiseDist attribute) numerator (PYME.IO.FileUtils.obf_support.Fraction property) numFluors (PYME.simulation.pointsets.WiglyFibreSource attribute) numFollowFrames (PYME.recipes.tracking.FitFusionTraces attribute) numLeadFrames (PYME.recipes.tracking.FitFusionTraces attribute) NumpyExporter (class in PYME.IO.dataExporter) NumpyTileIO (class in PYME.Analysis.tile_pyramid) numRadialBins (PYME.recipes.machine_learning.PointFeaturesVectorial attribute) numSamples (PYME.recipes.localisations.DensityMapping attribute) numToAlpha() (in module PYME.IO.FileUtils.nameUtils)

O

ob16() (in module PYME.misc.TiffImagePlugin) ob32() (in module PYME.misc.TiffImagePlugin) OBJECT (PYME.Acquire.stackSettings.StackSettings attribute) ObjectIdentifier (class in PYME.localization.ofind) (class in PYME.localization.ofind3d) (class in PYME.localization.ofind_nofilt) (class in PYME.localization.ofind_pri) (class in PYME.localization.ofind_split) (class in PYME.localization.ofind_xcorr) (class in PYME.localization.ofind_xcorr_fw) objectIndices() (in module PYME.Analysis.points.EdgeDB.edges) ObjectMeasurer (class in PYME.LMVis.Extras.objectMeasurements) ObjectTagger (class in PYME.DSView.modules.object_tagging) observe() (in module PYME.misc.mock_traits) Octree (class in PYME.recipes.pointcloud) OctreeRenderLayer (class in PYME.LMVis.layers.octree) of() (in module PYME.Analysis.optic_flow) offline_plotting (class in PYME.Analysis.graphing_filters) OffScreenHandler (class in PYME.LMVis.gl_offScreenHandler) Offset (class in PYME.recipes.processing) offset (PYME.recipes.base.NormalizeMean attribute) (PYME.recipes.processing.Deconvolve attribute) (PYME.recipes.surface_fitting.NthPointIsosurface attribute) offset_constant (PYME.recipes.processing.Offset attribute) offset_selection (PYME.recipes.processing.Offset attribute) OfindPoint (class in PYME.localization.ofind) (class in PYME.localization.ofind3d) (class in PYME.localization.ofind_nofilt) (class in PYME.localization.ofind_pri) (class in PYME.localization.ofind_split) (class in PYME.localization.ofind_xcorr) (class in PYME.localization.ofind_xcorr_fw) OITCompositorProgram (class in PYME.LMVis.shader_programs.oit_compositor) OITGouraudShaderProgram (class in PYME.LMVis.shader_programs.GouraudShaderProgram) OITShadedFaceEngine (class in PYME.LMVis.layers.mesh) ol16() (in module PYME.misc.TiffImagePlugin) ol32() (in module PYME.misc.TiffImagePlugin) oldData (PYME.IO.DataSources.BaseDataSource.XYTCDataSource attribute) oldSlice (PYME.IO.DataSources.BaseDataSource.XYTCDataSource attribute) OMDialog (class in PYME.LMVis.Extras.objectMeasurements) OMETiffExporter (class in PYME.IO.dataExporter) OMEXMLMDHandler (class in PYME.IO.MetaDataHandler) On3DIsosurf() (PYME.DSView.modules.vis3D.Visualiser method) On3DVolume() (PYME.DSView.modules.vis3D.Visualiser method) on_adjust_snake() (PYME.DSView.modules.annotation.LabelPanel method) on_cb_highspeed() (PYME.Acquire.ui.mpd_picosecond_delay_panel.DelayPanel method) on_change_lock_mode() (PYME.DSView.modules.annotation.LabelPanel method) on_copy() (PYME.ui.progress.TracebackDialog method) on_data_complete() (PYME.cluster.rules.LocalisationRule method) (PYME.cluster.rules.Rule method) (PYME.cluster.rules.SpoolLocalLocalizationRule method) on_edit() (PYME.LMVis.Extras.animation.VideoPanel method) on_eof() (PYME.Acquire.webui.ipy.IPYTermManager method) on_frame() (PYME.Acquire.xyztc.XYZTCAcquisition method) on_idle() (PYME.LMVis.layer_panel.LayerPane method) on_map() (in module PYME.DSView.modules.camera_maps) on_metadata_change() (PYME.DSView.modules.LMAnalysis.AnalysisSettingsView method) on_moveto() (PYME.Acquire.ui.positionUI.PositionPanel method) on_select_view() (PYME.LMVis.Extras.animation.VideoPanel method) on_SIGHUP() (in module PYME.cluster.ruleserver) (in module PYME.cluster.taskWorkerHTTP) on_slide() (PYME.Acquire.ui.mpd_picosecond_delay_panel.DelayPanel method) on_spool_event() (PYME.Acquire.htsms.rule_ui.ProtocolRules method) on_spool_start() (PYME.Acquire.htsms.rule_ui.ProtocolRules method) on_spool_stop() (PYME.Acquire.htsms.rule_ui.ProtocolRules method) on_toggle() (PYME.Acquire.ui.lasersliders.LaserSliders method) (PYME.Acquire.ui.multiview_select.MultiviewSelect method) on_toggle_loc_units() (PYME.LMVis.importTextDialog.ColumnMappingDialog method) on_trait_change() (in module PYME.misc.mock_traits) on_update() (PYME.DSView.OpenSequenceDialog.OpenSequenceDialog method) OnAbout() (PYME.ui.AUIFrame.AUIFrame method) OnAddAction() (PYME.Acquire.ui.actionUI.ActionPanel method) OnAddChan() (PYME.DSView.modules.composite.CompositeDialog method) OnAddLocalization() (PYME.Acquire.htsms.rule_ui.SMLMChainedAnalysisPage method) OnAddLocalizationRule() (PYME.Acquire.htsms.rule_ui.LocalizationSettingsPanel method) OnAddModule() (PYME.recipes.recipeGui.RecipeView method) OnAddMove() (PYME.Acquire.ui.actionUI.ActionPanel method) OnAddRecipe() (PYME.Acquire.htsms.rule_ui.ChainedAnalysisPage method) OnAddRecipeRule() (PYME.Acquire.htsms.rule_ui.RuleRecipeManager method) OnAddSequence() (PYME.Acquire.ui.actionUI.ActionPanel method) OnAddSlide() (PYME.Acquire.sampleInformation.SampleInfoDialog method) OnAddVSSetting() (PYME.Acquire.ui.voxelSizeDialog.VoxelSizeDialog method) OnAlignChannels() (PYME.DSView.modules.composite.Compositor method) OnApply() (PYME.DSView.modules.composite.ShiftPanel method) (PYME.DSView.modules.segmentation.SegmentationPanel method) OnApplyShiftmap() (PYME.DSView.modules.composite.Compositor method) OnApplyText() (PYME.recipes.recipeGui.RecipeView method) OnApplyThreshold() (PYME.DSView.modules.filtering.Filterer method) OnAqStart() (PYME.Acquire.zScanner.wavetableZScanner method) (PYME.Acquire.zScanner.zScanner method) OnAqStop() (PYME.Acquire.zScanner.wavetableZScanner method) (PYME.Acquire.zScanner.zScanner method) OnAstigQualityControl() (PYME.LMVis.Extras.multiviewMapping.MultiviewMapper method) OnAverageFramesByStep() (PYME.DSView.modules.filtering.Filterer method) OnBake() (PYME.recipes.recipeGui.BatchFrame method) OnBAnalyse() (PYME.Acquire.ui.HDFSpoolFrame.PanSpool method) OnBeginEdit() (PYME.ui.MetadataTree.MetadataPanel method) OnBeginLabelEdit() (PYME.DSView.modules.annotation.myListCtrl method) OnBEndHereButton() (PYME.Acquire.ui.seqdialog.seqPanel method) OnBLive() (PYME.Acquire.ui.seqdialog.seqPanel method) OnBMid_numRadiobutton() (PYME.Acquire.ui.seqdialog.seqPanel method) OnBOptimise() (PYME.DSView.displaySettingsPanel.dispSettingsPanel method) (PYME.DSView.displaySettingsPanel.dispSettingsPanel2 method) OnBSetAqProtocolButton() (PYME.Acquire.ui.HDFSpoolFrame.PanSpool method) OnBSetSpoolDirButton() (PYME.Acquire.ui.HDFSpoolFrame.PanSpool method) OnBSingle() (PYME.Acquire.ui.seqdialog.seqPanel method) OnBSt_endRadiobutton() (PYME.Acquire.ui.seqdialog.seqPanel method) OnBStartHereButton() (PYME.Acquire.ui.seqdialog.seqPanel method) OnBStartSpoolButton() (PYME.Acquire.ui.HDFSpoolFrame.PanSpool method) OnBStartStackButton() (PYME.Acquire.ui.HDFSpoolFrame.PanSpool method) OnBStopSpoolingButton() (PYME.Acquire.ui.HDFSpoolFrame.PanSpool method) OnCalcDecays() (PYME.LMVis.Extras.photophysics.DecayAnalyser method) OnCalcHarmonicRepresentation() (PYME.LMVis.Extras.spherical_harmonics.SphericalHarmonicShellManager method) OnCalcMSDs() (PYME.LMVis.Extras.particleTracking.ParticleTracker method) OnCalcShift() (PYME.DSView.modules.psfExtraction.PsfExtractor method) OnCalcShiftmap() (PYME.DSView.modules.blobFinding.BlobFinder method) (PYME.DSView.modules.shiftfield_estimation.BlobFinder method) OnCalculate() (PYME.DSView.modules.blobMeasure.Measurements method) (PYME.DSView.modules.deconvolution.WienerDeconvolver method) OnCalcWidths() (PYME.LMVis.Extras.particleTracking.ParticleTracker method) OnCalibrateMultiview() (PYME.DSView.modules.psfExtraction.PsfExtractor method) OnCalibrateShifts() (PYME.LMVis.Extras.multiviewMapping.MultiviewMapper method) OnCalibrateSplitter() (PYME.DSView.modules.LMAnalysis.FitDefaults method) OnCameraFrame() (PYME.Acquire.zScanner.zScanner method) OnCancel() (PYME.Deconv.deconvDialogs.DeconvProgressDialog method) (PYME.Deconv.deconvDialogs.DeconvProgressPanel method) OnCbOn() (PYME.Acquire.ui.lasersliders.LaserSliders method) (PYME.Acquire.ui.lasersliders.LaserToggles method) OnCCamera() (PYME.Acquire.ui.selectCameraPanel.CameraChooserPanel method) OnChanDown() (PYME.DSView.modules.composite.CompositeDialog method) OnChange() (PYME.DSView.displayOptions.DisplayOpts method) OnChange3D() (PYME.LMVis.displayPane.DisplayPane method) (PYME.LMVis.displayPane.DisplayPaneHorizontal method) (PYME.LMVis.displayPane.DisplayPaneLight method) OnChangeLineWidth() (PYME.DSView.modules.annotation.LabelPanel method) OnChangeMethod() (PYME.DSView.modules.blobFinding.BlobFinder method) (PYME.DSView.modules.shiftfield_estimation.BlobFinder method) OnChangePDye() (PYME.LMVis.colourPanel.colourPanel method) OnChangePointColour() (PYME.LMVis.pointSettingsPanel.PointSettingsPanel method) OnChangePOther() (PYME.LMVis.colourPanel.colourPanel method) OnChangeScaleBar() (PYME.LMVis.displayPane.DisplayPane method) (PYME.LMVis.displayPane.DisplayPaneHorizontal method) (PYME.LMVis.displayPane.DisplayPaneLight method) OnChangeStructure() (PYME.DSView.modules.annotation.LabelPanel method) OnChannelFold() (PYME.DSView.DisplayOptionsPanel.OptionsPanel method) OnChanUp() (PYME.DSView.modules.composite.CompositeDialog method) OnChar() (PYME.contrib.listctrlMixins.TextEditMixin method) (PYME.ui.MetadataTree.TextEditMixin method) OnCheckAstigmatismCalibration() (PYME.LMVis.Extras.multiviewMapping.MultiviewMapper method) OnCheckItem() (PYME.contrib.listctrlMixins.CheckListCtrlMixin method) (PYME.DSView.modules.particleTracking.TrackList method) OnCheckSpacing() (PYME.Acquire.Utils.sarcSpacing.SarcomereChecker method) OnChooseVS() (PYME.Acquire.ui.voxelSizeDialog.VoxelSizeDialog method) OnChPiezoChoice() (PYME.Acquire.ui.seqdialog.seqPanel method) OnClear() (PYME.Acquire.htsms.rule_ui.ChainedAnalysisPage method) (PYME.Acquire.positionTracker.TrackerPanel method) (PYME.Acquire.ui.intensity_trace.TraceROISelectPanel method) OnClearTags() (PYME.DSView.modules.object_tagging.ObjectTagger method) (PYME.DSView.modules.psfExtraction.PsfExtractor method) OnCLimChange() (PYME.LMVis.displayPane.DisplayPane method) OnCLimChanged() (PYME.DSView.DisplayOptionsPanel.OptionsPanel method) OnCLimHistChange() (PYME.LMVis.displayPane.DisplayPane method) OnClose() (PYME.LMVis.Extras.showShortcuts.ShowShortcuts method) (PYME.LMVis.VisGUI.VisGUIFrame method) OnCloseWindow() (PYME.Acquire.acquiremainframe.PYMEMainFrame method) (PYME.Acquire.acquirewx.PYMEMainFrame method) (PYME.DSView.dsviewer.DSViewFrame method) OnClumpDBSCAN() (PYME.LMVis.Extras.clusterAnalysis.ClusterAnalyser method) OnClustersInTime() (PYME.LMVis.Extras.clusterAnalysis.ClusterAnalyser method) OnCMapChange() (PYME.LMVis.displayPane.DisplayPane method) OnCMapChanged() (PYME.DSView.DisplayOptionsPanel.OptionsPanel method) OnCoalesce() (PYME.LMVis.Extras.particleTracking.ParticleTracker method) OnColNameChange() (PYME.LMVis.importTextDialog.ColumnMappingDialog method) OnColoc() (PYME.DSView.modules.coloc.Colocaliser method) (PYME.DSView.modules.fourierRingCorrelation.RingCorrelator method) OnColocBasic() (PYME.DSView.modules.coloc.Colocaliser method) OnColourChanged() (PYME.LMVis.displayPane.DisplayPaneHorizontal method) OnColourFilterChange() (PYME.LMVis.colourFilterGUI.ColourFilterPane method) onCombobox() (PYME.Acquire.ui.intsliders.IntegrationSliders method) (PYME.Acquire.ui.intsliders.IntegrationSliders_ method) OnComplexChanged() (PYME.DSView.DisplayOptionsPanel.OptionsPanel method) OnConfigure() (PYME.LMVis.Extras.pointSetGeneration.Generator method) OnCorrelate() (PYME.DSView.modules.composite.ShiftPanel method) OnCrop() (PYME.DSView.dsviewer.DSViewFrame method) (PYME.DSView.modules.cropping.Cropper method) OnDarkT() (PYME.LMVis.Extras.QPobjectSegment.QPObjectSegmenter method) OnDeconEnd() (PYME.DSView.modules.deconvolution.Deconvolver method) OnDeconTimer() (PYME.DSView.modules.deconvolution.Deconvolver method) (PYME.DSView.modules.deconvolution.WienerDeconvolver method) OnDeconvBead() (PYME.DSView.modules.deconvolution.Deconvolver method) OnDeconvICTM() (PYME.DSView.modules.deconvolution.Deconvolver method) OnDeconvMovie() (PYME.DSView.modules.deconvolution.Deconvolver method) OnDeconvWiener() (PYME.DSView.modules.deconvolution.Deconvolver method) OnDiagSplit() (PYME.DSView.modules.cropping.Cropper method) OnDNAPaint() (PYME.DSView.modules.LMAnalysis.FitDefaults method) OnDoChange() (PYME.DSView.DisplayOptionsPanel.OptionsPanel method) OnDocumentation() (PYME.LMVis.VisGUI.VisGUIFrame method) OnDone() (PYME.DSView.modules.segmentation.SegmentationPanel method) OnDoubleClick() (PYME.LMVis.view_clipping_pane.ClippingPanel method) OnDwellKillFocus() (PYME.Acquire.ui.seqdialog.seqPanel method) OnEditRuleChain() (PYME.Acquire.htsms.rule_ui.ChainedAnalysisPanel method) OnEndEdit() (PYME.ui.MetadataTree.MetadataPanel method) ones() (in module PYME.util.shmarray.shmarray) OnExport() (PYME.DSView.dsviewer.DSViewFrame method) (PYME.DSView.modules.visgui.visGuiExtras method) OnExportXls() (PYME.DSView.modules.blobMeasure.Measurements method) onExpReady() (PYME.Acquire.frameWrangler.FrameWrangler method) OnExtract() (PYME.DSView.modules.prebleachExtraction.PrebleachExtractor method) (PYME.DSView.modules.psfExtraction.PsfExtractor method) OnExtractMultiviewPSF() (PYME.DSView.modules.psfExtraction.PsfExtractor method) OnExtractPSF() (PYME.DSView.modules.psfExtraction.PsfExtractor method) OnExtractSplitPSF() (PYME.DSView.modules.psfExtraction.PsfExtractor method) OnFeaturesChanged() (PYME.recipes.tracking.TrackFeatures method) OnFileExit() (PYME.Acquire.acquiremainframe.PYMEMainFrame method) (PYME.Acquire.acquirewx.PYMEMainFrame method) OnFileOpenStack() (PYME.Acquire.acquiremainframe.PYMEMainFrame method) (PYME.Acquire.acquirewx.PYMEMainFrame method) OnFilterAdd() (PYME.DSView.modules.measure.filterPan.FilterPane method) (PYME.ui.custom_traits_editors.DictChoiceStrPanel method) (PYME.ui.filterPane.FilterPanel method) OnFilterChange() (PYME.Acquire.sampleInformation.SampleInfoDialog method) OnFilterClipToSelection() (PYME.DSView.modules.measure.filterPan.FilterPane method) (PYME.ui.filterPane.FilterPane method) OnFilterDelete() (PYME.DSView.modules.measure.filterPan.FilterPane method) (PYME.ui.custom_traits_editors.DictChoiceStrPanel method) (PYME.ui.filterPane.FilterPanel method) OnFilterEdit() (PYME.DSView.modules.measure.filterPan.FilterPane method) (PYME.ui.custom_traits_editors.DictChoiceStrPanel method) (PYME.ui.filterPane.FilterPanel method) OnFilterItemDeselected() (PYME.DSView.modules.measure.filterPan.FilterPane method) (PYME.ui.custom_traits_editors.DictChoiceStrPanel method) (PYME.ui.filterPane.FilterPanel method) OnFilterItemSelected() (PYME.DSView.modules.measure.filterPan.FilterPane method) (PYME.ui.custom_traits_editors.DictChoiceStrPanel method) (PYME.ui.filterPane.FilterPanel method) OnFilterListRightClick() (PYME.DSView.modules.measure.filterPan.FilterPane method) (PYME.ui.custom_traits_editors.DictChoiceStrPanel method) (PYME.ui.filterPane.FilterPanel method) OnFindClumps() (PYME.LMVis.Extras.multiviewMapping.MultiviewMapper method) (PYME.LMVis.Extras.particleTracking.ParticleTracker method) OnFindMixedClusters() (PYME.LMVis.Extras.clusterAnalysis.ClusterAnalyser method) OnFindObjects() (PYME.DSView.modules.blobFinding.BlobFinder method) OnFinish() (PYME.Acquire.protocol.Protocol method) (PYME.Acquire.protocol.TaskListProtocol method) (PYME.Acquire.protocol.ZStackTaskListProtocol method) OnFitModuleChanged() (PYME.Acquire.ui.AnalysisSettingsUI.AnalysisSettingsPanel method) (PYME.DSView.modules.LMAnalysis.AnalysisSettingsView method) OnFitObjects() (PYME.DSView.modules.blobFinding.BlobFinder method) (PYME.DSView.modules.shiftfield_estimation.BlobFinder method) OnFitQuadraticPatches() (PYME.LMVis.Extras.surface_fitting.SurfaceFitter method) OnFitROI() (PYME.LMVis.visCore.VisGUICore method) OnFlavourChange() (PYME.LMVis.importTextDialog.ImportTextDialog method) OnFold() (PYME.LMVis.Extras.multiviewMapping.MultiviewMapper method) (PYME.ui.autoFoldPanel.collapsingPane method) (PYME.ui.manualFoldPanel.collapsingPane method) OnFrame() (PYME.Acquire.protocol.Protocol method) (PYME.Acquire.protocol.TaskListProtocol method) (PYME.Acquire.protocol.ZStackTaskListProtocol method) (PYME.DSView.modules.playback.PlayPanel method) (PYME.IO.HDFSpooler.Spooler method) (PYME.IO.HTTPSpooler.Spooler method) (PYME.IO.HTTPSpooler_v2.Spooler method) (PYME.IO.QueueSpooler.Spooler method) (PYME.IO.Spooler.Spooler method) OnFrameGroup() (PYME.Acquire.autofocus.AutoFocus method) (PYME.Acquire.Utils.vibrationAnalysis.VibrAnal method) OnFRC() (PYME.DSView.modules.coloc.Colocaliser method) OnGaussianFilter() (PYME.DSView.modules.filtering.Filterer method) (PYME.DSView.modules.sparkprepare.filterer method) OnGaussianFit() (PYME.DSView.modules.profileFitting.Fitter method) OnGenEvents() (PYME.LMVis.Extras.pointSetGeneration.Generator method) OnGenPoints() (PYME.LMVis.Extras.pointSetGeneration.Generator method) OnGenShiftmap() (PYME.LMVis.Extras.shiftmapGenerator.ShiftmapGenerator method) OnGenShiftmapQuad() (PYME.LMVis.Extras.shiftmapGenerator.ShiftmapGenerator method) OnGenShiftmapQuadz() (PYME.LMVis.Extras.shiftmapGenerator.ShiftmapGenerator method) OnGetIDs() (PYME.LMVis.Extras.objectMeasurements.ObjectMeasurer method) (PYME.LMVis.Extras.QPobjectSegment.QPObjectSegmenter method) OnGetItemAttr() (PYME.DSView.modules.particleTracking.TrackList method) OnGetItemText() (PYME.Acquire.htsms.rule_ui.ProtocolRuleFactoryListCtrl method) (PYME.Acquire.sampleInformation.VirtList method) (PYME.Acquire.ui.actionUI.ActionList method) (PYME.DSView.modules.composite.ImageList method) (PYME.DSView.modules.particleTracking.TrackList method) OnGetMatches() (PYME.recipes.recipeGui.FileListPanel method) OnGo() (PYME.Acquire.ui.tile_panel.CircularTilePanel method) (PYME.Acquire.ui.tile_panel.MultiwellTilePanel method) (PYME.Acquire.ui.tile_panel.TilePanel method) (PYME.DSView.modules.LMAnalysis.LMAnalyser2 method) OnGoto() (PYME.DSView.modules.playback.PlayPanel method) OnHideObject() (PYME.DSView.modules.blobMeasure.Measurements method) OnHideTrack() (PYME.DSView.modules.particleTracking.TrackList method) OnHome() (PYME.LMVis.visCore.VisGUICore method) OnIdle() (PYME.DSView.DisplayOptionsPanel.OptionsPanel method) (PYME.LMVis.visCore.VisGUICore method) (PYME.recipes.vertical_recipe_display.RecipeDisplayPanel method) OnIDTransient() (PYME.LMVis.Extras.flagZMotionArtifacts.motionFlagger method) OnImagesPushed() (PYME.DSView.modules.LMAnalysis.LMAnalyser2 method) OnIsodataThresh() (PYME.DSView.DisplayOptionsPanel.OptionsPanel method) OnItemSelected() (PYME.contrib.listctrlMixins.TextEditMixin method) (PYME.ui.MetadataTree.TextEditMixin method) OnJoystickEnable() (PYME.Acquire.ui.positionUI.PositionPanel method) (PYME.Acquire.ui.positionUI.PositionSliders method) OnKeyPress() (PYME.LMVis.imageView.ImageViewPanel method) (PYME.LMVis.imageView2.ImageViewPanel method) (PYME.ui.histLimits.HistLimitPanel method) OnLabel() (PYME.DSView.modules.filtering.Filterer method) OnLabelActivate() (PYME.DSView.modules.annotation.myListCtrl method) OnLabelSizeThreshold() (PYME.DSView.modules.filtering.Filterer method) OnLabelWatershed() (PYME.DSView.modules.filtering.Filterer method) OnLCSMDoPopup() (PYME.contrib.listctrlMixins.ListCtrlSelectionManagerMix method) OnLCSMRightDown() (PYME.contrib.listctrlMixins.ListCtrlSelectionManagerMix method) OnLeftDown() (PYME.contrib.listctrlMixins.TextEditMixin method) (PYME.LMVis.imageView.ImageViewPanel method) (PYME.LMVis.imageView2.ImageViewPanel method) (PYME.LMVis.view_clipping_pane.ClippingPanel method) (PYME.ui.histLimits.HistLimitPanel method) (PYME.ui.MetadataTree.TextEditMixin method) OnLeftUp() (PYME.LMVis.imageView.ImageViewPanel method) (PYME.LMVis.imageView2.ImageViewPanel method) (PYME.LMVis.view_clipping_pane.ClippingPanel method) (PYME.ui.histLimits.HistLimitPanel method) OnLineThickness() (PYME.DSView.DisplayOptionsPanel.OptionsPanel method) OnListRightClick() (PYME.DSView.modules.particleTracking.TrackList method) OnLoadClassifier() (PYME.DSView.modules.annotation.Annotater method) OnLoadCustom() (PYME.DSView.modules.recipes.RecipePlugin method) OnLoadHarmonicRepresentation() (PYME.LMVis.Extras.spherical_harmonics.SphericalHarmonicShellManager method) OnLoadOutputs() (PYME.DSView.modules.recipes.RecipePlugin method) OnLoadRecipe() (PYME.recipes.recipeGui.RecipeManager method) OnLUTDrawCB() (PYME.LMVis.displayPane.DisplayPane method) (PYME.LMVis.displayPane.DisplayPaneHorizontal method) (PYME.LMVis.displayPane.DisplayPaneLight method) OnMakeComposites() (PYME.DSView.modules.composite.Compositor method) OnMapAstigmaticZ() (PYME.LMVis.Extras.multiviewMapping.MultiviewMapper method) OnMappingChange() (PYME.DSView.displaySettingsPanel.dispSettingsPanel method) (PYME.DSView.displaySettingsPanel.dispSettingsPanel2 method) OnMAquireOnePic() (PYME.Acquire.acquiremainframe.PYMEMainFrame method) (PYME.Acquire.acquirewx.PYMEMainFrame method) OnMAquireStack() (PYME.Acquire.acquiremainframe.PYMEMainFrame method) (PYME.Acquire.acquirewx.PYMEMainFrame method) OnMaxProject() (PYME.DSView.modules.filtering.Filterer method) OnMCA() (PYME.LMVis.Extras.multiColourAnalysis.MultiColAnalyzer method) OnMCamBin() (PYME.Acquire.acquiremainframe.PYMEMainFrame method) (PYME.Acquire.acquirewx.PYMEMainFrame method) OnMCamRoi() (PYME.Acquire.acquiremainframe.PYMEMainFrame method) (PYME.Acquire.acquirewx.PYMEMainFrame method) OnMCamSetPixelSize() (PYME.Acquire.acquire_server.PYMEAcquireServer method) (PYME.Acquire.acquiremainframe.PYMEMainFrame method) (PYME.Acquire.acquirewx.PYMEMainFrame method) OnMDChanged() (PYME.Acquire.ui.AnalysisSettingsUI.AnalysisDetailsPanel method) OnMDisplayClearSel() (PYME.Acquire.acquiremainframe.PYMEMainFrame method) (PYME.Acquire.acquirewx.PYMEMainFrame method) OnMeanProject() (PYME.DSView.modules.filtering.Filterer method) OnMeasure() (PYME.LMVis.Extras.objectMeasurements.ObjectMeasurer method) (PYME.LMVis.Extras.QPobjectSegment.QPObjectSegmenter method) OnMeasureClusters() (PYME.LMVis.Extras.clusterAnalysis.ClusterAnalyser method) OnMergeClumps() (PYME.LMVis.Extras.multiviewMapping.MultiviewMapper method) OnMethodChanged() (PYME.Deconv.deconvDialogs.DeconvSettingsDialog method) OnMiddleDown() (PYME.LMVis.imageView.ImageViewPanel method) (PYME.LMVis.imageView2.ImageViewPanel method) OnMiddleUp() (PYME.LMVis.imageView.ImageViewPanel method) (PYME.LMVis.imageView2.ImageViewPanel method) OnMotion() (PYME.LMVis.imageView.ImageViewPanel method) (PYME.LMVis.imageView2.ImageViewPanel method) OnMouseEnterPane() (PYME.ui.autoFoldPanel.foldPanel method) OnMouseLeave() (PYME.ui.autoFoldPanel.foldPanel method) OnMouseLeavePane() (PYME.ui.autoFoldPanel.foldPanel method) OnMouseMove() (PYME.LMVis.view_clipping_pane.ClippingPanel method) (PYME.ui.histLimits.HistLimitPanel method) OnMouseScrollEvent() (PYME.LMVis.view_clipping_pane.ClippingPanel method) (PYME.ui.histLimits.HistLimitPanel method) OnMove() (PYME.LMVis.VisGUI.VisGUIFrame method)

OnNearestNeighbor() (PYME.LMVis.Extras.clusterAnalysis.ClusterAnalyser method) OnNeuroglancer() (PYME.DSView.modules.neuroglancer.Neuroglancer method) OnNewRecipe() (PYME.recipes.recipeGui.RecipeView method) OnObjApplyThreshold() (PYME.LMVis.triBlobs.BlobSettingsPanel method) OnObjMeasure() (PYME.LMVis.triBlobs.BlobSettingsPanel method) OnOpen() (PYME.DSView.dsviewer.DSViewFrame method) OnOpenChannel() (PYME.LMVis.VisGUI.VisGUIFrame method) OnOpenFile() (PYME.LMVis.visCore.VisGUICore method) OnOpenRaw() (PYME.LMVis.VisGUI.VisGUIFrame method) OnOpenSequence() (PYME.DSView.dsviewer.DSViewFrame method) OnOptimise() (PYME.DSView.DisplayOptionsPanel.OptionsPanel method) OnPaint() (PYME.Acquire.ui.splashScreen.SplashPanel method) (PYME.DSView.eventLogViewer.eventLogPanel method) (PYME.DSView.eventLogViewer.eventLogTPanel method) (PYME.DSView.scrolledImagePanel.ImagePanel method) (PYME.DSView.splashScreen.SplashPanel method) (PYME.LMVis.imageView.ImageViewPanel method) (PYME.LMVis.imageView2.ImageViewPanel method) (PYME.LMVis.view_clipping_pane.ClippingPanel method) (PYME.recipes.vertical_recipe_display.RecipeDisplayPanel method) (PYME.ui.fastGraph.FastGraphPanel method) (PYME.ui.histLimits.HistLimitPanel method) OnPairwiseDistanceHistogram() (PYME.LMVis.Extras.clusterAnalysis.ClusterAnalyser method) OnParamChange() (PYME.recipes.tracking.TrackFeatures method) OnPauseActions() (PYME.Acquire.ui.actionUI.ActionPanel method) OnPercentileCLim() (PYME.LMVis.displayPane.DisplayPane method) OnPerFrame() (PYME.LMVis.Extras.perFrameVariable.PerFrameVar method) OnPick() (PYME.Acquire.htsms.rule_ui.ChainedAnalysisPage method) (PYME.recipes.recipeGui.RecipeView method) OnPlay() (PYME.DSView.modules.playback.PlayPanel method) OnPlayPosChanged() (PYME.DSView.modules.playback.PlayPanel method) OnPlaySpeedChanged() (PYME.DSView.modules.playback.PlayPanel method) OnPlotAxialProfile() (PYME.DSView.modules.profilePlotting.ProfilePlotter method) OnPlotProfile() (PYME.DSView.modules.multithreshold.MultiThreshold method) (PYME.DSView.modules.profilePlotting.ProfilePlotter method) OnPlotTemperature() (PYME.LMVis.Extras.temperaturePlot.TempPlotter method) OnPlotWavyProfile() (PYME.DSView.modules.profilePlotting.ProfilePlotter method) OnPointAlphaChange() (PYME.LMVis.pointSettingsPanel.PointSettingsPanel method) OnPointSelect() (PYME.DSView.modules.LMDisplay.LMDisplay method) OnPointSizeChange() (PYME.LMVis.pointSettingsPanel.PointSettingsPanel method) OnPointwiseColoc() (PYME.LMVis.Extras.pointwiseColoc.PointwiseColocaliser method) OnPostChoice() (PYME.Acquire.htsms.rule_ui.ChainedAnalysisPage method) OnPRI3D() (PYME.DSView.modules.LMAnalysis.FitDefaults method) OnProfile() (PYME.DSView.modules.profilePlotting.ProfilePlotter method) OnProtocolChoice() (PYME.Acquire.htsms.rule_ui.ChainedAnalysisPage method) OnPSFFileChanged() (PYME.Deconv.deconvDialogs.DeconvSettingsDialog method) (PYME.DSView.modules.deconvolution.WienerDeconvolver method) OnPSFFromPupil() (PYME.DSView.modules.pupilTools.PupilTools method) OnPSFFromZernikeModes() (PYME.DSView.modules.pupilTools.PupilTools method) OnPSFNotebookPageChanged() (PYME.Deconv.deconvDialogs.DeconvSettingsDialog method) OnPSFROI() (PYME.DSView.modules.object_tagging.ObjectTagger method) (PYME.DSView.modules.psfExtraction.PsfExtractor method) OnQTLeafChange() (PYME.LMVis.quadTreeSettings.QuadTreeSettingsPanel method) OnQueue() (PYME.Acquire.ui.tile_panel.MultiwellProtocolQueuePanel method) OnQuit() (PYME.ui.AUIFrame.AUIFrame method) OnRawDecay() (PYME.DSView.modules.profileFitting.Fitter method) OnRawDecaySimp() (PYME.DSView.modules.profileFitting.Fitter method) OnRecenter() (PYME.LMVis.visCore.VisGUICore method) OnRemoveChan() (PYME.DSView.modules.composite.CompositeDialog method) OnRemoveProtocolRule() (PYME.Acquire.htsms.rule_ui.ChainedAnalysisPanel method) OnResampleZStack() (PYME.DSView.modules.filtering.Filterer method) OnResetRotation() (PYME.LMVis.visCore.VisGUICore method) OnResize() (PYME.ui.manualFoldPanel.foldPanel method) OnRetrieveIntensitySteps() (PYME.LMVis.Extras.photophysics.DecayAnalyser method) OnRightDown() (PYME.ui.MetadataTree.MetadataPanel method) OnRightUp() (PYME.ui.histLimits.HistLimitPanel method) (PYME.ui.MetadataTree.MetadataPanel method) OnRingTest() (PYME.LMVis.Extras.clusterAnalysis.ClusterAnalyser method) OnRipleys() (PYME.LMVis.Extras.clusterAnalysis.ClusterAnalyser method) OnRipleysMasked() (PYME.LMVis.Extras.clusterAnalysis.ClusterAnalyser method) OnROIsFromFile() (PYME.Acquire.ui.actionUI.ActionPanel method) OnROIsFromTileviewer() (PYME.Acquire.ui.actionUI.ActionPanel method) OnRunCanned() (PYME.DSView.modules.recipes.RecipePlugin method) OnSave() (PYME.DSView.dsviewer.DSViewFrame method) (PYME.LMVis.visCore.VisGUICore method) (PYME.ui.recArrayView.ArrayPanel method) OnSaveClassifier() (PYME.DSView.modules.annotation.Annotater method) OnSaveMeasurements() (PYME.LMVis.VisGUI.VisGUIFrame method) OnSaveObjects() (PYME.DSView.modules.blobMeasure.Measurements method) OnSaveOutputOld() (PYME.DSView.modules.recipes.RecipePlugin method) OnSaveOutputs() (PYME.DSView.modules.recipes.RecipePlugin method) OnSavePoints() (PYME.LMVis.Extras.pointSetGeneration.Generator method) OnSaveRecipe() (PYME.recipes.recipeGui.RecipeManager method) OnSaveToCluster() (PYME.DSView.dsviewer.DSViewFrame method) OnScaleChanged() (PYME.DSView.DisplayOptionsPanel.OptionsPanel method) (PYME.DSView.displaySettingsPanel.dispSettingsPanel method) (PYME.DSView.displaySettingsPanel.dispSettingsPanel2 method) OnScrollX() (PYME.DSView.scrolledImagePanel.ScrolledImagePanel method) OnScrollY() (PYME.DSView.scrolledImagePanel.ScrolledImagePanel method) OnSearchChange() (PYME.recipes.recipeGui.ModuleSelectionDialog method) OnSeekStart() (PYME.DSView.modules.playback.PlayPanel method) OnSegmentAnneal() (PYME.DSView.modules.segmentation.Segmenter method) OnSelect() (PYME.recipes.recipeGui.ModuleSelectionDialog method) OnSelectCrosshairs() (PYME.DSView.DisplayOptionsPanel.OptionsPanel method) OnSelectLine() (PYME.DSView.DisplayOptionsPanel.OptionsPanel method) OnSelectObject() (PYME.DSView.DisplayOptionsPanel.OptionsPanel method) OnSelectRectangle() (PYME.DSView.DisplayOptionsPanel.OptionsPanel method) OnSelectSlide() (PYME.Acquire.sampleInformation.SampleInfoDialog method) OnSelectSquiggle() (PYME.DSView.DisplayOptionsPanel.OptionsPanel method) OnSelectTrack() (PYME.DSView.modules.particleTracking.ParticleTrackingView method) OnSetBlobColour() (PYME.LMVis.triBlobs.BlobSettingsPanel method) OnSetLabels() (PYME.DSView.modules.filtering.Filterer method) OnSetMapsDefault() (PYME.DSView.modules.LMAnalysis.FitDefaults method) OnSetShiftField() (PYME.DSView.modules.splitter.Unmixer method) OnSetShiftmap() (PYME.DSView.modules.composite.CompositeDialog method) OnSetSlide() (PYME.Acquire.sampleInformation.slidePanel method) OnSetSubtractionProfile() (PYME.Acquire.ui.focus_lock_gui.FocusLockPanel method) OnShiftCorrectFolded() (PYME.LMVis.Extras.multiviewMapping.MultiviewMapper method) OnShow() (PYME.LMVis.colourPanel.colourPanel method) OnShowChanged() (PYME.DSView.DisplayOptionsPanel.OptionsPanel method) OnShowThreshold() (PYME.DSView.DisplayOptionsPanel.OptionsPanel method) OnShowTrack() (PYME.DSView.modules.particleTracking.TrackList method) OnSignalFracThresh() (PYME.DSView.DisplayOptionsPanel.OptionsPanel method) OnSingleEnd() (PYME.Acquire.ui.seqdialog.seqPanel method) OnSize() (PYME.DSView.eventLogViewer.eventLogPanel method) (PYME.DSView.eventLogViewer.eventLogTPanel method) (PYME.DSView.modules.playback.PlayPanel method) (PYME.DSView.scrolledImagePanel.ScrolledImagePanel method) (PYME.LMVis.imageView.ImageViewPanel method) (PYME.LMVis.imageView2.ImageViewPanel method) (PYME.LMVis.pipelineView.PipelinePanel method) (PYME.LMVis.view_clipping_pane.ClippingPanel method) (PYME.ui.AUIFrame.AUIFrame method) (PYME.ui.fastGraph.FastGraphPanel method) (PYME.ui.histLimits.HistLimitPanel method) (PYME.ui.manualFoldPanel.foldingPane method) (PYME.ui.MetadataTree.MetadataPanel method) (PYME.ui.recArrayView.ArrayPanel method) OnSliceChanged() (PYME.DSView.DisplayOptionsPanel.OptionsPanel method) onSlide() (PYME.Acquire.ui.intsliders.IntegrationSliders method) (PYME.Acquire.ui.intsliders.IntegrationSliders_ method) (PYME.Acquire.ui.lasersliders.LaserSliders method) (PYME.Acquire.ui.lasersliders.LaserSliders_ method) (PYME.Acquire.ui.positionUI.PositionPanel method) (PYME.Acquire.ui.positionUI.PositionSliders method) OnSortOrderChanged() (PYME.contrib.listctrlMixins.ColumnSorterMixin method) OnSourceChange() (PYME.LMVis.visCore.VisGUICore method) OnSpecAdd() (PYME.LMVis.colourPanel.colourPanel method) OnSpecChange() (PYME.LMVis.colourPanel.colourPanel method) OnSpecDelete() (PYME.LMVis.colourPanel.colourPanel method) OnSpecGuess() (PYME.LMVis.colourPanel.colourPanel method) OnSpecListRightClick() (PYME.LMVis.colourPanel.colourPanel method) OnSplitChannels() (PYME.DSView.modules.composite.Compositor method) OnSplitter2D() (PYME.DSView.modules.LMAnalysis.FitDefaults method) OnSplitter3D() (PYME.DSView.modules.LMAnalysis.FitDefaults method) OnSpoolingStarted() (PYME.Acquire.ui.HDFSpoolFrame.PanSpool method) OnSpoolingStopped() (PYME.Acquire.ui.HDFSpoolFrame.PanSpool method) OnSpoolMethodChanged() (PYME.Acquire.ui.HDFSpoolFrame.PanSpool method) OnStandard2D() (PYME.DSView.modules.LMAnalysis.FitDefaults method) OnStandard3D() (PYME.DSView.modules.LMAnalysis.FitDefaults method) OnStart() (PYME.Acquire.ui.focus_lock_gui.FocusLogPanel method) OnStop() (PYME.Acquire.ui.focus_lock_gui.FocusLogPanel method) (PYME.Acquire.ui.tile_panel.MultiwellTilePanel method) (PYME.Acquire.ui.tile_panel.TilePanel method) OnSynchronise() (PYME.DSView.modules.synchronise.Syncer method) OnTagEdge() (PYME.Acquire.positionTracker.TrackerPanel method) OnTagObject() (PYME.DSView.modules.object_tagging.ObjectTagger method) OnTagPoints() (PYME.DSView.modules.psfExtraction.PsfExtractor method) OnTagPSF() (PYME.DSView.modules.psfExtraction.PsfExtractor method) onTarget() (PYME.Acquire.Utils.pointScanner.PointScanner method) (PYME.Acquire.Utils.pointScanner.PointScanner3D method) OnTcSpoolFileText() (PYME.Acquire.ui.HDFSpoolFrame.PanSpool method) OnTEndPosKillFocus() (PYME.Acquire.ui.seqdialog.seqPanel method) OnTest() (PYME.DSView.modules.LMAnalysis.LMAnalyser2 method) OnTestFrame() (PYME.DSView.modules.LMAnalysis.LMAnalyser2 method) OnTextCtrlEnter() (PYME.LMVis.view_clipping_pane.ClippingPanel method) OnTick() (PYME.Acquire.Utils.fastTiler.fastTiler method) OnTile() (PYME.DSView.modules.tiling.Tiler method) OnTilePyramid() (PYME.DSView.modules.tiling.Tiler method) OnTimedSpecies() (PYME.LMVis.Extras.sequentialSpecies.TimedSpecies method) OnTNumSlicesKillFocus() (PYME.Acquire.ui.seqdialog.seqPanel method) OnToggleActive() (PYME.Acquire.htsms.rule_ui.ChainedAnalysisPanel method) OnToggleBackground() (PYME.DSView.modules.LMAnalysis.LMAnalyser2 method) OnToggleLock() (PYME.Acquire.ui.focus_lock_gui.FocusLockPanel method) OnToggleModule() (PYME.DSView.dsviewer.DSViewFrame method) OnToggleScan() (PYME.Acquire.ui.scanner_panel.ScannerPanel method) OnToggleZStepping() (PYME.Acquire.ui.HDFSpoolFrame.PanSpool method) OnTrack() (PYME.DSView.modules.particleTracking.ParticleTrackingView method) OnTrackMolecules() (PYME.LMVis.Extras.particleTracking.ParticleTracker method) OnTStepSizeKillFocus() (PYME.Acquire.ui.seqdialog.seqPanel method) OnTStPosKillFocus() (PYME.Acquire.ui.seqdialog.seqPanel method) OnUnmix() (PYME.DSView.modules.splitter.Unmixer method) (PYME.DSView.modules.unmixing.Unmixer method) OnUnmixMax() (PYME.DSView.modules.splitter.Unmixer method) OnUpdateHome() (PYME.Acquire.ui.focus_lock_gui.FocusLockPanel method) OnUpdateSetpoint() (PYME.Acquire.ui.focus_lock_gui.FocusLockPanel method) OnView() (PYME.DSView.modules.blobMeasure.Measurements method) OnViewBackground() (PYME.DSView.modules.visgui.visGuiExtras method) OnViewBlobs() (PYME.LMVis.visCore.VisGUICore method) OnViewFront() (PYME.LMVis.displayPane.DisplayPaneHorizontal method) OnViewInterpTriangles() (PYME.LMVis.visCore.VisGUICore method) OnViewPoints() (PYME.LMVis.visCore.VisGUICore method) OnViewPointsprites() (PYME.LMVis.visCore.VisGUICore method) OnViewQuads() (PYME.LMVis.visCore.VisGUICore method) OnViewRight() (PYME.LMVis.displayPane.DisplayPaneHorizontal method) OnViewSelect() (PYME.DSView.modules.particleTracking.ParticleTrackingView method) OnViewShadedPoints() (PYME.LMVis.visCore.VisGUICore method) OnViewTop() (PYME.LMVis.displayPane.DisplayPaneHorizontal method) OnViewTracks() (PYME.LMVis.visCore.VisGUICore method) OnViewTriangles() (PYME.LMVis.visCore.VisGUICore method) OnViewTriangles3D() (PYME.LMVis.visCore.VisGUICore method) OnViewVoronoi() (PYME.LMVis.visCore.VisGUICore method) OnWheel() (PYME.DSView.eventLogViewer.eventLogPanel method) (PYME.DSView.eventLogViewer.eventLogTPanel method) (PYME.LMVis.imageView.ImageViewPanel method) (PYME.LMVis.imageView2.ImageViewPanel method) OnZBinChange() (PYME.LMVis.genImageDialog.GenImageDialog method) OnZero() (PYME.DSView.modules.composite.ShiftPanel method) OnZPlotProfile() (PYME.DSView.modules.profilePlotting.ProfilePlotter method) OnZProjChanged() (PYME.DSView.DisplayOptionsPanel.OptionsPanel method) OpaquePointShaderProgram (class in PYME.LMVis.shader_programs.DefaultShaderProgram) open_surface() (in module PYME.LMVis.Extras.extra_layers) OpenChannel() (PYME.LMVis.pipeline.Pipeline method) (PYME.LMVis.visCore.VisGUICore method) openDB() (in module PYME.IO.FileUtils.thumbnailDatabase) OpenEditor() (PYME.contrib.listctrlMixins.TextEditMixin method) (PYME.ui.MetadataTree.TextEditMixin method) openFile() (in module PYME.IO.unifiedIO) OpenFile() (PYME.LMVis.pipeline.Pipeline method) (PYME.LMVis.visCore.VisGUICore method) openH5() (in module PYME.IO.h5File) openH5R() (in module PYME.IO.h5rFile) OpenSequenceDialog (class in PYME.DSView.OpenSequenceDialog) OpticalFlow (class in PYME.recipes.processing) Optimise() (PYME.DSView.displayOptions.DisplayOpts method) optimize_path (PYME.recipes.acquisition.QueueAcquisitions attribute) OptionsPanel (class in PYME.DSView.DisplayOptionsPanel) orientationChoices (PYME.DSView.DisplayOptionsPanel.OptionsPanel attribute) origin (PYME.DSView.modules.composite.CompositeDialog property) (PYME.IO.image.ImageStack property) origin_nm() (in module PYME.IO.MetaDataHandler) OSXActivateKludge() (in module PYME.DSView.dsviewer) otsu() (in module PYME.Analysis.thresholding) Output (class in PYME.recipes.traits) output (PYME.LMVis.pipeline.Pipeline property) (PYME.recipes.base.Crop attribute) (PYME.recipes.base.Redimension attribute) (PYME.recipes.localisations.ProcessColour attribute) (PYME.recipes.localisations.TimeBlocks attribute) (PYME.recipes.machine_learning.LabelsToChannels attribute) (PYME.recipes.measurement.ChunkedTravelingSalesperson attribute) (PYME.recipes.measurement.IdentifyOverlappingROIs attribute) (PYME.recipes.measurement.TravelingSalesperson attribute) (PYME.recipes.pointcloud.DelaunayCircumcentres attribute) (PYME.recipes.pointcloud.DelaunayTesselation attribute) (PYME.recipes.pointcloud.LocalPointDensity attribute) (PYME.recipes.processing.AverageFramesByZStep attribute) (PYME.recipes.processing.Composite attribute) (PYME.recipes.processing.ResampleZ attribute) (PYME.recipes.simulation.RandomPoints attribute) (PYME.recipes.simulation.TheoreticalPSF attribute) (PYME.recipes.surface_fitting.DelaunayMarchingTetrahedra attribute) (PYME.recipes.surface_fitting.DistanceToMesh attribute) (PYME.recipes.surface_fitting.DualMarchingCubes attribute) (PYME.recipes.surface_fitting.FilterMeshComponentsByVolume attribute) (PYME.recipes.surface_fitting.ImageMaskFromSphericalHarmonicShell attribute) (PYME.recipes.surface_fitting.Isosurface attribute) (PYME.recipes.surface_fitting.NthPointIsosurface attribute) (PYME.recipes.surface_fitting.SHShellRadiusDensityEstimate attribute) (PYME.recipes.tablefilters.RandomSubset attribute) output_dark (PYME.recipes.processing.DarkAndVarianceMap attribute) output_files (PYME.cluster.rules.Rule property) output_fits_filtered (PYME.recipes.surface_fitting.FitSurfaceWithPatches attribute) output_fits_raw (PYME.recipes.surface_fitting.FitSurfaceWithPatches attribute) output_labeled (PYME.recipes.pointcloud.GaussianMixtureModel attribute) output_mapped (PYME.recipes.surface_fitting.AddSphericalHarmonicShellMappedCoords attribute) output_name (PYME.recipes.localisations.MapAstigZ attribute) (PYME.recipes.measurement.DetectPoints2D attribute) (PYME.recipes.multiview.CalibrateShifts attribute) (PYME.recipes.multiview.ExtractMultiviewChannel attribute) (PYME.recipes.multiview.FindClumps attribute) (PYME.recipes.multiview.Fold attribute) (PYME.recipes.multiview.MapAstigZ attribute) (PYME.recipes.multiview.MergeClumps attribute) (PYME.recipes.multiview.ShiftCorrect attribute) (PYME.recipes.processing.BackgroundSubtractionMovingAverage attribute) (PYME.recipes.processing.RawADUToElectronsPerSecond attribute) (PYME.recipes.processing.StatisticsByFrame attribute) (PYME.recipes.pyramid.SupertilePhysicalCoords attribute) (PYME.recipes.surface_fitting.SphericalHarmonicShell attribute) output_name_mapped (PYME.recipes.surface_fitting.SphericalHarmonicShell attribute) output_octree (PYME.recipes.pointcloud.Octree attribute) output_points (PYME.recipes.localisations.AddMeasurementsByLabel attribute) output_relative_positions (PYME.recipes.measurement.ExtractROIs attribute) output_rois (PYME.recipes.measurement.ExtractROIs attribute) output_shapes() (PYME.recipes.base.Filter method) output_surface_reconstruction (PYME.recipes.surface_fitting.FitSurfaceWithPatches attribute) output_variance (PYME.recipes.processing.DarkAndVarianceMap attribute) outputClumps (PYME.recipes.tracking.FindClumps attribute) outputColumnName (PYME.recipes.machine_learning.PointFeatureBase attribute) outputFiducials (PYME.recipes.localisations.FiducialCorrection attribute) outputImage (PYME.recipes.localisations.DensityMapping attribute) outputLocalizations (PYME.recipes.localisations.Pipelineify attribute) OutputModule (class in PYME.recipes.base) outputName (PYME.recipes.base.ArithmaticFilter attribute) (PYME.recipes.base.ExtractChannel attribute) (PYME.recipes.base.Filter attribute) (PYME.recipes.base.JoinChannels attribute) (PYME.recipes.fudges.EstimateFrameZFromStepMetadata attribute) (PYME.recipes.localisations.AutocorrelationDriftCorrection attribute) (PYME.recipes.localisations.ClusterCountVsImagingTime attribute) (PYME.recipes.localisations.DBSCANClustering attribute) (PYME.recipes.localisations.ExtractTableChannel attribute) (PYME.recipes.localisations.FiducialCorrection attribute) (PYME.recipes.localisations.IDTransientFrames attribute) (PYME.recipes.localisations.LabelsFromImage attribute) (PYME.recipes.localisations.MeasureClusters3D attribute) (PYME.recipes.localisations.MergeClumps attribute) (PYME.recipes.machine_learning.AnnotatePoints attribute) (PYME.recipes.machine_learning.PointFeaturesPairwiseDist attribute) (PYME.recipes.machine_learning.PointFeaturesVectorial attribute) (PYME.recipes.measurement.AddMetadataToMeasurements attribute) (PYME.recipes.measurement.BinnedHistogram attribute) (PYME.recipes.measurement.FitDumbells attribute) (PYME.recipes.measurement.FitPoints attribute) (PYME.recipes.measurement.Histogram attribute) (PYME.recipes.measurement.ImageCumulativeHistogram attribute) (PYME.recipes.measurement.ImageHistogram attribute) (PYME.recipes.measurement.IntensityAtPoints attribute) (PYME.recipes.measurement.MeanNeighbourDistances attribute) (PYME.recipes.measurement.Measure2D attribute) (PYME.recipes.measurement.MultifitBlobs attribute) (PYME.recipes.measurement.NearestNeighbourDistances attribute) (PYME.recipes.measurement.PairwiseDistanceHistogram attribute) (PYME.recipes.measurement.Plot attribute) (PYME.recipes.pointcloud.Ripleys attribute) (PYME.recipes.processing.FindCaWaves attribute) (PYME.recipes.processing.FlatfiledAndDarkCorrect attribute) (PYME.recipes.processing.VectorfieldNorm attribute) (PYME.recipes.processing.Watershed attribute) (PYME.recipes.processing.WavefrontDetection attribute) (PYME.recipes.processing.WavefrontVelocity attribute) (PYME.recipes.tablefilters.AggregateMeasurements attribute) (PYME.recipes.tablefilters.ConcatenateTables attribute) (PYME.recipes.tablefilters.FilterTable attribute) (PYME.recipes.tablefilters.FilterTableByIDs attribute) (PYME.recipes.tablefilters.Mapping attribute) (PYME.recipes.tablefilters.SelectTableColumns attribute) (PYME.recipes.tracking.FindClumps attribute) (PYME.recipes.tracking.LoadSpeckles attribute) outputNameP (PYME.recipes.processing.ProjectOnVector attribute) outputNameS (PYME.recipes.processing.ProjectOnVector attribute) outputNameX (PYME.recipes.processing.DirectionToMask3D attribute) (PYME.recipes.processing.Gradient2D attribute) (PYME.recipes.processing.Gradient3D attribute) (PYME.recipes.processing.OpticalFlow attribute) outputNameY (PYME.recipes.processing.DirectionToMask3D attribute) (PYME.recipes.processing.Gradient2D attribute) (PYME.recipes.processing.Gradient3D attribute) (PYME.recipes.processing.OpticalFlow attribute) outputNameZ (PYME.recipes.processing.DirectionToMask3D attribute) (PYME.recipes.processing.Gradient3D attribute) outputPhi (PYME.recipes.processing.VectorfieldAngle attribute) outputPlot (PYME.recipes.processing.ColocalisationEDT attribute) outputs (PYME.recipes.base.ModuleBase property) (PYME.recipes.recipe.Recipe property) outputs_in_namespace() (PYME.recipes.base.ModuleBase method) outputTable (PYME.recipes.processing.Colocalisation attribute) (PYME.recipes.processing.ColocalisationEDT attribute) outputTheta (PYME.recipes.processing.VectorfieldAngle attribute) outputTrackInfo (PYME.recipes.tracking.TrackFeatures attribute) outputTracks (PYME.recipes.tracking.ExtractTracks attribute) (PYME.recipes.tracking.FitFusionTraces attribute) (PYME.recipes.tracking.TrackFeatures attribute) outputX (PYME.recipes.processing.VectorfieldCurl attribute) outputY (PYME.recipes.processing.VectorfieldCurl attribute) outputZ (PYME.recipes.processing.VectorfieldCurl attribute) overlap (PYME.recipes.processing.Deconvolve attribute) overlap() (in module PYME.Analysis.Colocalisation.correlationCoeffs) Overlay (class in PYME.DSView.overlays) OverlayLayer (class in PYME.LMVis.layers.OverlayLayer) OverlayPanel (class in PYME.DSView.OverlaysPanel)

P

p_poisson() (in module PYME.Analysis.cramerRao) pa (PYME.Acquire.microscope.microscope property) pack() (PYME.contrib.lzw.BitPacker method) pack_results() (in module PYME.localization.FitFactories.fitCommon) padding (PYME.recipes.processing.Deconvolve attribute) PagingDecoder (class in PYME.contrib.lzw) PagingEncoder (class in PYME.contrib.lzw) pair_molecules() (in module PYME.Analysis.points.multiview) PairwiseDistanceHistogram (class in PYME.recipes.measurement) PanCamera() (PYME.Acquire.microscope.microscope method) PanSpool (class in PYME.Acquire.ui.HDFSpoolFrame) parameters (PYME.recipes.measurement.FitPoints attribute) ParamGroup (class in PYME.localization.MetaDataEdit) paramsToFit (PYME.recipes.tracking.FitFusionTraces attribute) parse() (in module PYME.LMVis.VisGUI) (PYME.DSView.logparser.logparser method) parse_csv_header() (in module PYME.IO.csv_flavours) parseLines() (PYME.misc.zemax.Surface method) Parser (class in PYME.util.mProfile.colorize_db_t) parseURL() (in module PYME.IO.clusterIO) partial_pyramid_depth (PYME.Analysis.distributed_pyramid.DistributedImagePyramid property) PartialPyramid (class in PYME.Analysis.distributed_pyramid) ParticleTracker (class in PYME.LMVis.Extras.particleTracking) ParticleTrackingView (class in PYME.DSView.modules.particleTracking) patch_log_verbosity() (in module PYME.util.log_verbosity) path_elem() (PYME.cluster.webdav.DAVRequestHandler method) path_elem_prev() (PYME.cluster.webdav.DAVRequestHandler method) PCA (PYME.recipes.machine_learning.PointFeatureBase attribute) PCA_components (PYME.recipes.machine_learning.PointFeatureBase attribute) pd() (PYME.Deconv.richardsonLucyMVM.MotionCompensatingRichardsonLucy method) pearson() (in module PYME.Analysis.Colocalisation.correlationCoeffs) percentile (PYME.recipes.processing.BackgroundSubtractionMovingAverage attribute) (PYME.recipes.processing.BackgroundSubtractionMovingPercentile attribute) performClassification() (in module PYME.Analysis.svmSegment) PerFrameVar (class in PYME.LMVis.Extras.perFrameVariable) persistLength (PYME.simulation.pointsets.WiglyFibreSource attribute) (PYME.simulation.pointsets.WormlikeSource attribute) Person (class in PYME.recipes.html_recipe_editor) PHASE (PYME.Acquire.stackSettings.StackSettings attribute) PhaseRampPupil (class in PYME.DSView.modules.psfGeneration) Phi (PYME.DSView.modules.blobMeasure.DataBlock property) pick_color() (PYME.LMVis.Extras.scaleBox.ScaleBoxPanel method) pickleSlice() (in module PYME.localization.FitFactories.fitCommon) pickResultsServer() (in module PYME.IO.clusterResults) piecewiseLinear() (in module PYME.Analysis.piecewise) piecewiseMap (class in PYME.Analysis.piecewiseMapping) piezoGoHome() (PYME.Acquire.stackSettings.StackSettings method) Pin() (PYME.ui.manualFoldPanel.foldingPane method) pin_bits (in module PYME.ui.autoFoldPanel) (in module PYME.ui.manualFoldPanel) pinhole_radius_nm (PYME.recipes.simulation.TheoreticalPSF attribute) PinOpen() (PYME.ui.autoFoldPanel.foldingPane method) (PYME.ui.manualFoldPanel.foldingPane method) Pipeline (class in PYME.LMVis.pipeline) pipeline_view (PYME.recipes.base.ModuleBase property) (PYME.recipes.recipe.Recipe property) pipeline_view_min (PYME.recipes.base.ModuleBase property) Pipelineify (class in PYME.recipes.localisations) PipelinePanel (class in PYME.LMVis.pipelineView) PipelineRecipeManager (class in PYME.recipes.recipeGui) pixel_index_of_points_in_image() (in module PYME.Analysis.points.coordinate_tools) pixel_to_screen_coordinates() (PYME.DSView.arrayViewPanel.ArrayViewPanel method) pixel_to_screen_coordinates3D() (PYME.DSView.arrayViewPanel.ArrayViewPanel method) pixelSize (PYME.DSView.modules.psfGeneration.PupilGenerator attribute) (PYME.IO.image.ImageStack property) pixelsize (PYME.LMVis.Extras.snapshot.SnapshotSettings attribute) pixelSize (PYME.recipes.localisations.DensityMapping attribute) pixelSizeNM (PYME.recipes.localisations.Pipelineify attribute) pkmod_onestate() (in module PYME.Analysis.BleachProfile.intensProf) play() (PYME.LMVis.Extras.animation.VideoPanel method) playback_running (PYME.DSView.modules.playback.PlayPanel property) (PYME.DSView.modules.playback.PlayZTPanel property) player (class in PYME.DSView.modules.playback) PlayEvents() (in module PYME.misc.eventSpy) PlayPanel (class in PYME.DSView.modules.playback) PlayZTPanel (class in PYME.DSView.modules.playback) pLinkCutoff (PYME.recipes.tracking.TrackFeatures attribute) Plot (class in PYME.recipes.graphing) (class in PYME.recipes.measurement) plot() (in module PYME.Analysis.graphing_filters) (PYME.Acquire.stage_leveling.StageLeveler method) (PYME.recipes.graphing.Plot method) plot_and_fit() (in module PYME.Analysis.points.qpaint) plot_fit_history() (PYME.localization.autopsf.autopsf.ZernikePSFModel method) plot_image_dist_coloc_figure() (in module PYME.Analysis.Colocalisation.edtColoc) plot_scan() (PYME.Acquire.stage_leveling.StageLeveler static method) plot_vertical() (in module PYME.recipes.recipeLayout) plotCRB() (in module PYME.Analysis.PSFGen.genCRBcurves) plotFolded() (in module PYME.LMVis.Extras.multiviewMapping) PlotOutput (class in PYME.recipes.output) PlotPanel (class in PYME.contrib.wxPlotPanel) plotProfile() (in module PYME.util.mProfile.tProfile) plotRes() (PYME.localization.Test.fitTestJig.fitTestJig method) (PYME.localization.Test.fitTestJigSCMOS.fitTestJig method) (PYME.localization.Test.fitTestJigWC.fitTestJig method) plotResSimp() (PYME.localization.Test.fitTestJigSCMOS.fitTestJig method) (PYME.localization.Test.fitTestJigWC.fitTestJig method) plotSample() (in module PYME.localization.autopsf.autopsf) PlotShiftField() (in module PYME.Analysis.points.twoColourPlot) PlotShiftField2() (in module PYME.Analysis.points.twoColourPlot) PlotShiftResiduals() (in module PYME.Analysis.points.twoColourPlot) PlotShiftResidualsS() (in module PYME.Analysis.points.twoColourPlot) plotting_context (class in PYME.recipes.graphing) Plug() (in module PYME.Acquire.ui.AnalysisSettingsUI) (in module PYME.DSView.modules.annotation) (in module PYME.DSView.modules.arrayView) (in module PYME.DSView.modules.blobFinding) (in module PYME.DSView.modules.blobMeasure) (in module PYME.DSView.modules.camera_maps) (in module PYME.DSView.modules.coloc) (in module PYME.DSView.modules.composite) (in module PYME.DSView.modules.convnet) (in module PYME.DSView.modules.cropping) (in module PYME.DSView.modules.dark_and_flatfield) (in module PYME.DSView.modules.deconvolution) (in module PYME.DSView.modules.eventView) (in module PYME.DSView.modules.fastGraphPanel) (in module PYME.DSView.modules.filtering) (in module PYME.DSView.modules.flowView) (in module PYME.DSView.modules.fourierRingCorrelation) (in module PYME.DSView.modules.gl_image_view) (in module PYME.DSView.modules.LMAnalysis) (in module PYME.DSView.modules.LMDisplay) (in module PYME.DSView.modules.metadataView) (in module PYME.DSView.modules.multithreshold) (in module PYME.DSView.modules.neuroglancer) (in module PYME.DSView.modules.object_tagging) (in module PYME.DSView.modules.particleTracking) (in module PYME.DSView.modules.playback) (in module PYME.DSView.modules.prebleachExtraction) (in module PYME.DSView.modules.profileFitting) (in module PYME.DSView.modules.profilePlotting) (in module PYME.DSView.modules.projections) (in module PYME.DSView.modules.psfExtraction) (in module PYME.DSView.modules.psfGeneration) (in module PYME.DSView.modules.pupilTools) (in module PYME.DSView.modules.recipes) (in module PYME.DSView.modules.redimension) (in module PYME.DSView.modules.segmentation) (in module PYME.DSView.modules.sheetView) (in module PYME.DSView.modules.shell) (in module PYME.DSView.modules.shiftfield_estimation) (in module PYME.DSView.modules.sparkprepare) (in module PYME.DSView.modules.splitter) (in module PYME.DSView.modules.synchronise) (in module PYME.DSView.modules.tiling) (in module PYME.DSView.modules.unmixing) (in module PYME.DSView.modules.vis3D) (in module PYME.DSView.modules.visgui) (in module PYME.DSView.modules.webview) (in module PYME.LMVis.Extras.animation) (in module PYME.LMVis.Extras.annotation) (in module PYME.LMVis.Extras.clusterAnalysis) (in module PYME.LMVis.Extras.dockedPanel) (in module PYME.LMVis.Extras.extra_layers) (in module PYME.LMVis.Extras.fiducial) (in module PYME.LMVis.Extras.flagZMotionArtifacts) (in module PYME.LMVis.Extras.fusionUtils) (in module PYME.LMVis.Extras.multiColourAnalysis) (in module PYME.LMVis.Extras.multiviewMapping) (in module PYME.LMVis.Extras.objectMeasurements) (in module PYME.LMVis.Extras.particleTracking) (in module PYME.LMVis.Extras.perFrameVariable) (in module PYME.LMVis.Extras.photophysics) (in module PYME.LMVis.Extras.pointSetGeneration) (in module PYME.LMVis.Extras.pointwiseColoc) (in module PYME.LMVis.Extras.QPobjectSegment) (in module PYME.LMVis.Extras.saved_views) (in module PYME.LMVis.Extras.scaleBox) (in module PYME.LMVis.Extras.sequentialSpecies) (in module PYME.LMVis.Extras.setBGImage) (in module PYME.LMVis.Extras.shiftmapGenerator) (in module PYME.LMVis.Extras.showShortcuts) (in module PYME.LMVis.Extras.snapshot) (in module PYME.LMVis.Extras.spherical_harmonics) (in module PYME.LMVis.Extras.subsets) (in module PYME.LMVis.Extras.surface_fitting) (in module PYME.LMVis.Extras.temperaturePlot) (in module PYME.LMVis.Extras.vibration) plug() (PYME.Acquire.htsms.rule_ui.ChainedAnalysisPanel static method) (PYME.Acquire.htsms.rule_ui.SMLMChainedAnalysisPanel static method) pNew (PYME.recipes.tracking.TrackFeatures attribute) Point (class in PYME.ui.selection) point_size (PYME.LMVis.layers.pointcloud.PointCloudRenderLayer attribute) point_spacing (PYME.simulation.pointsets.SHNucleusSource attribute) PointCloudRenderLayer (class in PYME.LMVis.layers.pointcloud) pointColour() (PYME.LMVis.visCore.VisGUICore method) pointDensityAtDistance() (in module PYME.Analysis.Colocalisation.edtColoc) PointDisplayOverlay (class in PYME.DSView.overlays) PointDisplaySettings (class in PYME.LMVis.pointSettingsPanel) (class in PYME.LMVis.view_clipping_pane) PointFeatureBase (class in PYME.recipes.machine_learning) PointFeaturesPairwiseDist (class in PYME.recipes.machine_learning) PointFeaturesVectorial (class in PYME.recipes.machine_learning) pointlHood() (PYME.Analysis.points.segmentLL.segmenter method) points() (PYME.simulation.pointsets.PointSource method) Points3DEngine (class in PYME.LMVis.layers.pointcloud) points_from_mask() (in module PYME.Analysis.points.ripleys) points_from_sdf() (in module PYME.simulation.locify) points_hit_test() (PYME.DSView.overlays.PointDisplayOverlay method) points_per_chunk (PYME.recipes.measurement.ChunkedTravelingSalesperson attribute) points_per_pixel (PYME.simulation.pointsets.ImageSource attribute) PointScanner (class in PYME.Acquire.Utils.MultiPointScanner) (class in PYME.Acquire.Utils.pointScanner) PointScanner3D (class in PYME.Acquire.Utils.pointScanner) PointSettingsPanel (class in PYME.LMVis.pointSettingsPanel) pointSize (PYME.LMVis.pointSettingsPanel.PointDisplaySettings attribute) (PYME.LMVis.view_clipping_pane.PointDisplaySettings attribute) PointSource (class in PYME.simulation.pointsets) PointSpritesEngine (class in PYME.LMVis.layers.pointcloud) PointSpriteShaderProgram (class in PYME.LMVis.shader_programs.PointSpriteShaderProgram) PointwiseColocaliser (class in PYME.LMVis.Extras.pointwiseColoc) poll_timeouts() (PYME.cluster.ruleserver.IntegerIDRule method) PopContext() (PYME.Analysis.processLogger.ContextManager method) populate() (PYME.ui.custom_traits_editors.DictChoiceStrPanel method) (PYME.ui.custom_traits_editors.DictFloatEditList method) (PYME.ui.filterPane.FilterPanel method) populate_filters() (in module PYME.reports.filters) PopulateMetadata() (PYME.Acquire.sampleInformation.SampleInfoDialog method) port (PYME.misc.sqlite_ns.NSInfo property) PositionPanel (class in PYME.Acquire.ui.positionUI) PositionSliders (class in PYME.Acquire.ui.positionUI) PositionTracker (class in PYME.Acquire.positionTracker) positivity() (in module PYME.Analysis.PSFEst.psfQuality) post_on (PYME.Acquire.htsms.rule_ui.RuleChain attribute) post_rule() (PYME.cluster.HTTPRulePusher.HTTPRulePusher method) Pow (class in PYME.recipes.base) power (PYME.recipes.base.Pow attribute) powerMod2D() (in module PYME.Analysis.Tracking.trackUtils) powerMod3D() (in module PYME.Analysis.Tracking.trackUtils) ppi (PYME.LMVis.Extras.snapshot.SnapshotSettings attribute) PrebleachExtractor (class in PYME.DSView.modules.prebleachExtraction) prefillSampleData() (in module PYME.Acquire.sampleInformation) PreflightCheck() (PYME.Acquire.protocol.Protocol method) (PYME.Acquire.protocol.TaskListProtocol method) PreflightCheckItem (class in PYME.Acquire.protocol) prep() (PYME.Deconv.dec.ClassicMappingFFTW method) (PYME.Deconv.dec.DeconvMappingBase method) Prepare() (PYME.Acquire.frameWrangler.FrameWrangler method) prepare() (PYME.Analysis.PSFEst.dec.dec_psf method) (PYME.cluster.rules.LocalisationRule method) (PYME.cluster.rules.RecipeRule method) (PYME.cluster.rules.Rule method) (PYME.Deconv.dec.dec_4pi_c method) preparePSF() (in module PYME.localization.ofind_pri) (in module PYME.localization.ofind_xcorr) (in module PYME.localization.ofind_xcorr_fw) principalAxis (PYME.DSView.modules.blobMeasure.DataBlock property) print_catalog_list() (in module PYME.misc.read_agf) print_cycles() (in module PYME.misc.findCycles) print_glass_list() (in module PYME.misc.read_agf) print_glass_report() (in module PYME.misc.read_agf) prob_predict() (in module PYME.Analysis.svmSegment) probabilities() (PYME.Analysis.svmSegment.svmClassifier method) probe_aware (PYME.recipes.multiview.FindClumps attribute) probePoint() (PYME.Analysis.points.segmentLL.segmenter method) ProcessColour (class in PYME.recipes.localisations) processFramesIndividually (PYME.recipes.base.ArithmaticFilter attribute) (PYME.recipes.base.ImageModuleBase property) (PYME.recipes.processing.DeconvolveMotionCompensating attribute) (PYME.recipes.processing.Watershed attribute) processIntensityTrace() (in module PYME.Analysis.BleachProfile.rawIntensity) processTag() (PYME.cluster.webdav.XMLDict_Parser method) procSkelFile() (in module PYME.Analysis.angleFilter) prof_callback() (PYME.util.fProfile.fProfile.ThreadProfiler method) (PYME.util.fProfile.fProfile.ThreadProfilerRegex method) profile_off() (in module PYME.util.mProfile.tProfile) (PYME.util.fProfile.fProfile.ThreadProfiler method) profile_on() (in module PYME.util.mProfile.tProfile) (PYME.util.fProfile.fProfile.ThreadProfiler method) (PYME.util.fProfile.fProfile.ThreadProfilerRegex method) profileOff() (in module PYME.util.mProfile.mProfile) (PYME.util.fProfile.fProfile.ThreadProfiler method) profileOn() (in module PYME.util.mProfile.mProfile) (PYME.util.fProfile.fProfile.ThreadProfiler method) ProfilePlotter (class in PYME.DSView.modules.profilePlotting) profiler() (in module PYME.util.mProfile.tProfile) profOff() (in module PYME.util.mProfile.p) profOn() (in module PYME.util.mProfile.p) progPanel (class in PYME.LMVis.progGraph) ProgressSelection() (PYME.LMVis.imageView.ImageViewPanel method) (PYME.LMVis.imageView2.ImageViewPanel method) project() (in module PYME.DSView.modules.projections) Project() (PYME.DSView.modules.filtering.Filterer method) Projection (class in PYME.recipes.processing) ProjectOnVector (class in PYME.recipes.processing) projectZ() (in module PYME.misc.zernike) projectZ_rays() (in module PYME.misc.zernike) propagate() (PYME.Analysis.PSFGen.fourier.FourierPropagator method) (PYME.Analysis.PSFGen.fourierHNA.FourierPropagatorClipHNA method) (PYME.Analysis.PSFGen.fourierHNA.FourierPropagatorHNA method) (PYME.Analysis.PSFGen.fourierHNA2.FourierPropagatorClipHNA method) (PYME.Analysis.PSFGen.fourierHNA2.FourierPropagatorHNA method) propagate_r() (PYME.Analysis.PSFGen.fourierHNA.FourierPropagatorHNA method) (PYME.Analysis.PSFGen.fourierHNA2.FourierPropagatorHNA method) Property (in module PYME.misc.mock_traits) Protocol (class in PYME.Acquire.protocol) protocol (PYME.Acquire.htsms.rule_ui.RuleChain attribute) protocol_version (PYME.cluster.HTTPDataServer.PYMEHTTPRequestHandler attribute) (PYME.util.webframework.JSONAPIRequestHandler attribute) ProtocolRuleFactoryListCtrl (class in PYME.Acquire.htsms.rule_ui) ProtocolRules (class in PYME.Acquire.htsms.rule_ui) ProvideStackMetadata() (PYME.Acquire.stackSettings.StackSettings method) prune_dependencies_from_namespace() (PYME.recipes.recipe.Recipe method) PseudoPointList (class in PYME.localization.ofind) (class in PYME.localization.ofind3d) (class in PYME.localization.ofind_nofilt) (class in PYME.localization.ofind_pri) (class in PYME.localization.ofind_split) (class in PYME.localization.ofind_xcorr) (class in PYME.localization.ofind_xcorr_fw) psf() (PYME.Analysis.PSFGen.fourierHNA.FourierPSF method) psf_calc() (PYME.Analysis.PSFEst.dec.dec_psf method) (PYME.Deconv.dec.ClassicMappingFFTW method) (PYME.Deconv.dec.ClassicMappingNP method) (PYME.Deconv.dec.dec_4pi method) (PYME.Deconv.dec.DeconvMappingBase method) (PYME.Deconv.dec.SpatialConvolutionMapping method) (PYME.Deconv.wiener.dec_wiener method) PSF_from_pupil_and_propagator() (in module PYME.Analysis.PSFGen.fourierHNA) (in module PYME.Analysis.PSFGen.fourierHNA2) psf_type (PYME.recipes.simulation.TheoreticalPSF attribute) PSFExporter (class in PYME.IO.dataExporter) PsfExtractor (class in PYME.DSView.modules.psfExtraction) PSFFile (class in PYME.recipes.processing) psfFilename (PYME.recipes.processing.Deconvolve attribute) PSFFitFactory (class in PYME.localization.FitFactories.InterpFitR) (class in PYME.localization.FitFactories.LatPSFFitR) (class in PYME.localization.FitFactories.PRInterpFitQR) (class in PYME.localization.FitFactories.PRInterpFitR) PSFFitResult (class in PYME.localization.FitFactories.LatPSFFitR) PSFFitResultR() (in module PYME.localization.FitFactories.InterpFitR) (in module PYME.localization.FitFactories.LatPSFFitR) (in module PYME.localization.FitFactories.MultiviewFitInterpNR) (in module PYME.localization.FitFactories.PRInterpFitQR) (in module PYME.localization.FitFactories.PRInterpFitR) (in module PYME.localization.FitFactories.SplitterFitInterpBNR) (in module PYME.localization.FitFactories.SplitterFitInterpNR) PsfFromPupil() (in module PYME.Analysis.PSFGen.fourierHNA) (in module PYME.Analysis.PSFGen.fourierHNA2) PsfFromPupilVect() (in module PYME.Analysis.PSFGen.fourierHNA) (in module PYME.Analysis.PSFGen.fourierHNA2) psfSigma (PYME.recipes.tracking.FitFusionTraces attribute) psfType (PYME.recipes.processing.Deconvolve attribute) pty_read() (PYME.Acquire.webui.ipy.IPYTermManager method) ptyproc (PYME.Acquire.webui.ipy.IPYWithClients property) Pupil (class in PYME.DSView.modules.psfGeneration) pupil (PYME.DSView.modules.psfGeneration.PupilGenerator attribute) PupilGenerator (class in PYME.DSView.modules.psfGeneration) pupils (PYME.DSView.modules.psfGeneration.PupilGenerator attribute) pupilSizeX (PYME.DSView.modules.psfGeneration.PupilGenerator attribute) PupilTools (class in PYME.DSView.modules.pupilTools) purge() (PYME.Acquire.frameWrangler.FrameWrangler method) (PYME.Analysis.tile_pyramid.TileCache method) push() (PYME.cluster.rules.Rule method) pushImages() (PYME.DSView.modules.LMAnalysis.AnalysisController method) pushImagesCluster() (PYME.DSView.modules.LMAnalysis.AnalysisController method) pushImagesDS() (PYME.DSView.modules.LMAnalysis.AnalysisController method) pushImagesHDF() (PYME.DSView.modules.LMAnalysis.AnalysisController method) pushImagesQueue() (PYME.DSView.modules.LMAnalysis.AnalysisController method) put() (PYME.IO.cluster_streaming.Stream method) (PYME.IO.cluster_streaming.Streamer method) put_file() (in module PYME.IO.clusterIO) (PYME.IO.h5File.H5File method) put_files() (in module PYME.IO.clusterIO) put_stream() (PYME.IO.cluster_streaming.Streamer method) PYME module PYME.Acquire module PYME.Acquire.acquire_client module PYME.Acquire.acquire_server module PYME.Acquire.acquiremainframe module PYME.Acquire.acquirewx module PYME.Acquire.ActionManager module PYME.Acquire.actions module PYME.Acquire.autofocus module PYME.Acquire.event_loop module PYME.Acquire.eventLog module PYME.Acquire.ExecTools module PYME.Acquire.frameWrangler module PYME.Acquire.htsms module PYME.Acquire.htsms.rule_ui module PYME.Acquire.htsms.tweeter module PYME.Acquire.microscope module PYME.Acquire.misc module PYME.Acquire.misc.tempLogger module PYME.Acquire.misc.tempLoggerDB module PYME.Acquire.misc.tempMonitor module PYME.Acquire.positionTracker module PYME.Acquire.protocol module PYME.Acquire.PYMEAcquire module PYME.Acquire.sampleInformation module PYME.Acquire.setup module PYME.Acquire.SpoolController module PYME.Acquire.stackSettings module PYME.Acquire.stage_leveling module PYME.Acquire.ui module PYME.Acquire.ui.actionUI module PYME.Acquire.ui.AnalysisSettingsUI module PYME.Acquire.ui.focus_lock_gui module PYME.Acquire.ui.HDFSpoolFrame module PYME.Acquire.ui.intensity_trace module PYME.Acquire.ui.intsliders module PYME.Acquire.ui.lasersliders module PYME.Acquire.ui.mpd_picosecond_delay_panel module PYME.Acquire.ui.multiview_select module PYME.Acquire.ui.positionUI module PYME.Acquire.ui.preflight module PYME.Acquire.ui.scanner_panel module PYME.Acquire.ui.selectCameraPanel module PYME.Acquire.ui.seqdialog module PYME.Acquire.ui.splashScreen module PYME.Acquire.ui.tile_panel module PYME.Acquire.ui.voxelSizeDialog module PYME.Acquire.Utils module PYME.Acquire.Utils.failsafe module PYME.Acquire.Utils.fastTiler module PYME.Acquire.Utils.MultiPointScanner module PYME.Acquire.Utils.pointScanner module PYME.Acquire.Utils.sarcSpacing module PYME.Acquire.Utils.strip_tiler module PYME.Acquire.Utils.tiler module PYME.Acquire.Utils.vibrationAnalysis module PYME.Acquire.webui module PYME.Acquire.webui.ipy module PYME.Acquire.xyztc module PYME.Acquire.zScanner module PYME.Analysis module PYME.Analysis.angleFilter module PYME.Analysis.annealThresh module PYME.Analysis.autoencoder_classifier module PYME.Analysis.binAvg module PYME.Analysis.BleachProfile module PYME.Analysis.BleachProfile.deMod module PYME.Analysis.BleachProfile.fitRecover module PYME.Analysis.BleachProfile.intensProf module PYME.Analysis.BleachProfile.kinModels module PYME.Analysis.BleachProfile.rawIntensity module PYME.Analysis.BleachProfile.rollins module PYME.Analysis.Colocalisation module PYME.Analysis.Colocalisation.colocScaleDep module PYME.Analysis.Colocalisation.correlationCoeffs module PYME.Analysis.Colocalisation.distColoc module PYME.Analysis.Colocalisation.edtColoc module PYME.Analysis.composite module PYME.Analysis.cramerRao module PYME.Analysis.density_filter module PYME.Analysis.deTile module PYME.Analysis.distributed_pyramid module PYME.Analysis.fiducial_matching module PYME.Analysis.gen_sCMOS_maps module PYME.Analysis.graphing_filters module PYME.Analysis.implicitFilter module PYME.Analysis.keep_pairs module PYME.Analysis.MetaData module PYME.Analysis.optic_flow module PYME.Analysis.piecewise module PYME.Analysis.piecewiseMapping module PYME.Analysis.piezo_movement_correction module PYME.Analysis.points module PYME.Analysis.points.arcfit module PYME.Analysis.points.arcfit.arcmf module PYME.Analysis.points.arcfit.setup module PYME.Analysis.points.astigmatism module PYME.Analysis.points.astigmatism.astiglookup module PYME.Analysis.points.astigmatism.astigTools module PYME.Analysis.points.astigmatism.setup module PYME.Analysis.points.cluster_morphology module PYME.Analysis.points.coordinate_tools module PYME.Analysis.points.DeClump module PYME.Analysis.points.DeClump.deClump module PYME.Analysis.points.DeClump.deClumpGUI module PYME.Analysis.points.DeClump.pyDeClump module PYME.Analysis.points.DeClump.setup module PYME.Analysis.points.DeClump.testClump module PYME.Analysis.points.DistHist module PYME.Analysis.points.DistHist.distHist module PYME.Analysis.points.DistHist.distHistThreaded module PYME.Analysis.points.DistHist.setup module PYME.Analysis.points.EdgeDB module PYME.Analysis.points.EdgeDB.edgeDB module PYME.Analysis.points.EdgeDB.edges module PYME.Analysis.points.EdgeDB.edgeTest module PYME.Analysis.points.EdgeDB.segment module PYME.Analysis.points.EdgeDB.setup module PYME.Analysis.points.features module PYME.Analysis.points.features.metal module PYME.Analysis.points.fiducials module PYME.Analysis.points.gen3DTriangs module PYME.Analysis.points.moments module PYME.Analysis.points.multiview module PYME.Analysis.points.objectMeasure module PYME.Analysis.points.qpaint module PYME.Analysis.points.QuadTree module PYME.Analysis.points.QuadTree.pointQT module PYME.Analysis.points.QuadTree.pointQTF module PYME.Analysis.points.QuadTree.QTrend module PYME.Analysis.points.QuadTree.rendQT module PYME.Analysis.points.rings module PYME.Analysis.points.ripleys module PYME.Analysis.points.segmentLL module PYME.Analysis.points.setup module PYME.Analysis.points.SoftRend module PYME.Analysis.points.SoftRend.setup module PYME.Analysis.points.SoftRend.testTetrahedra module PYME.Analysis.points.SoftRend.triRend module PYME.Analysis.points.spherical_harmonics module PYME.Analysis.points.surfit module PYME.Analysis.points.tCluster module PYME.Analysis.points.traveling_salesperson module PYME.Analysis.points.traveling_salesperson.queue_opt module PYME.Analysis.points.traveling_salesperson.sectioned_two_opt module PYME.Analysis.points.traveling_salesperson.setup module PYME.Analysis.points.traveling_salesperson.sort module PYME.Analysis.points.traveling_salesperson.two_opt module PYME.Analysis.points.traveling_salesperson.two_opt_utils module PYME.Analysis.points.twoColour module PYME.Analysis.points.twoColourPlot module PYME.Analysis.processLogger module PYME.Analysis.profile_extraction module PYME.Analysis.PSFEst module PYME.Analysis.PSFEst.dec module PYME.Analysis.PSFEst.extractImages module PYME.Analysis.PSFEst.psfQuality module PYME.Analysis.PSFGen module PYME.Analysis.PSFGen.fourier module PYME.Analysis.PSFGen.fourierHNA module PYME.Analysis.PSFGen.fourierHNA2 module PYME.Analysis.PSFGen.genCRBcurves module PYME.Analysis.PSFGen.nijboer_zernike module PYME.Analysis.PSFGen.ps_app module PYME.Analysis.PSFGen.setup module PYME.Analysis.PSFGen.test_ps_app module PYME.Analysis.setup module PYME.Analysis.splitting module PYME.Analysis.svmSegment module PYME.Analysis.thresholding module PYME.Analysis.tile_pyramid module PYME.Analysis.Tracking module PYME.Analysis.Tracking.msd module PYME.Analysis.Tracking.tracking module PYME.Analysis.Tracking.trackUtils module PYME.Analysis.widefieldify module PYME.cluster module PYME.cluster.cluster_of_one module PYME.cluster.dataserver_wsgi module PYME.cluster.distribution module PYME.cluster.HTTPDataServer module PYME.cluster.HTTPRulePusher module PYME.cluster.HTTPTaskPusher module PYME.cluster.PYMERuleNodeServer module PYME.cluster.PYMERuleServer module PYME.cluster.rulenodeserver module PYME.cluster.rules module PYME.cluster.ruleserver module PYME.cluster.status module PYME.cluster.taskWorkerHTTP module PYME.cluster.webdav module PYME.config module PYME.contrib module PYME.contrib.aniso module PYME.contrib.aniso.aniso module PYME.contrib.auiFloatBook module PYME.contrib.congrid module PYME.contrib.dispatch module PYME.contrib.dispatch.dispatcher module PYME.contrib.gohlke module PYME.contrib.gohlke.czifile module PYME.contrib.gohlke.fcsfiles module PYME.contrib.gohlke.setup module PYME.contrib.gohlke.tifffile module PYME.contrib.listctrlMixins module PYME.contrib.lzw module PYME.contrib.pad module PYME.contrib.pad.info_pad module PYME.contrib.pad.pad module PYME.contrib.setup module PYME.contrib.TextCtrlAutoComplete module PYME.contrib.wxPlotPanel module PYME.Deconv module PYME.Deconv.beadGen module PYME.Deconv.dec module PYME.Deconv.dec_test module PYME.Deconv.deconvDialogs module PYME.Deconv.decTask module PYME.Deconv.decThread module PYME.Deconv.fftwWisdom module PYME.Deconv.richardsonLucy module PYME.Deconv.richardsonLucyMV module PYME.Deconv.richardsonLucyMVM module PYME.Deconv.test_block_dec module PYME.Deconv.wiener module PYME.DSView module PYME.DSView.arrayViewPanel module PYME.DSView.displayOptions module PYME.DSView.DisplayOptionsPanel module PYME.DSView.displaySettingsPanel module PYME.DSView.dsviewer module PYME.DSView.eventLogViewer module PYME.DSView.fitInfo module PYME.DSView.htmlServe module PYME.DSView.logparser module PYME.DSView.LUT module PYME.DSView.LUT.lut module PYME.DSView.LUT.setup module PYME.DSView.modules module PYME.DSView.modules.annotation module PYME.DSView.modules.arrayView module PYME.DSView.modules.blobFinding module PYME.DSView.modules.blobMeasure module PYME.DSView.modules.camera_maps module PYME.DSView.modules.coloc module PYME.DSView.modules.composite module PYME.DSView.modules.convnet module PYME.DSView.modules.cropping module PYME.DSView.modules.dark_and_flatfield module PYME.DSView.modules.deconvolution module PYME.DSView.modules.eventView module PYME.DSView.modules.extractBlobs module

PYME.DSView.modules.fastGraphPanel module PYME.DSView.modules.filtering module PYME.DSView.modules.flowView module PYME.DSView.modules.fourierRingCorrelation module PYME.DSView.modules.gl_image_view module PYME.DSView.modules.LMAnalysis module PYME.DSView.modules.LMDisplay module PYME.DSView.modules.measure module PYME.DSView.modules.measure.filterPan module PYME.DSView.modules.metadataView module PYME.DSView.modules.multithreshold module PYME.DSView.modules.neuroglancer module PYME.DSView.modules.object_tagging module PYME.DSView.modules.particleTracking module PYME.DSView.modules.playback module PYME.DSView.modules.prebleachExtraction module PYME.DSView.modules.profileFitting module PYME.DSView.modules.profilePlotting module PYME.DSView.modules.projections module PYME.DSView.modules.psfExtraction module PYME.DSView.modules.psfGeneration module PYME.DSView.modules.pupilTools module PYME.DSView.modules.recipes module PYME.DSView.modules.redimension module PYME.DSView.modules.segmentation module PYME.DSView.modules.sheetView module PYME.DSView.modules.shell module PYME.DSView.modules.shiftfield_estimation module PYME.DSView.modules.sparkprepare module PYME.DSView.modules.splitter module PYME.DSView.modules.synchronise module PYME.DSView.modules.tiling module PYME.DSView.modules.unmixing module PYME.DSView.modules.vis3D module PYME.DSView.modules.visgui module PYME.DSView.modules.webview module PYME.DSView.OpenSequenceDialog module PYME.DSView.overlays module PYME.DSView.OverlaysPanel module PYME.DSView.scrolledImagePanel module PYME.DSView.setup module PYME.DSView.splashScreen module PYME.DSView.voxSizeDialog module PYME.IO module PYME.IO.acquisition_backends module PYME.IO.buffer_helpers module PYME.IO.buffers module PYME.IO.cluster_directory module PYME.IO.cluster_streaming module PYME.IO.clusterDuplication module PYME.IO.clusterExport module PYME.IO.clusterGlob module PYME.IO.clusterIO module PYME.IO.clusterListing module PYME.IO.clusterResults module PYME.IO.clusterUpload module PYME.IO.compatibility module PYME.IO.countdir module PYME.IO.countdir.countdir module PYME.IO.countdir.setup module PYME.IO.csv_flavours module PYME.IO.dataExporter module PYME.IO.DataSources module PYME.IO.DataSources.AlignDataSource module PYME.IO.DataSources.ArrayDataSource module PYME.IO.DataSources.BaseDataSource module PYME.IO.DataSources.BGSDataSource module PYME.IO.DataSources.BioformatsDataSource module PYME.IO.DataSources.BufferedDataSource module PYME.IO.DataSources.ClusterPZFDataSource module PYME.IO.DataSources.ConcatenatedDataSource module PYME.IO.DataSources.CropDataSource module PYME.IO.DataSources.DcimgDataSource module PYME.IO.DataSources.ElectronsPerSecondDataSource module PYME.IO.DataSources.FlatFieldDataSource module PYME.IO.DataSources.HDFDataSource module PYME.IO.DataSources.HTTPDataSource module PYME.IO.DataSources.ImageSeriesDataSource module PYME.IO.DataSources.MultiviewDataSource module PYME.IO.DataSources.OBFDataSource module PYME.IO.DataSources.RandomDataSource module PYME.IO.DataSources.SupertileDatasource module PYME.IO.DataSources.TiffDataSource module PYME.IO.DataSources.TQDataSource module PYME.IO.DataSources.UnsplitDataSource module PYME.IO.dataWrap module PYME.IO.dcimg module PYME.IO.events module PYME.IO.FileUtils module PYME.IO.FileUtils.compHdf module PYME.IO.FileUtils.fileID module PYME.IO.FileUtils.fnlGen module PYME.IO.FileUtils.freeSpace module PYME.IO.FileUtils.h5ExFrames module PYME.IO.FileUtils.h5rFormatDef module PYME.IO.FileUtils.h5rToTxt module PYME.IO.FileUtils.h5ToTiffSeries module PYME.IO.FileUtils.IJLut module PYME.IO.FileUtils.nameUtils module PYME.IO.FileUtils.obf_support module PYME.IO.FileUtils.ply module PYME.IO.FileUtils.RawToHdf5 module PYME.IO.FileUtils.readSpeckle module PYME.IO.FileUtils.readTiff module PYME.IO.FileUtils.saveTiffStack module PYME.IO.FileUtils.setup module PYME.IO.FileUtils.SPAD module PYME.IO.FileUtils.stl module PYME.IO.FileUtils.thumbnailDatabase module PYME.IO.FileUtils.TiffSeqToHdf5 module PYME.IO.h5File module PYME.IO.h5rFile module PYME.IO.HDFSpooler module PYME.IO.HTTPSpooler module PYME.IO.HTTPSpooler_v2 module PYME.IO.image module PYME.IO.load_psf module PYME.IO.MetaDataHandler module PYME.IO.pyme_h5ls module PYME.IO.PZFFormat module PYME.IO.QueueSpooler module PYME.IO.ragged module PYME.IO.rgb_image module PYME.IO.setup module PYME.IO.Spooler module PYME.IO.tabular module PYME.IO.testClusterSpooling module PYME.IO.unifiedIO module PYME.LMVis module PYME.LMVis.colourFilterGUI module PYME.LMVis.colourPanel module PYME.LMVis.displayPane module PYME.LMVis.dyeRatios module PYME.LMVis.Extras module PYME.LMVis.Extras.animation module PYME.LMVis.Extras.annotation module PYME.LMVis.Extras.clusterAnalysis module PYME.LMVis.Extras.dockedPanel module PYME.LMVis.Extras.extra_layers module PYME.LMVis.Extras.fiducial module PYME.LMVis.Extras.flagZMotionArtifacts module PYME.LMVis.Extras.fusionUtils module PYME.LMVis.Extras.multiColourAnalysis module PYME.LMVis.Extras.multiviewMapping module PYME.LMVis.Extras.objectMeasurements module PYME.LMVis.Extras.particleTracking module PYME.LMVis.Extras.perFrameVariable module PYME.LMVis.Extras.photophysics module PYME.LMVis.Extras.pointSetGeneration module PYME.LMVis.Extras.pointwiseColoc module PYME.LMVis.Extras.QPobjectSegment module PYME.LMVis.Extras.saved_views module PYME.LMVis.Extras.scaleBox module PYME.LMVis.Extras.sequentialSpecies module PYME.LMVis.Extras.setBGImage module PYME.LMVis.Extras.shiftmapGenerator module PYME.LMVis.Extras.showShortcuts module PYME.LMVis.Extras.snapshot module PYME.LMVis.Extras.spherical_harmonics module PYME.LMVis.Extras.subsets module PYME.LMVis.Extras.surface_fitting module PYME.LMVis.Extras.temperaturePlot module PYME.LMVis.Extras.vibration module PYME.LMVis.genImageDialog module PYME.LMVis.gl_offScreenHandler module PYME.LMVis.gl_render3D_shaders module PYME.LMVis.imageView module PYME.LMVis.imageView2 module PYME.LMVis.importTextDialog module PYME.LMVis.layer_panel module PYME.LMVis.layers module PYME.LMVis.layers.AxesOverlayLayer module PYME.LMVis.layers.base module PYME.LMVis.layers.image_layer module PYME.LMVis.layers.layer_defaults module PYME.LMVis.layers.LUTOverlayLayer module PYME.LMVis.layers.mesh module PYME.LMVis.layers.octree module PYME.LMVis.layers.OverlayLayer module PYME.LMVis.layers.pointcloud module PYME.LMVis.layers.quiver module PYME.LMVis.layers.ScaleBarOverlayLayer module PYME.LMVis.layers.ScaleBoxOverlayLayer module PYME.LMVis.layers.SelectionOverlayLayer module PYME.LMVis.layers.text module PYME.LMVis.layers.tracks module PYME.LMVis.objectDarkMeasure module PYME.LMVis.pipeline module PYME.LMVis.pipelineView module PYME.LMVis.pointSettingsPanel module PYME.LMVis.progGraph module PYME.LMVis.quadTreeSettings module PYME.LMVis.renderers module PYME.LMVis.rendGauss module PYME.LMVis.setup module PYME.LMVis.setup_exe module PYME.LMVis.shader_programs module PYME.LMVis.shader_programs.DefaultShaderProgram module PYME.LMVis.shader_programs.GLProgram module PYME.LMVis.shader_programs.GouraudShaderProgram module PYME.LMVis.shader_programs.oit_compositor module PYME.LMVis.shader_programs.PointSpriteShaderProgram module PYME.LMVis.shader_programs.shader_loader module PYME.LMVis.shader_programs.shader_program module PYME.LMVis.shader_programs.ShaderProgramFactory module PYME.LMVis.shader_programs.TesselShaderProgram module PYME.LMVis.shader_programs.WireFrameShaderProgram module PYME.LMVis.statusLog module PYME.LMVis.tests module PYME.LMVis.triBlobs module PYME.LMVis.view_clipping_pane module PYME.LMVis.views module PYME.LMVis.visCore module PYME.LMVis.VisGUI module PYME.LMVis.visHelpers module PYME.LMVis.visHelpersMin module PYME.localization module PYME.localization.autopsf module PYME.localization.autopsf.autopsf module PYME.localization.autopsf.roifit module PYME.localization.cInterp module PYME.localization.cInterp.cInterp module PYME.localization.cInterp.setup module PYME.localization.cModels module PYME.localization.cModels.gauss_app module PYME.localization.cModels.setup module PYME.localization.FitFactories module PYME.localization.FitFactories.AstigGaussFitFR module PYME.localization.FitFactories.AstigGaussGPUFitFR module PYME.localization.FitFactories.BeadConvolvedAstigGaussFit module PYME.localization.FitFactories.ChecksumFR module PYME.localization.FitFactories.ChecksumGPUFR module PYME.localization.FitFactories.ChecksumMultifitSR module PYME.localization.FitFactories.ConfocCOIR module PYME.localization.FitFactories.Dumbell3DFitR module PYME.localization.FitFactories.DumbellFitR module PYME.localization.FitFactories.FFBase module PYME.localization.FitFactories.fitCommon module PYME.localization.FitFactories.Gauss3DFitR module PYME.localization.FitFactories.GaussFitConstrR module PYME.localization.FitFactories.GaussMultifitLinesR module PYME.localization.FitFactories.GaussMultifitR module PYME.localization.FitFactories.GaussMultifitSR module PYME.localization.FitFactories.InterpFitR module PYME.localization.FitFactories.InterpFitWFR module PYME.localization.FitFactories.Interpolators module PYME.localization.FitFactories.Interpolators.baseInterpolator module PYME.localization.FitFactories.Interpolators.CSInterpolator module PYME.localization.FitFactories.Interpolators.CubeSInterpolatorP module PYME.localization.FitFactories.Interpolators.CubicSplineInterpolator module PYME.localization.FitFactories.Interpolators.LinearInterpolator module PYME.localization.FitFactories.Interpolators.LinearPInterpolatorP module PYME.localization.FitFactories.LatFitCOIR module PYME.localization.FitFactories.LatGaussFitFR module PYME.localization.FitFactories.LatObjFindFR module PYME.localization.FitFactories.LatPSFFitR module PYME.localization.FitFactories.MultiviewFitInterpNR module PYME.localization.FitFactories.PRInterpFitQR module PYME.localization.FitFactories.PRInterpFitR module PYME.localization.FitFactories.ROIExtractNR module PYME.localization.FitFactories.SpecGaussFitFR module PYME.localization.FitFactories.SplitterFitCOIR module PYME.localization.FitFactories.SplitterFitFNR module PYME.localization.FitFactories.SplitterFitFusionR module PYME.localization.FitFactories.SplitterFitInterpBNR module PYME.localization.FitFactories.SplitterFitInterpNR module PYME.localization.FitFactories.SplitterFitScavNR module PYME.localization.FitFactories.SplitterMultifitSR module PYME.localization.FitFactories.SplitterObjFindR module PYME.localization.FitFactories.SplitterROIExtractNR module PYME.localization.FitFactories.SplitterShiftEstFR module PYME.localization.FitFactories.zEstimators module PYME.localization.FitFactories.zEstimators.astigEstimator module PYME.localization.FitFactories.zEstimators.biplaneEstimator module PYME.localization.FitFactories.zEstimators.genericDualEstimator module PYME.localization.FitFactories.zEstimators.genericEstimator module PYME.localization.FitFactories.zEstimators.priEstimator module PYME.localization.lev_gfit module PYME.localization.lev_gfit.setup module PYME.localization.MetaDataEdit module PYME.localization.ofind module PYME.localization.ofind3d module PYME.localization.ofind_nofilt module PYME.localization.ofind_pri module PYME.localization.ofind_split module PYME.localization.ofind_xcorr module PYME.localization.ofind_xcorr_fw module PYME.localization.remFitBuf module PYME.localization.setup module PYME.localization.splitting module PYME.localization.Test module PYME.localization.Test.fitTestJig module PYME.localization.Test.fitTestJigSCMOS module PYME.localization.Test.fitTestJigWC module PYME.localization.twist module PYME.misc module PYME.misc.aligned_array module PYME.misc.aniso module PYME.misc.big_sur_fix module PYME.misc.check_for_updates module PYME.misc.colormaps module PYME.misc.colorsys module PYME.misc.computerName module PYME.misc.coverslipGeometries module PYME.misc.cython_numpy_monkey module PYME.misc.depGraph module PYME.misc.dirSize module PYME.misc.diskCleanup module PYME.misc.django_widgets module PYME.misc.djangoRecarray module PYME.misc.editgrid module PYME.misc.eventSpy module PYME.misc.exceptions module PYME.misc.facsPlot module PYME.misc.fbpIcons module PYME.misc.fftw_compat module PYME.misc.findCycles module PYME.misc.fortran_interrupt_defeat module PYME.misc.glassModel module PYME.misc.hash32 module PYME.misc.hillcurve module PYME.misc.hybrid_ns module PYME.misc.kdFit module PYME.misc.locate module PYME.misc.memmap module PYME.misc.memUsage module PYME.misc.mock_ctypes module PYME.misc.mock_traits module PYME.misc.mock_traitsui module PYME.misc.pyme_zeroconf module PYME.misc.pyro_tracebacks module PYME.misc.read_agf module PYME.misc.sffake module PYME.misc.snells module PYME.misc.sqlite_ns module PYME.misc.sqlitendarray module PYME.misc.taskDef module PYME.misc.tempDB module PYME.misc.TiffImagePlugin module PYME.misc.TiSettings module PYME.misc.VolProj module PYME.misc.wxThread module PYME.misc.zemax module PYME.misc.zernike module PYME.recipes module PYME.recipes.acquisition module PYME.recipes.bakeshop module PYME.recipes.base module PYME.recipes.batchProcess module PYME.recipes.filters module PYME.recipes.fudges module PYME.recipes.graphing module PYME.recipes.html_recipe_editor module PYME.recipes.localisations module PYME.recipes.machine_learning module PYME.recipes.measurement module PYME.recipes.modules module PYME.recipes.multiview module PYME.recipes.output module PYME.recipes.pointcloud module PYME.recipes.processing module PYME.recipes.pyramid module PYME.recipes.recipe module PYME.recipes.recipeGui module PYME.recipes.recipeLayout module PYME.recipes.runRecipe module PYME.recipes.setup module PYME.recipes.simulation module PYME.recipes.skfilters module PYME.recipes.surface_fitting module PYME.recipes.tablefilters module PYME.recipes.tracking module PYME.recipes.traits module PYME.recipes.vertical_recipe_display module PYME.reports module PYME.reports.filters module PYME.resources module PYME.resources.setup module PYME.setup module PYME.setup_exe module PYME.simulation module PYME.simulation.locify module PYME.simulation.pointsets module PYME.simulation.wormlike module PYME.simulation.wormlike2 module PYME.simulation.wormlike3 module PYME.simulation.wormlike_curled module PYME.tileviewer module PYME.tileviewer.tileviewer module PYME.ui module PYME.ui.about_dlg module PYME.ui.AUIFrame module PYME.ui.autoFoldPanel module PYME.ui.crop_dialog module PYME.ui.custom_traits_editors module PYME.ui.editFilterDialog module PYME.ui.editList module PYME.ui.fastGraph module PYME.ui.filterPane module PYME.ui.histLimits module PYME.ui.layerFoldPanel module PYME.ui.manualFoldPanel module PYME.ui.MetadataTree module PYME.ui.mytimer module PYME.ui.progress module PYME.ui.recArrayView module PYME.ui.selection module PYME.ui.wx_compat module PYME.update_version module PYME.util module PYME.util.authenticate module PYME.util.execfile module PYME.util.fProfile module PYME.util.fProfile.convertProfile module PYME.util.fProfile.fProfile module PYME.util.fProfile.viewProfile module PYME.util.install_dependencies module PYME.util.log_verbosity module PYME.util.mProfile module PYME.util.mProfile.colorize_db_t module PYME.util.mProfile.mProfile module PYME.util.mProfile.p module PYME.util.mProfile.tProfile module PYME.util.pymelauncher module PYME.util.shmarray module PYME.util.shmarray.shmarray module PYME.util.shmarray.shmTest module PYME.util.webframework module PYME.version module PYME.warnings module PYMEAcquireServer (class in PYME.Acquire.acquire_server) PYMEDeprecationWarning PYMEHTTPRequestHandler (class in PYME.cluster.HTTPDataServer) PYMEMainFrame (class in PYME.Acquire.acquiremainframe) (class in PYME.Acquire.acquirewx) pzf_index (PYME.IO.DataSources.HDFDataSource.DataSource property) (PYME.IO.h5File.H5File property) PZFCompression (PYME.IO.h5File.H5File attribute) PZFTileCache (class in PYME.Analysis.tile_pyramid) PZFTileIO (class in PYME.Analysis.tile_pyramid)

Q

qpaint1mod() (in module PYME.Analysis.points.qpaint) qpaint2mod() (in module PYME.Analysis.points.qpaint) QPObjectSegmenter (class in PYME.LMVis.Extras.QPobjectSegment) qsToRecarray() (in module PYME.misc.djangoRecarray) qtBranchNode (class in PYME.Analysis.points.QuadTree.pointQT) (class in PYME.Analysis.points.QuadTree.pointQTF) qtLeafNode (class in PYME.Analysis.points.QuadTree.pointQT) (class in PYME.Analysis.points.QuadTree.pointQTF) qtNode (class in PYME.Analysis.points.QuadTree.pointQT) (class in PYME.Analysis.points.QuadTree.pointQTF) qtRec (class in PYME.Analysis.points.QuadTree.pointQT) (class in PYME.Analysis.points.QuadTree.pointQTF) QTRendererNode (class in PYME.Analysis.points.QuadTree.QTrend) qtRoot (class in PYME.Analysis.points.QuadTree.pointQT) (class in PYME.Analysis.points.QuadTree.pointQTF) quad_rot_surf_misfit() (in module PYME.Analysis.points.surfit)

quad_surf_mf() (in module PYME.Analysis.points.arcfit.arcmf) quad_surf_mf_fpos() (in module PYME.Analysis.points.arcfit.arcmf) QuadTreeRenderer (class in PYME.LMVis.renderers) QuadTreeSettings (class in PYME.LMVis.quadTreeSettings) QuadTreeSettingsPanel (class in PYME.LMVis.quadTreeSettings) queue_action() (PYME.Acquire.ActionManager.ActionManagerWebWrapper method) queue_actions() (PYME.Acquire.ActionManager.ActionManager method) (PYME.Acquire.ActionManager.ActionManagerWebWrapper method) queue_base_tile_update() (PYME.Analysis.distributed_pyramid.PartialPyramid method) queue_two_opt() (PYME.Analysis.points.traveling_salesperson.queue_opt.TSPQueue method) QueueAcquisitions (class in PYME.recipes.acquisition) QueueAction() (PYME.Acquire.ActionManager.ActionManager method) QueueEventLogger (class in PYME.IO.events) QueueMDHandler (class in PYME.IO.MetaDataHandler) QuiverEngine (class in PYME.LMVis.layers.quiver) QuiverRenderLayer (class in PYME.LMVis.layers.quiver)

R

R (PYME.DSView.modules.blobMeasure.DataBlock property) r (PYME.DSView.modules.blobMeasure.DataBlock property) r0 (PYME.recipes.tracking.TrackFeatures attribute) r_bin_spacing (PYME.recipes.surface_fitting.SHShellRadiusDensityEstimate attribute) r_sph_harm() (in module PYME.Analysis.points.spherical_harmonics) radial_analysis_tabular() (in module PYME.Analysis.points.rings) radial_distance_to_shell() (PYME.Analysis.points.spherical_harmonics.ScaledShell method) radialBinWidth (PYME.recipes.machine_learning.PointFeaturesVectorial attribute) RadialDistN() (PYME.DSView.modules.blobMeasure.BlobObject method) radialDistN() (PYME.DSView.modules.blobMeasure.BlobObject method) radii (PYME.recipes.measurement.IntensityAtPoints attribute) radius (PYME.recipes.processing.BinaryDilation attribute) (PYME.recipes.processing.BinaryErosion attribute) (PYME.recipes.processing.BinaryFillHoles attribute) (PYME.recipes.processing.GreyDilation attribute) (PYME.recipes.processing.GreyErosion attribute) (PYME.recipes.processing.WhiteTophat attribute) radius_offset (PYME.recipes.multiview.FindClumps attribute) radius_scale (PYME.recipes.multiview.FindClumps attribute) RaggedBase (class in PYME.IO.ragged) RaggedCache (class in PYME.IO.ragged) RaggedJSON (class in PYME.IO.ragged) RaggedVLArray (class in PYME.IO.ragged) rand() (in module PYME.Analysis.Colocalisation.colocScaleDep) (in module PYME.simulation.locify) RandomPoints (class in PYME.recipes.simulation) RandomSelectionFilter (class in PYME.IO.tabular) randomSelectionFilter() (in module PYME.IO.tabular) RandomSource (class in PYME.IO.tabular) randomSource() (in module PYME.IO.tabular) RandomSubset (class in PYME.recipes.tablefilters) RangeParam (class in PYME.localization.MetaDataEdit) rasterize() (PYME.DSView.modules.annotation.AnnotationList method) Rater (class in PYME.cluster.rulenodeserver) ratios_from_metadata (PYME.recipes.localisations.ProcessColour attribute) RawADUToElectronsPerSecond (class in PYME.recipes.processing) read() (in module PYME.IO.unifiedIO) (PYME.Acquire.webui.ipy.TTYDummy method) (PYME.misc.TiSettings.TiSettings method) read3DTiff() (in module PYME.IO.FileUtils.readTiff) read_bead_data() (in module PYME.Analysis.points.twoColour) read_cached_zar() (in module PYME.misc.zemax) read_cat_from_lines() (in module PYME.misc.read_agf) read_cat_from_string() (in module PYME.misc.read_agf) read_file() (PYME.LMVis.shader_programs.shader_loader.ShaderLoader method) read_file_with_path() (PYME.LMVis.shader_programs.shader_loader.ShaderLoader method) read_glasscat() (in module PYME.misc.read_agf) read_h5f_cols() (in module PYME.Analysis.points.twoColour) read_shader() (in module PYME.LMVis.shader_programs.shader_program) readbytes() (in module PYME.contrib.lzw) readline() (PYME.Acquire.webui.ipy.TTYDummy method) readSpeckles() (in module PYME.IO.FileUtils.readSpeckle) readZar() (in module PYME.misc.zemax) rebin() (in module PYME.Analysis.Colocalisation.distColoc) Rebuild() (PYME.LMVis.pipeline.Pipeline method) rebuild() (PYME.ui.MetadataTree.MetadataPanel method) recArrayInput() (in module PYME.IO.tabular) RecArraySource (class in PYME.IO.tabular) receiver() (in module PYME.contrib.dispatch.dispatcher) Recipe (class in PYME.recipes.recipe) RecipeDisplayPanel (class in PYME.recipes.vertical_recipe_display) RecipeError RecipeExecutionError RecipeManager (class in PYME.recipes.recipeGui) RecipeModuleNotFoundError RecipePlotPanel (class in PYME.recipes.recipeGui) RecipePlugin (class in PYME.DSView.modules.recipes) RecipePusher (class in PYME.cluster.HTTPRulePusher) (class in PYME.cluster.HTTPTaskPusher) RecipeRule (class in PYME.cluster.rules) RecipeRuleFactory (class in PYME.cluster.rules) RecipeTaskError (class in PYME.cluster.taskWorkerHTTP) RecipeView (class in PYME.recipes.recipeGui) recolor() (in module PYME.Analysis.BleachProfile.intensProf) recommendedVariables (PYME.LMVis.importTextDialog.ColumnMappingDialog attribute) reconstruct_pipeline_from_image() (PYME.LMVis.VisGUI.VisGUIFrame method) reconstruct_pipeline_from_image_file() (PYME.LMVis.VisGUI.VisGUIFrame method) reconstruct_pipeline_from_open_image() (PYME.LMVis.VisGUI.VisGUIFrame method) reconstruct_quad_surf() (in module PYME.Analysis.points.surfit) reconstruct_quad_surf_region_cropped() (in module PYME.Analysis.points.surfit) reconstruct_quad_surfaces() (in module PYME.Analysis.points.surfit) reconstruct_quad_surfaces_P() (in module PYME.Analysis.points.surfit) reconstruct_quad_surfaces_P_region_cropped() (in module PYME.Analysis.points.surfit) reconstruct_quad_surfaces_Pr() (in module PYME.Analysis.points.surfit) reconstruct_quad_surfaces_Pr_region_cropped() (in module PYME.Analysis.points.surfit) reconstruct_shell() (in module PYME.Analysis.points.spherical_harmonics) reconstruction_point_spacing (PYME.recipes.surface_fitting.FitSurfaceWithPatches attribute) reconstruction_radius (PYME.recipes.surface_fitting.FitSurfaceWithPatches attribute) record_pyme_version() (PYME.IO.MetaDataHandler.MDHandlerBase method) recreate() (PYME.IO.MetaDataHandler.CachingMDHandler class method) (PYME.misc.eventSpy.eventInfo method) recvMember() (PYME.cluster.webdav.DirCollection method) (PYME.cluster.webdav.TempDirCollection method) Red() (in module PYME.misc.colormaps) Redimension (class in PYME.recipes.base) redimension() (in module PYME.DSView.modules.redimension) RedimensionDialog (class in PYME.DSView.modules.redimension) Redraw() (PYME.DSView.arrayViewPanel.ArrayViewPanel method) reduce_catalog() (in module PYME.misc.read_agf) reducePhi (PYME.recipes.machine_learning.PointFeaturesVectorial attribute) reduceTheta (PYME.recipes.machine_learning.PointFeaturesVectorial attribute) refill() (PYME.LMVis.Extras.animation.VideoPanel method) refr() (PYME.ui.fastGraph.SpecGraphPanel method) refract (PYME.misc.zemax.DefaultGlass attribute) RefrData() (PYME.DSView.displaySettingsPanel.dispSettingsPanel method) (PYME.DSView.displaySettingsPanel.dispSettingsPanel2 method) refresh() (PYME.Acquire.ui.focus_lock_gui.FocusLockPanel method) (PYME.LMVis.colourPanel.colourPanel method) refresh_analysis() (PYME.DSView.modules.LMAnalysis.LMAnalyser2 method) refresh_canvas() (PYME.LMVis.Extras.scaleBox.ScaleBoxPanel method) refresh_choices() (PYME.simulation.pointsets.ImageSource method) (PYME.simulation.pointsets.PointSource method) refresh_settings() (PYME.IO.buffers.backgroundBufferM method) refresh_warpdrive() (PYME.localization.FitFactories.AstigGaussGPUFitFR.GaussianFitFactory method) (PYME.localization.FitFactories.ChecksumGPUFR.ChecksumFitFactory method) RefreshHists() (PYME.DSView.DisplayOptionsPanel.OptionsPanel method) RefreshRows() (PYME.contrib.listctrlMixins.ListRowHighlighter method) RefreshScrollbars() (PYME.DSView.scrolledImagePanel.ScrolledImagePanel method) RefreshView() (PYME.LMVis.visCore.VisGUICore method) reg_of() (in module PYME.Analysis.optic_flow) RegenFilter() (PYME.LMVis.visCore.VisGUICore method) RegenSizer() (PYME.ui.autoFoldPanel.foldPanel method) (PYME.ui.manualFoldPanel.foldPanel method) register() (PYME.cluster.rules.RuleGroupWatcher method) (PYME.misc.hybrid_ns.HybridNS method) (PYME.misc.pyme_zeroconf.ZeroConfNS method) (PYME.misc.sqlite_ns.SQLiteNS method) register_camera() (PYME.Acquire.microscope.microscope method) register_cmap() (PYME.misc.colormaps.CMapDict method) register_endpoint() (in module PYME.util.webframework) register_file() (PYME.IO.cluster_directory.DirectoryInfoManager method) register_legacy_module() (in module PYME.recipes.base) register_module() (in module PYME.recipes.base) register_piezo() (PYME.Acquire.microscope.microscope method) register_service() (PYME.misc.hybrid_ns.HybridNS method) (PYME.misc.pyme_zeroconf.ZeroConfNS method) (PYME.misc.sqlite_ns.SQLiteNS method) registerChangeListener() (PYME.Acquire.microscope.StateManager method) registerHandler() (PYME.Acquire.microscope.StateManager method) regularisationLambda (PYME.recipes.processing.Deconvolve attribute) regularizationLambda (PYME.recipes.processing.OpticalFlow attribute) reject_key (PYME.recipes.measurement.IdentifyOverlappingROIs attribute) rel_path_as_posix() (in module PYME.IO.FileUtils.nameUtils) rel_tolerance (PYME.recipes.base.IsClose attribute) release() (PYME.IO.DataSources.AlignDataSource.DataSource method) (PYME.IO.DataSources.BGSDataSource.XTZCBackgroundSource method) (PYME.IO.DataSources.BioformatsDataSource.DataSource method) (PYME.IO.DataSources.BufferedDataSource.DataSource method) (PYME.IO.DataSources.ConcatenatedDataSource.DataSource method) (PYME.IO.DataSources.CropDataSource.DataSource method) (PYME.IO.DataSources.DcimgDataSource.DataSource method) (PYME.IO.DataSources.FlatFieldDataSource.DataSource method) (PYME.IO.DataSources.HDFDataSource.DataSource method) (PYME.IO.DataSources.ImageSeriesDataSource.DataSource method) (PYME.IO.DataSources.MultiviewDataSource.DataSource method) (PYME.IO.DataSources.OBFDataSource.DataSource method) (PYME.IO.DataSources.SupertileDatasource.SupertileDataSource method) (PYME.IO.DataSources.TiffDataSource.DataSource method) (PYME.IO.DataSources.UnsplitDataSource.DataSource method) release_rule_tasks() (PYME.cluster.ruleserver.RuleServer method) release_VM() (in module PYME.IO.DataSources.BioformatsDataSource) reloadData() (PYME.IO.DataSources.AlignDataSource.DataSource method) (PYME.IO.DataSources.BGSDataSource.XTZCBackgroundSource method) (PYME.IO.DataSources.BGSDataSource.XYZTCBgsSource method) (PYME.IO.DataSources.BioformatsDataSource.DataSource method) (PYME.IO.DataSources.BufferedDataSource.DataSource method) (PYME.IO.DataSources.ConcatenatedDataSource.DataSource method) (PYME.IO.DataSources.CropDataSource.DataSource method) (PYME.IO.DataSources.DcimgDataSource.DataSource method) (PYME.IO.DataSources.HDFDataSource.DataSource method) (PYME.IO.DataSources.ImageSeriesDataSource.DataSource method) (PYME.IO.DataSources.MultiviewDataSource.DataSource method) (PYME.IO.DataSources.OBFDataSource.DataSource method) (PYME.IO.DataSources.SupertileDatasource.SupertileDataSource method) (PYME.IO.DataSources.TiffDataSource.DataSource method) (PYME.IO.DataSources.UnsplitDataSource.DataSource method) remap_data_2d() (in module PYME.Analysis.composite) remap_splitter_coords() (in module PYME.localization.splitting) remap_splitter_coords_() (in module PYME.localization.splitting) remesh (PYME.recipes.surface_fitting.DelaunayMarchingTetrahedra attribute) (PYME.recipes.surface_fitting.DualMarchingCubes attribute) (PYME.recipes.surface_fitting.Isosurface attribute) (PYME.recipes.surface_fitting.NthPointIsosurface attribute) remove() (PYME.Analysis.tile_pyramid.TileCache method) remove_inactive_services() (PYME.misc.pyme_zeroconf.ZeroConfNS method) (PYME.misc.sqlite_ns.SQLiteNS method) remove_service() (PYME.misc.pyme_zeroconf.ZCListener method) removeFrame() (PYME.IO.buffers.bgFrameBuffer method) (PYME.IO.buffers.bgFrameBufferC method) (PYME.IO.DataSources.BGSDataSource.bgFrameBuffer method) removeInternalFaces() (in module PYME.Analysis.points.gen3DTriangs) rend() (in module PYME.Analysis.points.surfit) rend_density_estimate() (in module PYME.LMVis.visHelpers) render() (PYME.DSView.modules.annotation.AnnotateBase method) (PYME.LMVis.Extras.annotation.AnnotationOverlayLayer method) (PYME.LMVis.layers.AxesOverlayLayer.AxesOverlayLayer method) (PYME.LMVis.layers.base.BaseEngine method) (PYME.LMVis.layers.base.BaseLayer method) (PYME.LMVis.layers.base.EngineLayer method) (PYME.LMVis.layers.image_layer.ImageEngine method) (PYME.LMVis.layers.LUTOverlayLayer.LUTOverlayLayer method) (PYME.LMVis.layers.mesh.FlatFaceEngine method) (PYME.LMVis.layers.mesh.OITShadedFaceEngine method) (PYME.LMVis.layers.mesh.ShadedFaceEngine method) (PYME.LMVis.layers.mesh.TesselEngine method) (PYME.LMVis.layers.mesh.WireframeEngine method) (PYME.LMVis.layers.OverlayLayer.OverlayLayer method) (PYME.LMVis.layers.pointcloud.Points3DEngine method) (PYME.LMVis.layers.quiver.QuiverEngine method) (PYME.LMVis.layers.ScaleBarOverlayLayer.ScaleBarOverlayLayer method) (PYME.LMVis.layers.ScaleBoxOverlayLayer.ScaleBoxOverlayLayer method) (PYME.LMVis.layers.SelectionOverlayLayer.SelectionOverlayLayer method) (PYME.LMVis.layers.text.Text method) (PYME.LMVis.layers.tracks.Track3DEngine method) renderFit() (PYME.localization.FitFactories.Gauss3DFitR.GaussFitResult method) (PYME.localization.FitFactories.LatPSFFitR.PSFFitResult method) renderingModule (PYME.recipes.localisations.DensityMapping attribute) renderTetrahedra() (in module PYME.Analysis.points.gen3DTriangs) RenderTetrahedra() (in module PYME.Analysis.points.SoftRend.triRend) rendGauss() (in module PYME.LMVis.rendGauss) (in module PYME.LMVis.visHelpers) rendGauss3D() (in module PYME.LMVis.visHelpers) rendGaussNested() (in module PYME.LMVis.rendGauss) rendGaussNestedPS() (in module PYME.LMVis.rendGauss) rendGaussNestedXYCorr() (in module PYME.LMVis.rendGauss) rendGaussP() (in module PYME.LMVis.rendGauss) rendGaussProd() (in module PYME.LMVis.visHelpers) rendHist() (in module PYME.LMVis.rendGauss) (in module PYME.LMVis.visHelpers) (in module PYME.LMVis.visHelpersMin) rendHist3D() (in module PYME.LMVis.visHelpers) (in module PYME.LMVis.visHelpersMin) rendHistF() (in module PYME.LMVis.rendGauss)

rendJitTet() (in module PYME.LMVis.visHelpers) (in module PYME.LMVis.visHelpersMin) rendJitTri() (in module PYME.LMVis.visHelpers) (in module PYME.LMVis.visHelpersMin) rendJitTri2() (in module PYME.LMVis.visHelpers) rendJitTriang() (in module PYME.LMVis.visHelpers) (in module PYME.LMVis.visHelpersMin) rendJitTriang2() (in module PYME.LMVis.visHelpers) rendJTet() (in module PYME.LMVis.visHelpers) rendP() (in module PYME.Analysis.Colocalisation.colocScaleDep) rendQT() (in module PYME.Analysis.points.QuadTree.QTrend) (in module PYME.Analysis.points.QuadTree.rendQT) rendQTa() (in module PYME.Analysis.points.QuadTree.QTrend) (in module PYME.Analysis.points.QuadTree.rendQT) rendQTan() (in module PYME.Analysis.points.QuadTree.QTrend) (in module PYME.Analysis.points.QuadTree.rendQT) rendQTe() (in module PYME.Analysis.points.QuadTree.QTrend) (in module PYME.Analysis.points.QuadTree.rendQT) rendS() (in module PYME.Analysis.Colocalisation.colocScaleDep) rendSurfs() (in module PYME.Analysis.points.surfit) rendSurfsT() (in module PYME.Analysis.points.surfit) rendTri() (in module PYME.LMVis.visHelpers) (in module PYME.LMVis.visHelpersMin) rendTri2() (in module PYME.LMVis.visHelpers) rendVoronoi() (in module PYME.LMVis.visHelpers) repair (PYME.recipes.surface_fitting.DelaunayMarchingTetrahedra attribute) (PYME.recipes.surface_fitting.DualMarchingCubes attribute) (PYME.recipes.surface_fitting.NthPointIsosurface attribute) replace_names() (in module PYME.IO.csv_flavours) replNoneWith1() (in module PYME.localization.FitFactories.fitCommon) (in module PYME.localization.FitFactories.Gauss3DFitR) (in module PYME.localization.FitFactories.SpecGaussFitFR) (in module PYME.localization.FitFactories.SplitterMultifitSR) (in module PYME.localization.FitFactories.SplitterObjFindR) (in module PYME.localization.FitFactories.SplitterShiftEstFR) report() (in module PYME.util.mProfile.mProfile) (in module PYME.util.mProfile.p) ReportForEachOutput (class in PYME.recipes.output) ReportOutput (class in PYME.recipes.output) requeue_missed() (PYME.Acquire.ui.tile_panel.MultiwellProtocolQueuePanel method) requiredVariables (PYME.LMVis.importTextDialog.ColumnMappingDialog attribute) ResampleZ (class in PYME.recipes.processing) reset() (PYME.misc.TiffImagePlugin.ImageFileDirectory method) ResetDataStack() (PYME.DSView.arrayViewPanel.ArrayViewPanel method) ResetSelection() (PYME.DSView.displayOptions.DisplayOpts method) resident() (in module PYME.misc.memUsage) resize_to_smallest() (PYME.Acquire.webui.ipy.IPYWithClients method) resizeColumn() (PYME.contrib.listctrlMixins.ListCtrlAutoWidthMixin method) resizeLastColumn() (PYME.contrib.listctrlMixins.ListCtrlAutoWidthMixin method) resizePSF() (in module PYME.Deconv.wiener) resolve() (PYME.misc.hybrid_ns.HybridNS method) (PYME.misc.pyme_zeroconf.ZeroConfNS method) (PYME.misc.sqlite_ns.SQLiteNS method) resolveDependencies() (PYME.recipes.recipe.Recipe method) ResponseNotAllowed() (in module PYME.cluster.dataserver_wsgi) ResponseNotFound() (in module PYME.cluster.dataserver_wsgi) ResponseOK() (in module PYME.cluster.dataserver_wsgi) result_params (PYME.localization.Test.fitTestJigSCMOS.fitTestJig property) results (PYME.localization.Test.fitTestJigSCMOS.fitTestJig property) ResultsFilter (class in PYME.IO.tabular) resultsFilter() (in module PYME.IO.tabular) ResultsView (class in PYME.DSView.modules.sheetView) RetrieveObjects() (PYME.DSView.modules.blobMeasure.Measurements method) retrieveValue() (PYME.localization.MetaDataEdit.BoolFloatParam method) (PYME.localization.MetaDataEdit.BoolParam method) (PYME.localization.MetaDataEdit.ChoiceParam method) (PYME.localization.MetaDataEdit.FilenameParam method) (PYME.localization.MetaDataEdit.FloatListParam method) (PYME.localization.MetaDataEdit.FloatParam method) (PYME.localization.MetaDataEdit.IntParam method) (PYME.localization.MetaDataEdit.RangeParam method) (PYME.localization.MetaDataEdit.ShiftFieldParam method) (PYME.localization.MetaDataEdit.StringParam method) returnLoop() (PYME.cluster.taskWorkerHTTP.taskWorker method) reversal_swap() (in module PYME.Analysis.points.traveling_salesperson.sectioned_two_opt) reversal_two_opt() (in module PYME.Analysis.points.traveling_salesperson.sectioned_two_opt) reverseDependancyGraph() (PYME.recipes.recipe.Recipe method) rgb_to_hls() (in module PYME.misc.colorsys) rgb_to_hsv() (in module PYME.misc.colorsys) rgb_to_yiq() (in module PYME.misc.colorsys) RGBImageOutput (class in PYME.recipes.output) RichardsonLucyDeconvolution (class in PYME.Deconv.richardsonLucy) right (PYME.recipes.measurement.BinnedHistogram attribute) (PYME.recipes.measurement.Histogram attribute) (PYME.recipes.measurement.ImageHistogram attribute) right() (PYME.LMVis.views.View method) ring() (in module PYME.Analysis.points.rings) ring_corr() (in module PYME.Analysis.points.rings) ring_corr_goal() (in module PYME.Analysis.points.rings) ring_paint() (in module PYME.Analysis.points.rings) ring_theory() (in module PYME.Analysis.points.rings) ring_theory_cdf() (in module PYME.Analysis.points.rings) RingCorrelator (class in PYME.DSView.modules.fourierRingCorrelation) Ripleys (class in PYME.recipes.pointcloud) ripleys_dh() (in module PYME.Analysis.points.ripleys) ripleys_dl() (in module PYME.Analysis.points.ripleys) ripleys_h() (in module PYME.Analysis.points.ripleys) ripleys_k() (in module PYME.Analysis.points.ripleys) ripleys_k_from_mask_points() (in module PYME.Analysis.points.ripleys) ripleys_l() (in module PYME.Analysis.points.ripleys) rlbead (class in PYME.Deconv.richardsonLucy) (class in PYME.Deconv.richardsonLucyMV) (class in PYME.Deconv.richardsonLucyMVM) robustLin2Lhood() (in module PYME.Analysis.points.twoColour) robustLin3Lhood() (in module PYME.Analysis.points.twoColour) robustLin3zLhood() (in module PYME.Analysis.points.twoColour) robustLinLhood() (in module PYME.Analysis.points.twoColour) roi_at() (in module PYME.Analysis.angleFilter) roi_crop_image() (in module PYME.IO.DataSources.CropDataSource) roi_half_size (PYME.recipes.measurement.ExtractROIs attribute) roi_list (PYME.tileviewer.tileviewer.TileServer attribute) roi_size_pixels (PYME.recipes.measurement.IdentifyOverlappingROIs attribute) roiHalfSize (PYME.recipes.measurement.FitPoints attribute) rootdir() (PYME.cluster.webdav.DirCollection method) ROT90 (PYME.DSView.displayOptions.DisplayOpts attribute) Rotate180 (class in PYME.recipes.processing) rough_knot_spacing (PYME.recipes.localisations.MapAstigZ attribute) (PYME.recipes.multiview.MapAstigZ attribute) round_sf() (in module PYME.reports.filters) Rp() (in module PYME.misc.snells) Rs() (in module PYME.misc.snells) Rule (class in PYME.cluster.rules) (class in PYME.cluster.ruleserver) rule_chain (PYME.Acquire.htsms.rule_ui.ChainedAnalysisPage property) rule_timeout (PYME.Acquire.htsms.rule_ui.RuleTile attribute) rule_type (PYME.cluster.rules.RuleFactory property) RuleChain (class in PYME.Acquire.htsms.rule_ui) RuleFactory (class in PYME.cluster.rules) RuleGroupWatcher (class in PYME.cluster.rules) RulePlotPanel (class in PYME.Acquire.htsms.rule_ui) RuleRecipeManager (class in PYME.Acquire.htsms.rule_ui) RuleRecipeView (class in PYME.Acquire.htsms.rule_ui) RuleServer (class in PYME.cluster.ruleserver) RuleTile (class in PYME.Acquire.htsms.rule_ui) RuleWatcher (class in PYME.cluster.rules) run() (in module PYME.recipes.processing) (PYME.Acquire.acquire_server.AcquireHTTPServer method) (PYME.Acquire.acquirewx.PYMEMainFrame method) (PYME.Acquire.ExecTools.GUIInitTask method) (PYME.cluster.cluster_of_one.ClusterOfOne method) (PYME.cluster.HTTPDataServer.statusPoller method) (PYME.cluster.rulenodeserver.ServerThread method) (PYME.cluster.ruleserver.ServerThread method) (PYME.Deconv.decThread.decThread method) (PYME.IO.testClusterSpooling.TestSpooler method) (PYME.LMVis.Extras.animation.VideoPanel method) (PYME.misc.wxThread.wxThread method) (PYME.recipes.base.ArithmaticFilter method) (PYME.recipes.base.Crop method) (PYME.recipes.base.ExtractChannel method) (PYME.recipes.base.Filter method) (PYME.recipes.base.JoinChannels method) (PYME.recipes.base.ModuleBase method) (PYME.recipes.base.Redimension method) (PYME.recipes.localisations.AddMeasurementsByLabel method) (PYME.recipes.localisations.AutocorrelationDriftCorrection method) (PYME.recipes.localisations.ClusterCountVsImagingTime method) (PYME.recipes.localisations.DBSCANClustering method) (PYME.recipes.localisations.DensityMapping method) (PYME.recipes.localisations.ExtractTableChannel method) (PYME.recipes.localisations.FiducialCorrection method) (PYME.recipes.localisations.IDTransientFrames method) (PYME.recipes.localisations.LabelsFromImage method) (PYME.recipes.localisations.MeasureClusters3D method) (PYME.recipes.localisations.MergeClumps method) (PYME.recipes.localisations.Pipelineify method) (PYME.recipes.localisations.ProcessColour method) (PYME.recipes.localisations.TimeBlocks method) (PYME.recipes.machine_learning.AnnotatePoints method) (PYME.recipes.machine_learning.LabelsToChannels method) (PYME.recipes.machine_learning.PointFeaturesPairwiseDist method) (PYME.recipes.machine_learning.PointFeaturesVectorial method) (PYME.recipes.measurement.AddMetadataToMeasurements method) (PYME.recipes.measurement.BinnedHistogram method) (PYME.recipes.measurement.DetectPoints2D method) (PYME.recipes.measurement.ExtractROIs method) (PYME.recipes.measurement.FitDumbells method) (PYME.recipes.measurement.FitPoints method) (PYME.recipes.measurement.Histogram method) (PYME.recipes.measurement.IdentifyOverlappingROIs method) (PYME.recipes.measurement.ImageCumulativeHistogram method) (PYME.recipes.measurement.ImageHistogram method) (PYME.recipes.measurement.IntensityAtPoints method) (PYME.recipes.measurement.MeanNeighbourDistances method) (PYME.recipes.measurement.Measure2D method) (PYME.recipes.measurement.MultifitBlobs method) (PYME.recipes.measurement.NearestNeighbourDistances method) (PYME.recipes.measurement.PairwiseDistanceHistogram method) (PYME.recipes.processing.AverageFramesByZStep method) (PYME.recipes.processing.BackgroundSubtractionMovingAverage method) (PYME.recipes.processing.Colocalisation method) (PYME.recipes.processing.ColocalisationEDT method) (PYME.recipes.processing.DarkAndVarianceMap method) (PYME.recipes.processing.DeconvolveMotionCompensating method) (PYME.recipes.processing.DirectionToMask3D method) (PYME.recipes.processing.FindCaWaves method) (PYME.recipes.processing.FlatfiledAndDarkCorrect method) (PYME.recipes.processing.Gradient2D method) (PYME.recipes.processing.Gradient3D method) (PYME.recipes.processing.Label method) (PYME.recipes.processing.OpticalFlow method) (PYME.recipes.processing.ProjectOnVector method) (PYME.recipes.processing.RawADUToElectronsPerSecond method) (PYME.recipes.processing.ResampleZ method) (PYME.recipes.processing.StatisticsByFrame method) (PYME.recipes.processing.VectorfieldCurl method) (PYME.recipes.processing.VectorfieldNorm method) (PYME.recipes.processing.Watershed method) (PYME.recipes.processing.WavefrontDetection method) (PYME.recipes.processing.WavefrontVelocity method) (PYME.recipes.pyramid.SupertilePhysicalCoords method) (PYME.recipes.simulation.RandomPoints method) (PYME.recipes.simulation.TheoreticalPSF method) (PYME.recipes.surface_fitting.NthPointIsosurface method) (PYME.recipes.tablefilters.AggregateMeasurements method) (PYME.recipes.tablefilters.ConcatenateTables method) (PYME.recipes.tablefilters.FilterTable method) (PYME.recipes.tablefilters.FilterTableByIDs method) (PYME.recipes.tablefilters.Mapping method) (PYME.recipes.tablefilters.RandomSubset method) (PYME.recipes.tablefilters.SelectTableColumns method) (PYME.util.mProfile.tProfile.T method) run_recipe_for_locations (PYME.tileviewer.tileviewer.TileServer attribute) run_t() (in module PYME.Analysis.points.SoftRend.testTetrahedra) RunCurrentRecipe() (PYME.DSView.modules.recipes.RecipePlugin method) RunCurrentRecipeAndSave() (PYME.DSView.modules.recipes.RecipePlugin method) runRec() (in module PYME.recipes.batchProcess) runRecipe() (in module PYME.recipes.runRecipe) runTests() (in module PYME.Analysis.PSFEst.psfQuality) (in module PYME.util.mProfile.tProfile) (PYME.localization.Test.fitTestJig.fitTestJig method) (PYME.localization.Test.fitTestJigSCMOS.fitTestJig method) (PYME.localization.Test.fitTestJigWC.fitTestJig method)

S

SA (PYME.DSView.modules.blobMeasure.DataBlock property) safe_read() (in module PYME.IO.unifiedIO) SampleInfoDialog (class in PYME.Acquire.sampleInformation) samples_per_node (PYME.recipes.pointcloud.Octree attribute) sampling (PYME.recipes.pointcloud.Ripleys attribute) sampling_method (PYME.recipes.surface_fitting.SHShellRadiusDensityEstimate attribute) sampling_nm (PYME.recipes.surface_fitting.SHShellRadiusDensityEstimate attribute) SarcomereChecker (class in PYME.Acquire.Utils.sarcSpacing) satCheck() (PYME.Acquire.microscope.microscope method) save() (PYME.Analysis.svmSegment.svmClassifier method) (PYME.Analysis.tile_pyramid.TileCache method) (PYME.Analysis.Tracking.trackUtils.Clump method) Save() (PYME.IO.image.ImageStack method) save() (PYME.LMVis.Extras.animation.VideoPanel method) (PYME.misc.TiffImagePlugin.ImageFileDirectory method) (PYME.recipes.acquisition.QueueAcquisitions method) (PYME.recipes.base.OutputModule method) (PYME.recipes.output.CSVOutput method) (PYME.recipes.output.HDFOutput method) (PYME.recipes.output.ImageOutput method) (PYME.recipes.output.PlotOutput method) (PYME.recipes.output.ReportForEachOutput method) (PYME.recipes.output.ReportOutput method) (PYME.recipes.output.RGBImageOutput method) (PYME.recipes.output.STLOutput method) (PYME.recipes.output.XLSOutput method) (PYME.recipes.pyramid.TilePyramid method) (PYME.recipes.recipe.Recipe method) save_as_png() (in module PYME.DSView.modules.arrayView) save_as_series_of_png() (in module PYME.DSView.modules.arrayView) save_attachments() (PYME.contrib.gohlke.czifile.CziFile method) save_hdf() (PYME.LMVis.pipeline.Pipeline method) save_ply() (in module PYME.IO.FileUtils.ply) save_snapshot() (in module PYME.LMVis.Extras.snapshot) save_stl() (PYME.DSView.modules.vis3D.Visualiser method) save_stl_binary() (in module PYME.IO.FileUtils.stl) save_surface() (in module PYME.LMVis.Extras.extra_layers) (PYME.DSView.modules.vis3D.MeshViewFrame method) save_tile() (PYME.Analysis.tile_pyramid.NumpyTileIO method) (PYME.Analysis.tile_pyramid.SqliteTileIO method) (PYME.Analysis.tile_pyramid.TileIO method) save_txt() (PYME.LMVis.pipeline.Pipeline method) save_u3d() (PYME.DSView.modules.vis3D.Visualiser method) save_view() (PYME.LMVis.Extras.saved_views.ViewPanel method) save_wisdom() (in module PYME.Deconv.fftwWisdom) save_x3d() (PYME.DSView.modules.vis3D.Visualiser method) save_yaml() (PYME.recipes.recipe.Recipe method) saveBlobs() (in module PYME.DSView.modules.extractBlobs) saved (PYME.Analysis.tile_pyramid.CacheEntry property) saveDataFrame() (in module PYME.recipes.runRecipe) saveDeconvolution() (PYME.DSView.modules.deconvolution.Deconvolver method) saveFilter() (in module PYME.IO.FileUtils.h5rToTxt) saveFits() (PYME.DSView.modules.blobFinding.BlobFinder method) (PYME.DSView.modules.shiftfield_estimation.BlobFinder method) SaveMetadata() (PYME.LMVis.Extras.sequentialSpecies.TimedSpecies method) (PYME.LMVis.visCore.VisGUICore method) saveOutput() (in module PYME.recipes.runRecipe) SavePerspective() (PYME.Acquire.acquiremainframe.PYMEMainFrame method) (PYME.Acquire.acquirewx.PYMEMainFrame method) savePositions() (PYME.DSView.modules.blobFinding.BlobFinder method) (PYME.DSView.modules.shiftfield_estimation.BlobFinder method) saveResultsToFile() (PYME.localization.autopsf.autopsf.ZernikePSFModel method) saveShiftmaps() (PYME.DSView.modules.blobFinding.BlobFinder method) (PYME.DSView.modules.shiftfield_estimation.BlobFinder method) saveTabular() (in module PYME.recipes.runRecipe) saveTiffMultipage() (in module PYME.IO.FileUtils.saveTiffStack) SaveTracks() (PYME.DSView.modules.particleTracking.ParticleTrackingView method) sc (PYME.Analysis.points.twoColour.lin3Model attribute) (PYME.Analysis.points.twoColour.lin3zModel attribute) scalar_column_source() (in module PYME.IO.tabular) scalar_dict_source() (in module PYME.IO.tabular) Scale (class in PYME.recipes.base) scale (PYME.DSView.arrayViewPanel.ArrayViewPanel property) (PYME.recipes.base.Scale attribute) (PYME.recipes.measurement.MultifitBlobs attribute) ScaleBarOverlay (class in PYME.DSView.overlays) ScaleBarOverlayLayer (class in PYME.LMVis.layers.ScaleBarOverlayLayer) ScaleBoxOverlayLayer (class in PYME.LMVis.layers.ScaleBoxOverlayLayer) ScaleBoxPanel (class in PYME.LMVis.Extras.scaleBox) scaled_projection() (in module PYME.Analysis.points.coordinate_tools) scaled_shell_from_hdf() (in module PYME.Analysis.points.spherical_harmonics) ScaledShell (class in PYME.Analysis.points.spherical_harmonics) scaleFactor (PYME.LMVis.Extras.pointSetGeneration.Generator attribute) scaling (PYME.LMVis.layers.quiver.QuiverRenderLayer attribute) (PYME.recipes.output.RGBImageOutput attribute) scaling_factor (PYME.recipes.output.RGBImageOutput attribute) scaling_factors (PYME.Analysis.points.spherical_harmonics.SHShell property) SCAN_MODES (PYME.Acquire.stackSettings.StackSettings attribute) ScannerPanel (class in PYME.Acquire.ui.scanner_panel) scatterdens() (in module PYME.LMVis.Extras.multiColourAnalysis) scheme (PYME.recipes.base.OutputModule attribute) schemes() (PYME.DSView.modules.blobMeasure.Measurements method) schemes3D() (PYME.DSView.modules.blobMeasure.Measurements method) scope_state_longpoll() (PYME.Acquire.acquire_server.PYMEAcquireServer method) scope_tweet() (PYME.Acquire.htsms.tweeter.LazyScopeTweeter method) Scroll() (PYME.DSView.scrolledImagePanel.ScrolledImagePanel method) ScrolledImagePanel (class in PYME.DSView.scrolledImagePanel) se_diff_l2_mean() (in module PYME.Analysis.BleachProfile.rollins) search_radius_nm (PYME.recipes.multiview.CalibrateShifts attribute) searchRadius (PYME.recipes.localisations.DBSCANClustering attribute) secondaryAxis (PYME.DSView.modules.blobMeasure.DataBlock property) sefm() (in module PYME.Analysis.BleachProfile.rollins) segment() (in module PYME.Analysis.points.EdgeDB.edgeDB) (in module PYME.Analysis.points.EdgeDB.segment) (in module PYME.Analysis.points.gen3DTriangs) (PYME.Analysis.points.EdgeDB.edges.EdgeDB method) SegmentationPanel (class in PYME.DSView.modules.segmentation) segmenter (class in PYME.Analysis.points.segmentLL) Segmenter (class in PYME.DSView.modules.segmentation) segmentNR() (in module PYME.Analysis.points.gen3DTriangs) segments() (PYME.contrib.gohlke.czifile.CziFile method) select_annotation() (PYME.DSView.modules.annotation.AnnotateBase method) select_rule_chain() (PYME.Acquire.htsms.rule_ui.ChainedAnalysisPage method) selectBeforePopup() (in module PYME.contrib.listctrlMixins) selectDataSource() (PYME.LMVis.pipeline.Pipeline method) selectedDataSource (PYME.LMVis.pipeline.Pipeline property) selectedLineWidth (PYME.DSView.modules.particleTracking.ParticleTrackingView attribute) Selection (class in PYME.ui.selection) SelectionFilter (class in PYME.IO.tabular) SelectionOverlayLayer (class in PYME.LMVis.layers.SelectionOverlayLayer) SelectionSettings (class in PYME.LMVis.gl_render3D_shaders) SelectLabel (class in PYME.recipes.processing) SelectLargestLabel (class in PYME.recipes.processing) SelectTableColumns (class in PYME.recipes.tablefilters) Sellmeier() (in module PYME.misc.glassModel) send() (PYME.contrib.dispatch.dispatcher.Signal method) send_error() (PYME.cluster.HTTPDataServer.PYMEHTTPRequestHandler method) send_head() (PYME.cluster.HTTPDataServer.PYMEHTTPRequestHandler method) send_robust() (PYME.contrib.dispatch.dispatcher.Signal method) sendData() (PYME.cluster.webdav.DirCollection method) (PYME.cluster.webdav.FileMember method) seqPanel (class in PYME.Acquire.ui.seqdialog) SeqProgressPanel (class in PYME.Acquire.ui.seqdialog) sequence_id (PYME.IO.acquisition_backends.Backend property) SequencePanel (class in PYME.DSView.OpenSequenceDialog) serialise() (PYME.Acquire.actions.Action method) series (PYME.contrib.gohlke.tifffile.TIFFfile attribute) seriesName (PYME.Acquire.SpoolController.SpoolController property) server_for_chunk() (in module PYME.Analysis.distributed_pyramid) server_version (PYME.cluster.webdav.DAVRequestHandler attribute) ServerThread (class in PYME.cluster.rulenodeserver) (class in PYME.cluster.ruleserver) set_box_dimensions() (PYME.LMVis.layers.ScaleBoxOverlayLayer.ScaleBoxOverlayLayer method) set_c() (PYME.Acquire.xyztc.XYZTCAcquisition method) set_clipping_uniforms() (PYME.LMVis.shader_programs.GLProgram.GLProgram method) set_color() (PYME.LMVis.layers.ScaleBoxOverlayLayer.ScaleBoxOverlayLayer method) set_dim_order_and_size() (PYME.IO.DataSources.BaseDataSource.XYZTCDataSource method) set_fitting_points() (PYME.Analysis.points.spherical_harmonics.ScaledShell method) set_lock_mode() (PYME.DSView.modules.annotation.AnnotateBase method) set_lut() (PYME.LMVis.layers.image_layer.ImageEngine method) set_offset() (PYME.LMVis.layers.OverlayLayer.OverlayLayer method) set_readonly() (PYME.IO.MetaDataHandler.DictMDHandler method) set_recipe_text() (PYME.recipes.recipeGui.RecipeView method) set_roi_locations (PYME.tileviewer.tileviewer.TileServer attribute) set_scale_bar_depth() (PYME.LMVis.layers.ScaleBarOverlayLayer.ScaleBarOverlayLayer method) set_scale_bar_length() (PYME.LMVis.layers.ScaleBarOverlayLayer.ScaleBarOverlayLayer method) set_server() (in module PYME.Acquire.webui) set_shader_program() (PYME.LMVis.layers.base.BaseEngine method) (PYME.LMVis.layers.base.SimpleLayer method) (PYME.LMVis.shader_programs.GLProgram.GLProgram method) set_starts() (PYME.LMVis.layers.ScaleBoxOverlayLayer.ScaleBoxOverlayLayer method) set_t() (PYME.Acquire.xyztc.XYZTCAcquisition method) set_texture() (PYME.LMVis.layers.image_layer.ImageEngine method) (PYME.LMVis.layers.text.Text method) set_tick_distance() (PYME.LMVis.layers.ScaleBoxOverlayLayer.ScaleBoxOverlayLayer method) set_tile_source (PYME.tileviewer.tileviewer.TileServer attribute) set_values() (PYME.LMVis.layers.pointcloud.PointCloudRenderLayer method) set_variables() (PYME.IO.tabular.MappingFilter method) set_view() (PYME.LMVis.Extras.saved_views.ViewPanel method) set_view_x() (PYME.LMVis.Extras.saved_views.ViewPanel method) set_view_y() (PYME.LMVis.Extras.saved_views.ViewPanel method) set_view_z() (PYME.LMVis.Extras.saved_views.ViewPanel method) set_well_positions() (PYME.Acquire.Utils.tiler.MultiwellCircularTiler method) set_z() (PYME.Acquire.xyztc.XYZTCAcquisition method) SetAspect() (PYME.DSView.displayOptions.DisplayOpts method) SetBackend() (PYME.Analysis.processLogger.ContextManager method) setBackgroundBufferPCT() (PYME.IO.DataSources.BGSDataSource.XTZCBackgroundSource method) (PYME.IO.DataSources.BGSDataSource.XYZTCBgsSource method) SetCameraShutter() (in module PYME.Acquire.protocol) SetCaption() (PYME.ui.manualFoldPanel.foldingPane method) SetCentredRoi() (PYME.Acquire.acquiremainframe.PYMEMainFrame method) (PYME.Acquire.acquirewx.PYMEMainFrame method) SetCharts() (PYME.DSView.eventLogViewer.eventLogPanel method) (PYME.DSView.eventLogViewer.eventLogTPanel method) SetClumps() (PYME.DSView.modules.particleTracking.TrackList method) SetCMap() (PYME.DSView.displayOptions.DisplayOpts method) SetColor() (PYME.contrib.wxPlotPanel.PlotPanel method) setColour() (PYME.IO.tabular.ColourFilter method) SetColumnCount() (PYME.contrib.listctrlMixins.ColumnSorterMixin method) SetContinuousMode() (in module PYME.Acquire.protocol) setCreatorChoices() (PYME.Acquire.sampleInformation.SampleInfoDialog method) SetData() (PYME.IO.image.ImageStack method) (PYME.ui.fastGraph.FastGraphPanel method) (PYME.ui.histLimits.HistLimitPanel method) SetDataStack() (PYME.DSView.arrayViewPanel.ArrayViewPanel method) (PYME.DSView.displayOptions.DisplayOpts method) setDefaultNamespace() (in module PYME.Acquire.ExecTools) SetDirection() (PYME.Acquire.stackSettings.StackSettings method) setDyeChoices() (PYME.Acquire.sampleInformation.SampleInfoDialog method) SetEMGain() (in module PYME.Acquire.protocol) SetEndPos() (PYME.Acquire.stackSettings.StackSettings method) setEntry() (PYME.IO.MetaDataHandler.CachingMDHandler method) (PYME.IO.MetaDataHandler.CopyOnWriteMDHandler method) (PYME.IO.MetaDataHandler.DictMDHandler method) (PYME.IO.MetaDataHandler.HDFMDHandler method) (PYME.IO.MetaDataHandler.MDHandlerBase method) (PYME.IO.MetaDataHandler.NestedClassMDHandler method) (PYME.IO.MetaDataHandler.QueueMDHandler method) (PYME.IO.MetaDataHandler.XMLMDHandler method) setEventNumbers() (PYME.ui.filterPane.FilterPane method) SetEventSource() (PYME.DSView.eventLogViewer.eventLogPanel method) (PYME.DSView.eventLogViewer.eventLogTPanel method) SetFilter() (PYME.Acquire.sampleInformation.VirtList method) SetFit() (PYME.LMVis.visCore.VisGUICore method) SetFitInfo() (PYME.DSView.modules.LMAnalysis.LMAnalyser2 method) (PYME.DSView.modules.LMDisplay.LMDisplay method) SetFitResults() (PYME.DSView.fitInfo.fitDispPanel method) SetGain() (PYME.DSView.displayOptions.DisplayOpts method) SetHighlightColor() (PYME.contrib.listctrlMixins.ListRowHighlighter method) SetHighlightMode() (PYME.contrib.listctrlMixins.ListRowHighlighter method) SetIntegTime() (in module PYME.Acquire.protocol) setItem() (PYME.Acquire.microscope.StateManager method) setItems() (PYME.Acquire.microscope.StateManager method) setMapping() (PYME.IO.tabular.MappingFilter method) (PYME.LMVis.Extras.QPobjectSegment.QPObjectSegmenter method) SetMaster() (PYME.DSView.modules.composite.CompositeDialog method) SetMessage() (PYME.Acquire.ui.splashScreen.SplashScreen method) (PYME.DSView.splashScreen.SplashScreen method) SetMinMax() (PYME.ui.histLimits.HistLimitPanel method) SetOffset() (PYME.DSView.displayOptions.DisplayOpts method) SetOrientation() (PYME.DSView.displayOptions.DisplayOpts method) SetPattern() (PYME.Acquire.Utils.MultiPointScanner.PointScanner method) SetPercentile() (PYME.ui.histLimits.HistLimitPanel method) setPopupMenu() (PYME.contrib.listctrlMixins.ListCtrlSelectionManagerMix method) SetPos() (PYME.Acquire.microscope.microscope method) SetPrevPos() (PYME.Acquire.stackSettings.StackSettings method) SetPropagate() (PYME.Acquire.ui.AnalysisSettingsUI.AnalysisSettings method) SetProtocol() (PYME.Acquire.SpoolController.SpoolController method) SetRange() (PYME.DSView.eventLogViewer.eventLogPanel method) (PYME.DSView.eventLogViewer.eventLogTPanel method) SetRecipe() (PYME.recipes.vertical_recipe_display.RecipeDisplayPanel method) setResizeColumn() (PYME.contrib.listctrlMixins.ListCtrlAutoWidthMixin method) SetResults() (PYME.DSView.fitInfo.FitInfoPanel method) setResults() (PYME.IO.tabular.FitResultsSource method) SetScale() (PYME.DSView.displayOptions.DisplayOpts method) SetScanChannel() (PYME.Acquire.stackSettings.StackSettings method) SetSelection() (PYME.DSView.displayOptions.DisplayOpts method) SetSeqLength() (PYME.Acquire.stackSettings.StackSettings method) SetShiftField() (PYME.Analysis.splitting.Unmixer method) (PYME.IO.DataSources.UnsplitDataSource.DataSource method) SetShiftmap() (PYME.DSView.modules.composite.ImageList method) SetShifts() (PYME.IO.DataSources.AlignDataSource.DataSource method) SetSlice() (PYME.DSView.displayOptions.DisplayOpts method) setSlideChoices() (PYME.Acquire.sampleInformation.SampleInfoDialog method) SetSpoolDir() (PYME.Acquire.SpoolController.SpoolController method) SetSpoolMethod() (PYME.Acquire.SpoolController.SpoolController method) SetStartMode() (PYME.Acquire.stackSettings.StackSettings method) SetStartPos() (PYME.Acquire.stackSettings.StackSettings method) setStatus() (PYME.LMVis.statusLog.StatusLogger method) SetStatus() (PYME.LMVis.visCore.VisGUICore method) SetStatusDispFcn() (in module PYME.LMVis.statusLog) SetStepSize() (PYME.Acquire.stackSettings.StackSettings method) setStructureChoices() (PYME.Acquire.sampleInformation.SampleInfoDialog method) SetThresholdMode() (PYME.ui.histLimits.HistLimitPanel method) SetTimedSpecies() (PYME.LMVis.Extras.sequentialSpecies.TimedSpecies method) settings() (PYME.Acquire.SpoolController.SpoolControllerWrapper method) (PYME.Acquire.stackSettings.StackSettings method) settings_longpoll() (PYME.Acquire.stackSettings.StackSettings method) settingsDB (PYME.Acquire.microscope.microscope property) SetTracks() (PYME.DSView.modules.particleTracking.ParticleTrackingView method) setup_logging() (in module PYME.Acquire.PYMEAcquire) setup_off_screen() (PYME.LMVis.gl_offScreenHandler.OffScreenHandler method) setValue() (PYME.Acquire.microscope.StateHandler method) SetValue() (PYME.ui.histLimits.HistLimitPanel method) SetValueAndFire() (PYME.ui.histLimits.HistLimitPanel method) SetVirtualSize() (PYME.DSView.scrolledImagePanel.ScrolledImagePanel method) SetVoxelSize() (PYME.Acquire.microscope.microscope method) sffake (class in PYME.Analysis.points.twoColour) (class in PYME.misc.sffake) ShadedFaceEngine (class in PYME.LMVis.layers.mesh) ShadedPointsEngine (class in PYME.LMVis.layers.pointcloud) shader_program (PYME.LMVis.layers.base.BaseEngine property) (PYME.LMVis.layers.base.SimpleLayer property) ShaderLoader (class in PYME.LMVis.shader_programs.shader_loader) ShaderProgram (class in PYME.LMVis.shader_programs.shader_program) ShaderProgramFactory (class in PYME.LMVis.shader_programs.ShaderProgramFactory) shape (PYME.Acquire.xyztc.XYZTCAcquisition property) (PYME.contrib.gohlke.czifile.CziFile attribute) (PYME.DSView.modules.composite.CompositeDialog property) (PYME.IO.DataSources.ArrayDataSource.ArrayDataSource property) (PYME.IO.DataSources.ArrayDataSource.XYZTCArrayDataSource property) (PYME.IO.DataSources.BaseDataSource.BaseDataSource property) (PYME.IO.DataSources.BaseDataSource.XYTCDataSource property) (PYME.IO.DataSources.BaseDataSource.XYZSubvolume property) (PYME.IO.DataSources.BaseDataSource.XYZTCDataSource property) (PYME.IO.dataWrap.ListWrapper property) shell_coordinates() (PYME.Analysis.points.spherical_harmonics.ScaledShell method) shell_properties_output (PYME.recipes.surface_fitting.SHShellRadiusDensityEstimate attribute) shift_and_rot_model() (in module PYME.Analysis.points.twoColour) shift_and_rot_model_eval() (in module PYME.Analysis.points.twoColour) shift_map_path (PYME.recipes.multiview.ShiftCorrect attribute) shift_x (PYME.localization.FitFactories.FFBase.FFBase property) shift_y (PYME.localization.FitFactories.FFBase.FFBase property)

ShiftCorrect (class in PYME.recipes.multiview) ShiftFieldParam (class in PYME.localization.MetaDataEdit) ShiftItem() (PYME.DSView.modules.composite.ImageList method) shiftmap0 (PYME.recipes.processing.Composite attribute) shiftmap1 (PYME.recipes.processing.Composite attribute) shiftmap2 (PYME.recipes.processing.Composite attribute) shiftmap3 (PYME.recipes.processing.Composite attribute) ShiftmapGenerator (class in PYME.LMVis.Extras.shiftmapGenerator) ShiftmapSelectionDialog (class in PYME.DSView.modules.composite) ShiftModel (class in PYME.Analysis.points.twoColour) ShiftPanel (class in PYME.DSView.modules.composite) shininess (PYME.LMVis.shader_programs.GouraudShaderProgram.GouraudShaderProgram attribute) shmarray (class in PYME.util.shmarray.shmarray) SHNucleusSource (class in PYME.simulation.pointsets) shortAxisDist() (PYME.DSView.modules.blobMeasure.BlobObject method) show (PYME.ui.manualFoldPanel.CaptionButton property) Show() (PYME.DSView.displayOptions.DisplayOpts method) show() (PYME.LMVis.Extras.dockedPanel.DockedPanel static method) (PYME.LMVis.layers.ScaleBoxOverlayLayer.ScaleBoxOverlayLayer method) show_about_dlg() (in module PYME.ui.about_dlg) show_bounds (PYME.LMVis.layers.LUTOverlayLayer.LUTOverlayLayer attribute) show_box() (PYME.LMVis.Extras.scaleBox.ScaleBoxPanel method) show_lut (PYME.LMVis.layers.base.EngineLayer attribute) show_shortcuts() (in module PYME.LMVis.Extras.showShortcuts) show_traceback_dialog() (in module PYME.ui.progress) showCandidates (PYME.DSView.modules.particleTracking.ParticleTrackingView attribute) ShowDataGrid() (in module PYME.misc.editgrid) showFlow (PYME.DSView.modules.flowView.FlowView attribute) showGLFrame() (in module PYME.LMVis.gl_render3D_shaders) ShowHistLimitFrame() (in module PYME.ui.histLimits) ShowIso() (PYME.misc.VolProj.Isosurf method) ShowPreflightResults() (in module PYME.Acquire.ui.preflight) ShowProj() (PYME.misc.VolProj.Isosurf method) showSelectedTrack (PYME.DSView.modules.particleTracking.ParticleTrackingView attribute) ShowShortcuts (class in PYME.LMVis.Extras.showShortcuts) ShowTextCtrl() (PYME.LMVis.view_clipping_pane.ClippingPanel method) showTrackIDs (PYME.DSView.modules.particleTracking.ParticleTrackingView attribute) showTracks (PYME.DSView.modules.particleTracking.ParticleTrackingView attribute) SHShell (class in PYME.Analysis.points.spherical_harmonics) SHShellRadiusDensityEstimate (class in PYME.recipes.surface_fitting) shutdown (PYME.Acquire.webui.ipy.IPYTermManager attribute) shutdown() (PYME.cluster.cluster_of_one.ClusterOfOne method) (PYME.cluster.rulenodeserver.ServerThread method) (PYME.cluster.ruleserver.ServerThread method) sigma2s (PYME.recipes.filters.DoGFilter property) sigma2X (PYME.recipes.filters.DoGFilter attribute) sigma2Y (PYME.recipes.filters.DoGFilter attribute) sigma2Z (PYME.recipes.filters.DoGFilter attribute) sigmas (PYME.recipes.filters.DespeckleFilter property) (PYME.recipes.filters.DoGFilter property) (PYME.recipes.filters.GaussianFilter property) (PYME.recipes.filters.MaxFilter property) (PYME.recipes.filters.MeanFilter property) (PYME.recipes.filters.MedianFilter property) (PYME.recipes.filters.MinFilter property) sigmaT (PYME.recipes.filters.GaussianFilter attribute) sigmaX (PYME.recipes.filters.DoGFilter attribute) (PYME.recipes.filters.GaussianFilter attribute) sigmaY (PYME.recipes.filters.DoGFilter attribute) (PYME.recipes.filters.GaussianFilter attribute) sigmaZ (PYME.recipes.filters.DoGFilter attribute) (PYME.recipes.filters.GaussianFilter attribute) Signal (class in PYME.contrib.dispatch.dispatcher) signalFraction() (in module PYME.Analysis.thresholding) significance (PYME.recipes.pointcloud.Ripleys attribute) sim_params (PYME.localization.Test.fitTestJigSCMOS.fitTestJig property) sim_pic() (PYME.Analysis.PSFEst.dec.dec method) (PYME.Deconv.dec.ICTMDeconvolution method) SimpleLayer (class in PYME.LMVis.layers.base) SimpleMDHandler (class in PYME.IO.MetaDataHandler) SimpleSampleInfoPanel (class in PYME.Acquire.sampleInformation) SimpleThreshold (class in PYME.recipes.processing) simplify_catalog() (in module PYME.misc.read_agf) Single() (PYME.Acquire.zScanner.zScanner method) SingleTargetTimer() (PYME.Acquire.event_loop.EventLoop method) Singleton (class in PYME.Analysis.points.features.metal) SIUnit (class in PYME.IO.FileUtils.obf_support) size (PYME.IO.clusterListing.FileInfo property) (PYME.ui.layerFoldPanel.LUTBitmap property) (PYME.ui.manualFoldPanel.CaptionButton property) size_c (PYME.recipes.base.Redimension attribute) size_t (PYME.recipes.base.Redimension attribute) size_x() (in module PYME.Analysis.PSFEst.psfQuality) size_z (PYME.recipes.base.Redimension attribute) (PYME.recipes.simulation.TheoreticalPSF attribute) sizeC (PYME.IO.DataSources.BaseDataSource.XYTCDataSource attribute) (PYME.IO.DataSources.BGSDataSource.XTZCBackgroundSource property) sizeT (PYME.recipes.filters.MaxFilter attribute) (PYME.recipes.filters.MeanFilter attribute) (PYME.recipes.filters.MedianFilter attribute) (PYME.recipes.filters.MinFilter attribute) sizeX (PYME.DSView.modules.pupilTools.PupilTools attribute) (PYME.recipes.filters.DespeckleFilter attribute) (PYME.recipes.filters.MaxFilter attribute) (PYME.recipes.filters.MeanFilter attribute) (PYME.recipes.filters.MedianFilter attribute) (PYME.recipes.filters.MinFilter attribute) sizeY (PYME.recipes.filters.DespeckleFilter attribute) (PYME.recipes.filters.MaxFilter attribute) (PYME.recipes.filters.MeanFilter attribute) (PYME.recipes.filters.MedianFilter attribute) (PYME.recipes.filters.MinFilter attribute) sizeZ (PYME.DSView.modules.pupilTools.PupilTools attribute) (PYME.recipes.filters.DespeckleFilter attribute) (PYME.recipes.filters.MaxFilter attribute) (PYME.recipes.filters.MeanFilter attribute) (PYME.recipes.filters.MedianFilter attribute) (PYME.recipes.filters.MinFilter attribute) SKFilter (class in PYME.recipes.skfilters) SLICE_XY (PYME.DSView.displayOptions.DisplayOpts attribute) SLICE_XZ (PYME.DSView.displayOptions.DisplayOpts attribute) SLICE_YZ (PYME.DSView.displayOptions.DisplayOpts attribute) SliceBuffer (class in PYME.IO.buffers) sliceChoices (PYME.DSView.DisplayOptionsPanel.OptionsPanel attribute) sliceSize (PYME.IO.image.ImageStack property) slidePanel (class in PYME.Acquire.sampleInformation) SlowComputation (class in PYME.ui.progress) SMLMChainedAnalysisPage (class in PYME.Acquire.htsms.rule_ui) SMLMChainedAnalysisPanel (class in PYME.Acquire.htsms.rule_ui) smooth (PYME.recipes.processing.SplineFitBackgroundEstimate attribute) smooth_curvature (PYME.recipes.surface_fitting.DualMarchingCubes attribute) (PYME.recipes.surface_fitting.NthPointIsosurface attribute) snake_refine_trace() (PYME.DSView.modules.annotation.AnnotateBase method) SnapshotSettings (class in PYME.LMVis.Extras.snapshot) snr_threshold (PYME.recipes.measurement.DetectPoints2D attribute) softRender (PYME.recipes.localisations.DensityMapping attribute) sorted_selection (PYME.DSView.displayOptions.DisplayOpts property) SortListItems() (PYME.contrib.listctrlMixins.ColumnSorterMixin method) source (PYME.LMVis.Extras.pointSetGeneration.Generator attribute) sources (PYME.LMVis.Extras.pointSetGeneration.Generator attribute) SpatialConvolutionMapping (class in PYME.Deconv.dec) specAddDialog (class in PYME.LMVis.colourPanel) SpecFromMetadata() (PYME.LMVis.colourPanel.colourPanel method) SpecGraphPanel (class in PYME.ui.fastGraph) species_dyes (PYME.recipes.localisations.ProcessColour attribute) species_ratios (PYME.recipes.localisations.ProcessColour attribute) SpeciesDialog (class in PYME.LMVis.Extras.sequentialSpecies) speckleFilename (PYME.recipes.tracking.LoadSpeckles attribute) sphere_expansion() (in module PYME.Analysis.points.spherical_harmonics) sphere_expansion_clean() (in module PYME.Analysis.points.spherical_harmonics) SpheresEngine (class in PYME.LMVis.layers.pointcloud) spherical_to_cartesian() (in module PYME.Analysis.points.coordinate_tools) SphericalHarmonicShell (class in PYME.recipes.surface_fitting) SphericalHarmonicShellManager (class in PYME.LMVis.Extras.spherical_harmonics) SplashPanel (class in PYME.Acquire.ui.splashScreen) (class in PYME.DSView.splashScreen) SplashScreen (class in PYME.Acquire.ui.splashScreen) (class in PYME.DSView.splashScreen) SplineFitBackgroundEstimate (class in PYME.recipes.processing) split_cluster_url() (in module PYME.IO.unifiedIO) split_image() (in module PYME.localization.splitting) split_path() (PYME.cluster.webdav.DAVRequestHandler method) split_points_by_grid() (in module PYME.Analysis.points.traveling_salesperson.sectioned_two_opt) split_points_kmeans() (in module PYME.Analysis.points.traveling_salesperson.sectioned_two_opt) splitattrs() (in module PYME.cluster.webdav) splitGaussWeightedMisfit() (in module PYME.localization.cModels.gauss_app) splWrap() (in module PYME.localization.FitFactories.SplitterFitFNR) (in module PYME.localization.FitFactories.SplitterFitFusionR) (in module PYME.localization.FitFactories.SplitterFitScavNR) spoof_focus_events_from_ontarget() (in module PYME.Analysis.piezo_movement_correction) spool_settings (PYME.recipes.acquisition.QueueAcquisitions attribute) SpoolController (class in PYME.Acquire.SpoolController) SpoolControllerWrapper (class in PYME.Acquire.SpoolController) spoolData() (PYME.IO.clusterExport.ImageFrameSource method) Spooler (class in PYME.IO.HDFSpooler) (class in PYME.IO.HTTPSpooler) (class in PYME.IO.HTTPSpooler_v2) (class in PYME.IO.QueueSpooler) (class in PYME.IO.Spooler) spoolImageFromFile() (PYME.IO.clusterExport.ImageFrameSource method) SpoolLocalLocalizationRule (class in PYME.cluster.rules) SpoolLocalLocalizationRuleFactory (class in PYME.cluster.rules) SpoolSeries (class in PYME.Acquire.actions) SpoolStopped() (PYME.Acquire.SpoolController.SpoolController method) SQLiteNS (class in PYME.misc.sqlite_ns) SqliteTileIO (class in PYME.Analysis.tile_pyramid) Stack (class in PYME.IO.FileUtils.obf_support) stack_footer_v1_unpack() (in module PYME.IO.FileUtils.obf_support) stack_footer_v1a_unpack() (in module PYME.IO.FileUtils.obf_support) stack_footer_v2_unpack() (in module PYME.IO.FileUtils.obf_support) stack_footer_v3_unpack() (in module PYME.IO.FileUtils.obf_support) stack_footer_v4_unpack() (in module PYME.IO.FileUtils.obf_support) stack_footer_v5_unpack() (in module PYME.IO.FileUtils.obf_support) stack_footer_v5a_unpack() (in module PYME.IO.FileUtils.obf_support) stack_footer_v6_unpack() (in module PYME.IO.FileUtils.obf_support) stack_header_unpack() (in module PYME.IO.FileUtils.obf_support) StackSettings (class in PYME.Acquire.stackSettings) stacksize() (in module PYME.misc.memUsage) StageLeveler (class in PYME.Acquire.stage_leveling) start (PYME.contrib.gohlke.czifile.CziFile attribute) (PYME.recipes.processing.DarkAndVarianceMap attribute) (PYME.ui.selection.Selection property) start() (PYME.Acquire.frameWrangler.FrameWrangler method) (PYME.Acquire.Utils.MultiPointScanner.PointScanner method) (PYME.Acquire.Utils.pointScanner.PointScanner method) (PYME.Acquire.Utils.pointScanner.PointScanner3D method) (PYME.Acquire.Utils.strip_tiler.StripTiler method) (PYME.Acquire.Utils.tiler.MultiwellCircularTiler method) (PYME.Acquire.Utils.tiler.Tiler method) (PYME.Acquire.xyztc.XYZTCAcquisition method) Start() (PYME.Acquire.zScanner.zScanner method) START_AND_END (PYME.Acquire.stackSettings.StackSettings attribute) start_frame (PYME.recipes.processing.CaWave property) start_from_corner (PYME.recipes.measurement.TravelingSalesperson attribute) start_ind (PYME.Analysis.points.traveling_salesperson.queue_opt.TSPQueue property) start_ipython() (PYME.Acquire.webui.ipy.IPY method) start_next() (PYME.Acquire.Utils.tiler.MultiwellCircularTiler method) start_poll() (PYME.Acquire.htsms.tweeter.LazyScopeTweeter method) start_reading() (PYME.Acquire.webui.ipy.IPYTermManager method) start_spooling() (PYME.Acquire.acquire_client.AcquireClient method) (PYME.Acquire.SpoolController.SpoolController method) (PYME.Acquire.SpoolController.SpoolControllerWrapper method) startDuplicator() (in module PYME.IO.clusterDuplication) startEstROI() (in module PYME.localization.autopsf.roifit) startFrameWrangler() (PYME.Acquire.microscope.microscope method) startGuess() (PYME.Deconv.dec.ICTMDeconvolution method) (PYME.Deconv.richardsonLucy.RichardsonLucyDeconvolution method) startParams (PYME.recipes.tracking.FitFusionTraces attribute) StartSelection() (PYME.LMVis.imageView.ImageViewPanel method) (PYME.LMVis.imageView2.ImageViewPanel method) StartServing() (in module PYME.DSView.htmlServe) (PYME.DSView.modules.blobMeasure.Measurements method) StartSpool() (PYME.IO.HTTPSpooler.Spooler method) (PYME.IO.HTTPSpooler_v2.Spooler method) (PYME.IO.Spooler.Spooler method) stat() (in module PYME.IO.clusterIO) state (PYME.Acquire.acquire_client.AcquireClient property) StateAction (class in PYME.Acquire.actions) StateHandler (class in PYME.Acquire.microscope) StateManager (class in PYME.Acquire.microscope) StaticFileHandler (class in PYME.util.webframework) statistics (PYME.recipes.pointcloud.Ripleys attribute) StatisticsByFrame (class in PYME.recipes.processing) status() (PYME.cluster.rules.Rule method) (PYME.cluster.ruleserver.RuleServer method) (PYME.IO.Spooler.Spooler method) StatusBarUpdate() (PYME.Acquire.acquiremainframe.PYMEMainFrame method) (PYME.Acquire.acquirewx.PYMEMainFrame method) StatusInfo (class in PYME.cluster.status) StatusLogger (class in PYME.LMVis.statusLog) statusPoller (class in PYME.cluster.HTTPDataServer) sted_saturation (PYME.recipes.simulation.TheoreticalPSF attribute) sted_wavelength (PYME.recipes.simulation.TheoreticalPSF attribute) step (PYME.recipes.filters.Subsample attribute) (PYME.recipes.localisations.AutocorrelationDriftCorrection attribute) step_size (PYME.recipes.machine_learning.CNNFilter attribute) steplength (PYME.simulation.pointsets.WormlikeSource attribute) stepSize (PYME.recipes.localisations.ClusterCountVsImagingTime attribute) STLOutput (class in PYME.recipes.output) stokesEinstein() (in module PYME.Analysis.Tracking.msd) stop() (PYME.Acquire.event_loop.EventLoop method) (PYME.Acquire.frameWrangler.FrameWrangler method) (PYME.Acquire.Utils.MultiPointScanner.PointScanner method) (PYME.Acquire.Utils.pointScanner.PointScanner method) (PYME.Acquire.Utils.pointScanner.PointScanner3D method) (PYME.Acquire.Utils.tiler.MultiwellCircularTiler method) Stop() (PYME.Acquire.zScanner.zScanner method) stop() (PYME.cluster.HTTPDataServer.statusPoller method) (PYME.cluster.rulenodeserver.NodeServer method) (PYME.cluster.ruleserver.RuleServer method) stop_spooling() (PYME.Acquire.SpoolController.SpoolControllerWrapper method) stopDuplicator() (in module PYME.IO.clusterDuplication) StopSpool() (PYME.IO.Spooler.Spooler method) StopSpooling() (PYME.Acquire.SpoolController.SpoolController method) store_frame() (PYME.IO.acquisition_backends.Backend method) (PYME.IO.acquisition_backends.ClusterBackend method) (PYME.IO.acquisition_backends.HDFBackend method) (PYME.IO.acquisition_backends.MemoryBackend method) store_scan() (PYME.Acquire.stage_leveling.StageLeveler method) Str (in module PYME.misc.mock_traits) str_presenter() (in module PYME.cluster.taskWorkerHTTP) Stream (class in PYME.IO.cluster_streaming) Streamer (class in PYME.IO.cluster_streaming) strength (PYME.DSView.modules.psfGeneration.PhaseRampPupil attribute) strict (PYME.recipes.tablefilters.RandomSubset attribute) string_length (PYME.recipes.measurement.AddMetadataToMeasurements attribute) StringParam (class in PYME.localization.MetaDataEdit) StripTiler (class in PYME.Acquire.Utils.strip_tiler) stylesheet (PYME.util.mProfile.colorize_db_t.Parser attribute) subblock_directory (PYME.contrib.gohlke.czifile.CziFile attribute) subblocks() (PYME.contrib.gohlke.czifile.CziFile method) subsampidx() (in module PYME.LMVis.Extras.multiColourAnalysis) Subsample (class in PYME.recipes.filters) subsearch() (PYME.Analysis.PSFEst.dec.dec method) (PYME.Deconv.dec.ICTMDeconvolution method) Subtract (class in PYME.recipes.base) suffix1 (PYME.recipes.tablefilters.AggregateMeasurements attribute) suffix2 (PYME.recipes.tablefilters.AggregateMeasurements attribute) suffix3 (PYME.recipes.tablefilters.AggregateMeasurements attribute) suffix4 (PYME.recipes.tablefilters.AggregateMeasurements attribute) suggest_cluster_filename() (in module PYME.IO.clusterExport) sum (PYME.DSView.modules.blobMeasure.DataBlock property) SupertileDataSource (class in PYME.IO.DataSources.SupertileDatasource) SupertilePhysicalCoords (class in PYME.recipes.pyramid) supportRadius (PYME.recipes.processing.OpticalFlow attribute) Surface (class in PYME.misc.zemax) SurfaceFitter (class in PYME.LMVis.Extras.surface_fitting) svm_segment() (PYME.DSView.modules.annotation.Annotater method) svmClassifier (class in PYME.Analysis.svmSegment) SVMSegment (class in PYME.recipes.machine_learning) sync_to_display_opts() (PYME.LMVis.layers.image_layer.ImageRenderLayer method) Syncer (class in PYME.DSView.modules.synchronise) Synchronise() (PYME.DSView.displayOptions.DisplayOpts method)

T

T (class in PYME.util.mProfile.tProfile) (in module PYME.Acquire.protocol) t1() (in module PYME.util.mProfile.tProfile) t_pos (PYME.LMVis.layers.image_layer.ImageRenderLayer attribute) t_range (PYME.recipes.base.Crop attribute) table_representation (PYME.Analysis.points.spherical_harmonics.ScaledShell property) TablesBackend (class in PYME.Analysis.processLogger) TabularBase (class in PYME.IO.tabular) Tag (class in PYME.cluster.webdav) Tag() (PYME.Acquire.positionTracker.PositionTracker method) Task (class in PYME.misc.taskDef) task_advertisements() (PYME.cluster.ruleserver.RuleServer method) TASK_DONE (PYME.Acquire.ExecTools.BGInitTask attribute) TASK_FAILED (PYME.Acquire.ExecTools.BGInitTask attribute) TASK_INFO_DTYPE (PYME.cluster.ruleserver.IntegerIDRule attribute) TASK_RUNNING (PYME.Acquire.ExecTools.BGInitTask attribute) task_timeout (PYME.Acquire.htsms.rule_ui.RuleTile attribute) TaskError (class in PYME.cluster.taskWorkerHTTP) TaskListProtocol (class in PYME.Acquire.protocol) TaskListTask (class in PYME.Acquire.protocol) TaskResult (class in PYME.misc.taskDef) tasksLoop() (PYME.cluster.taskWorkerHTTP.taskWorker method) taskWorker (class in PYME.cluster.taskWorkerHTTP) te() (in module PYME.util.mProfile.mProfile) (in module PYME.util.mProfile.p) TempDirCollection (class in PYME.cluster.webdav) template (PYME.cluster.taskWorkerHTTP.RecipeTaskError attribute) (PYME.cluster.taskWorkerHTTP.TaskError attribute) (PYME.recipes.output.ReportForEachOutput attribute) (PYME.recipes.output.ReportOutput attribute) template_fill() (in module PYME.cluster.rulenodeserver) temporalFilter (PYME.recipes.localisations.FiducialCorrection attribute) temporalFilterScale (PYME.recipes.localisations.FiducialCorrection attribute) TempPlotter (class in PYME.LMVis.Extras.temperaturePlot) terminate() (PYME.Acquire.webui.ipy.IPYWithClients method) tertiaryAxis (PYME.DSView.modules.blobMeasure.DataBlock property) Tesselation (class in PYME.recipes.pointcloud) TesselEngine (class in PYME.LMVis.layers.mesh) TesselShaderProgram (class in PYME.LMVis.shader_programs.TesselShaderProgram) test() (in module PYME.Analysis.points.EdgeDB.edgeTest) (in module PYME.contrib.pad) (in module PYME.util.shmarray.shmTest) test_function() (in module PYME.util.mProfile.tProfile) test_method() (PYME.util.mProfile.tProfile.T method) test_ps_app() (in module PYME.Analysis.PSFGen.test_ps_app) test_value (PYME.LMVis.shader_programs.GouraudShaderProgram.GouraudShaderProgram attribute) TestCurrentRecipe() (PYME.DSView.modules.recipes.RecipePlugin method) testFrame() (PYME.DSView.modules.LMAnalysis.LMAnalyser2 method) testObj() (in module PYME.Analysis.points.gen3DTriangs) testPattern() (in module PYME.simulation.locify) TestSpooler (class in PYME.IO.testClusterSpooling) Text (class in PYME.LMVis.layers.text) text (PYME.LMVis.layers.text.Text property) TextEditMixin (class in PYME.contrib.listctrlMixins) (class in PYME.ui.MetadataTree) TextfileSource (class in PYME.IO.tabular) textfileSource() (in module PYME.IO.tabular) TextShaderProgram (class in PYME.LMVis.shader_programs.DefaultShaderProgram) tfoef() (in module PYME.Analysis.BleachProfile.rollins) tformat() (PYME.IO.MetaDataHandler.MDHandlerBase static method) th() (in module PYME.Analysis.angleFilter) th2() (in module PYME.Analysis.angleFilter) then() (PYME.Acquire.actions.StateAction method) TheoreticalPSF (class in PYME.recipes.simulation) Theta (PYME.DSView.modules.blobMeasure.DataBlock property) theta_t() (in module PYME.misc.snells) thiolInt() (in module PYME.Analysis.BleachProfile.deMod) thread_profiler (in module PYME.util.fProfile.fProfile) threaded (PYME.recipes.measurement.PairwiseDistanceHistogram attribute) (PYME.recipes.pointcloud.Ripleys attribute) ThreadedHTTPServer (class in PYME.cluster.HTTPDataServer) ThreadProfiler (class in PYME.util.fProfile.fProfile) ThreadProfilerRegex (class in PYME.util.fProfile.fProfile) three_d (PYME.recipes.pointcloud.DelaunayTesselation attribute) (PYME.recipes.pointcloud.LocalPointDensity attribute) (PYME.recipes.pointcloud.Ripleys attribute) threeD (PYME.recipes.machine_learning.PointFeaturesPairwiseDist attribute) Threshold (class in PYME.recipes.processing) threshold (PYME.recipes.measurement.DetectPoints2D attribute) (PYME.recipes.measurement.MultifitBlobs attribute) (PYME.recipes.processing.LocalMaxima attribute) (PYME.recipes.processing.SimpleThreshold attribute) (PYME.recipes.surface_fitting.Isosurface attribute) threshold_density (PYME.recipes.surface_fitting.DelaunayMarchingTetrahedra attribute) (PYME.recipes.surface_fitting.DualMarchingCubes attribute) thresholdedManders() (in module PYME.Analysis.Colocalisation.correlationCoeffs) thresholds (PYME.DSView.displayOptions.DisplayOpts property) Tick() (PYME.Acquire.ActionManager.ActionManager method) (PYME.Acquire.positionTracker.PositionTracker method) (PYME.Acquire.ui.HDFSpoolFrame.PanSpool method) (PYME.Acquire.ui.seqdialog.SeqProgressPanel method) (PYME.Acquire.ui.splashScreen.SplashScreen method) tick() (PYME.Acquire.Utils.MultiPointScanner.PointScanner method) (PYME.Acquire.Utils.pointScanner.PointScanner method) (PYME.Acquire.Utils.pointScanner.PointScanner3D method) (PYME.Acquire.Utils.tiler.Tiler method) Tick() (PYME.Deconv.deconvDialogs.DeconvProgressDialog method) (PYME.Deconv.deconvDialogs.DeconvProgressPanel method) (PYME.DSView.modules.segmentation.SegmentationPanel method) (PYME.DSView.splashScreen.SplashScreen method) TIFFfile (class in PYME.contrib.gohlke.tifffile) TiffMP (class in PYME.IO.FileUtils.saveTiffStack) TiffSeriesExporter (class in PYME.IO.dataExporter) TiffStackExporter (class in PYME.IO.dataExporter) tile() (in module PYME.Analysis.deTile) tile_coords (PYME.IO.DataSources.SupertileDatasource.SupertileDataSource property) tile_coords_um (PYME.IO.DataSources.SupertileDatasource.SupertileDataSource property) tile_exists() (PYME.Analysis.tile_pyramid.NumpyTileIO method) (PYME.Analysis.tile_pyramid.SqliteTileIO method) (PYME.Analysis.tile_pyramid.TileIO method) tile_pyramid() (in module PYME.Analysis.tile_pyramid) tile_size (PYME.recipes.pyramid.TilePyramid attribute) TileCache (class in PYME.Analysis.tile_pyramid) TileIO (class in PYME.Analysis.tile_pyramid)

TilePanel (class in PYME.Acquire.ui.tile_panel) TilePyramid (class in PYME.recipes.pyramid) Tiler (class in PYME.Acquire.Utils.tiler) (class in PYME.DSView.modules.tiling) TileServer (class in PYME.tileviewer.tileviewer) time_block_subset() (in module PYME.LMVis.Extras.subsets) time_gap_tolerance (PYME.recipes.multiview.FindClumps attribute) TimeBlocks (class in PYME.recipes.localisations) TimedSpecies (class in PYME.LMVis.Extras.sequentialSpecies) timeout (PYME.cluster.HTTPDataServer.PYMEHTTPRequestHandler attribute) (PYME.recipes.acquisition.QueueAcquisitions attribute) timeout_two_opt() (in module PYME.Analysis.points.traveling_salesperson.two_opt) timeoutTesting (PYME.cluster.HTTPDataServer.PYMEHTTPRequestHandler attribute) times_to_frames() (in module PYME.Analysis.piecewiseMapping) timeWindow (PYME.recipes.localisations.FiducialCorrection attribute) (PYME.recipes.processing.WavefrontVelocity attribute) (PYME.recipes.tracking.FindClumps attribute) TiSettings (class in PYME.misc.TiSettings) to_bytes() (in module PYME.IO.clusterIO) to_csv() (PYME.IO.tabular.TabularBase method) to_hdf() (PYME.Analysis.points.spherical_harmonics.ScaledShell method) (PYME.IO.ragged.RaggedBase method) (PYME.IO.tabular.TabularBase method) to_html() (PYME.recipes.recipe.Recipe method) to_JSON() (PYME.Analysis.points.twoColour.ShiftModel method) (PYME.IO.events.MemoryEventLogger method) (PYME.IO.MetaDataHandler.MDHandlerBase method) to_json() (PYME.IO.ragged.RaggedBase method) to_JSON() (PYME.IO.tabular.TabularBase method) to_json() (PYME.LMVis.views.VideoView method) (PYME.LMVis.views.View method) to_pyoptic() (PYME.misc.zemax.ZMX method) to_recarray() (PYME.Analysis.points.spherical_harmonics.ScaledShell method) (PYME.IO.events.MemoryEventLogger method) (PYME.IO.tabular.TabularBase method) (PYME.LMVis.pipeline.Pipeline method) to_string() (PYME.cluster.taskWorkerHTTP.TaskError method) to_svg() (in module PYME.recipes.recipeLayout) (PYME.recipes.recipe.Recipe method) toDataFrame() (PYME.IO.tabular.TabularBase method) (PYME.LMVis.pipeline.Pipeline method) toggle_new_style() (PYME.DSView.modules.LMAnalysis.LMAnalyser2 method) toggle_roi (PYME.tileviewer.tileviewer.TileServer attribute) ToggleFold() (PYME.ui.manualFoldPanel.foldingPane method) ToggleItem() (PYME.contrib.listctrlMixins.CheckListCtrlMixin method) TogglePin() (PYME.ui.autoFoldPanel.foldingPane method) (PYME.ui.manualFoldPanel.foldingPane method) toJSON() (PYME.recipes.recipe.Recipe method) top() (PYME.LMVis.views.View method) toPyOptic() (PYME.misc.zemax.ZMX method) total_frames (PYME.cluster.rules.LocalisationRule property) (PYME.cluster.rules.SpoolLocalLocalizationRule property) total_nglasses() (in module PYME.misc.read_agf) toXls() (PYME.DSView.modules.blobMeasure.Measurements method) toYAML() (PYME.recipes.base.ModuleBase method) (PYME.recipes.recipe.Recipe method) ToZarr() (PYME.DSView.modules.neuroglancer.Neuroglancer method) tp (PYME.DSView.displayOptions.DisplayOpts property) Tp() (in module PYME.misc.snells) tq (PYME.DSView.modules.LMAnalysis.LMAnalyser2 property) tqPopFcn() (in module PYME.localization.remFitBuf) TracebackDialog (class in PYME.ui.progress) traceModel() (in module PYME.Analysis.BleachProfile.intensProf) traceModelDE() (in module PYME.Analysis.BleachProfile.intensProf) traceModelDE1() (in module PYME.Analysis.BleachProfile.intensProf) TraceROISelectPanel (class in PYME.Acquire.ui.intensity_trace) Track (class in PYME.Analysis.Tracking.trackUtils) Track() (PYME.recipes.tracking.TrackFeatures method) Track3DEngine (class in PYME.LMVis.layers.tracks) trackDetail (PYME.DSView.modules.particleTracking.ParticleTrackingView attribute) Tracker (class in PYME.Analysis.Tracking.tracking) tracker (PYME.DSView.modules.particleTracking.ParticleTrackingView attribute) TrackerPanel (class in PYME.Acquire.positionTracker) TrackerPlotPanel (class in PYME.Acquire.positionTracker) TrackFeatures (class in PYME.recipes.tracking) trackLineWidth (PYME.DSView.modules.particleTracking.ParticleTrackingView attribute) TrackList (class in PYME.DSView.modules.particleTracking) TrackManager (class in PYME.Analysis.Tracking.trackUtils) TrackRenderLayer (class in PYME.LMVis.layers.tracks) TrackWithPipeline() (PYME.recipes.tracking.TrackFeatures method) train() (PYME.Analysis.svmSegment.svmClassifier method) train_naive_bayes() (PYME.DSView.modules.annotation.Annotater method) train_svm() (PYME.DSView.modules.annotation.Annotater method) trainAndClassify() (PYME.Analysis.svmSegment.svmClassifier method) trainClassifier() (in module PYME.Analysis.svmSegment) trait_view() (PYME.recipes.base.ModuleBase method) trajectory (PYME.Analysis.Tracking.trackUtils.Track property) translate_path() (PYME.cluster.dataserver_wsgi.dataserver method) (PYME.cluster.HTTPDataServer.PYMEHTTPRequestHandler method) translateSeparators() (in module PYME.IO.FileUtils.nameUtils) TransparentPointsEngine (class in PYME.LMVis.layers.pointcloud) TravelingSalesperson (class in PYME.recipes.measurement) Triangle3DRenderer (class in PYME.LMVis.renderers) TriangleRenderer (class in PYME.LMVis.renderers) TriangleRendererW (class in PYME.LMVis.renderers) TriangleRenderLayer (class in PYME.LMVis.layers.mesh) trianglesEqual() (in module PYME.Analysis.points.gen3DTriangs) Ts() (in module PYME.misc.snells) tsoef() (in module PYME.Analysis.BleachProfile.rollins) tsp_chunk_two_opt_multiproc() (in module PYME.Analysis.points.traveling_salesperson.sectioned_two_opt) tsp_sort() (in module PYME.Analysis.points.traveling_salesperson.sort) TSPQueue (class in PYME.Analysis.points.traveling_salesperson.queue_opt) ttest_ind() (in module PYME.Analysis.points.moments) TTYDummy (class in PYME.Acquire.webui.ipy) turnAllLasersOff() (PYME.Acquire.microscope.microscope method) twistCal() (in module PYME.localization.twist) two_opt() (in module PYME.Analysis.points.traveling_salesperson.two_opt) two_opt_section() (in module PYME.Analysis.points.traveling_salesperson.sectioned_two_opt) two_opt_swap() (in module PYME.Analysis.points.traveling_salesperson.two_opt) two_opt_test() (in module PYME.Analysis.points.traveling_salesperson.two_opt) (in module PYME.Analysis.points.traveling_salesperson.two_opt_utils) TxtExporter (class in PYME.IO.dataExporter) type (PYME.IO.clusterListing.FileInfo property) (PYME.recipes.measurement.Plot attribute)

U

U() (in module PYME.Analysis.PSFGen.nijboer_zernike) Unfold() (PYME.ui.autoFoldPanel.foldingPane method) (PYME.ui.manualFoldPanel.foldingPane method) UnifiedLoader (class in PYME.reports) uniform_blob_paint() (in module PYME.Analysis.points.rings) uniform_random_radial_density() (PYME.Analysis.points.spherical_harmonics.ScaledShell method) uniform_theory() (in module PYME.Analysis.points.rings) uniform_theory_cdf() (in module PYME.Analysis.points.rings) unitnames (PYME.IO.FileUtils.obf_support.SIUnit attribute) units (PYME.IO.MetaDataHandler.VoxelSize attribute) (PYME.recipes.processing.Gradient2D attribute) (PYME.recipes.processing.Gradient3D attribute) unixdate2httpdate() (in module PYME.cluster.webdav) unixdate2iso8601() (in module PYME.cluster.webdav) Unmix() (PYME.Analysis.splitting.Unmixer method) Unmix_() (PYME.Analysis.splitting.Unmixer method) Unmixer (class in PYME.Analysis.splitting) (class in PYME.DSView.modules.splitter) (class in PYME.DSView.modules.unmixing) UnMixSettingsDlg (class in PYME.DSView.modules.unmixing) unnest_dtype() (in module PYME.IO.tabular) unNestDtype() (in module PYME.IO.tabular) unNestNames() (in module PYME.IO.tabular) unpack() (PYME.contrib.lzw.BitUnpacker method) unpackbyte() (in module PYME.contrib.lzw) unpickleSlice() (in module PYME.localization.FitFactories.fitCommon) UnPin() (PYME.ui.autoFoldPanel.foldingPane method) (PYME.ui.manualFoldPanel.foldingPane method) Unplug() (in module PYME.DSView.modules.flowView) unregister() (PYME.misc.hybrid_ns.HybridNS method) (PYME.misc.pyme_zeroconf.ZeroConfNS method) (PYME.misc.sqlite_ns.SQLiteNS method) Update() (in module PYME.DSView.modules.eventView) update() (PYME.Acquire.htsms.rule_ui.ChainedAnalysisPage method) (PYME.Acquire.htsms.rule_ui.ProtocolRules method) (PYME.Acquire.htsms.tweeter.LazyScopeTweeter method) (PYME.Acquire.microscope.StateManager method) (PYME.Acquire.sampleInformation.slidePanel method) (PYME.Acquire.stackSettings.StackSettings method) (PYME.Acquire.ui.actionUI.ActionList method) (PYME.Acquire.ui.AnalysisSettingsUI.AnalysisSettingsPanel method) (PYME.Acquire.ui.intsliders.IntegrationSliders method) (PYME.Acquire.ui.intsliders.IntegrationSliders_ method) (PYME.Acquire.ui.lasersliders.LaserSliders method) (PYME.Acquire.ui.lasersliders.LaserSliders_ method) (PYME.Acquire.ui.lasersliders.LaserToggles method) (PYME.Acquire.ui.mpd_picosecond_delay_panel.DelayPanel method) (PYME.Acquire.ui.multiview_select.MultiviewSelect method) (PYME.Acquire.ui.positionUI.PositionPanel method) (PYME.Acquire.ui.positionUI.PositionSliders method) (PYME.DSView.dsviewer.DSViewFrame method) (PYME.DSView.modules.deconvolution.Deconvolver method) (PYME.DSView.modules.LMAnalysis.LMAnalyser2 method) (PYME.DSView.modules.LMDisplay.LMDisplay method) (PYME.DSView.modules.playback.PlayPanel method) (PYME.DSView.modules.playback.PlayZTPanel method) (PYME.LMVis.layer_panel.LayerPane method) (PYME.LMVis.layers.image_layer.ImageRenderLayer method) (PYME.LMVis.layers.mesh.TriangleRenderLayer method) (PYME.LMVis.layers.pointcloud.PointCloudRenderLayer method) (PYME.LMVis.layers.quiver.QuiverRenderLayer method) (PYME.LMVis.layers.tracks.TrackRenderLayer method) (PYME.recipes.recipeGui.RecipeView method) (PYME.ui.custom_traits_editors.DictChoiceStrPanel method) (PYME.ui.filterPane.FilterPane method) (PYME.ui.filterPane.FilterPanel method) update_base_tile() (PYME.Analysis.distributed_pyramid.DistributedImagePyramid method) (PYME.Analysis.tile_pyramid.ImagePyramid method)

update_base_tiles_from_frame() (PYME.Analysis.tile_pyramid.ImagePyramid method) update_cache() (PYME.IO.clusterListing.DirCache method) update_config() (in module PYME.config) update_data() (PYME.LMVis.layers.pointcloud.PointCloudRenderLayer method) update_datasource_panel() (PYME.LMVis.visCore.VisGUICore method) update_display() (PYME.Acquire.ui.intensity_trace.IntensityTracePanel method) update_from_datasource() (PYME.LMVis.layers.image_layer.ImageRenderLayer method) (PYME.LMVis.layers.mesh.TriangleRenderLayer method) (PYME.LMVis.layers.octree.OctreeRenderLayer method) (PYME.LMVis.layers.pointcloud.PointCloudRenderLayer method) (PYME.LMVis.layers.quiver.QuiverRenderLayer method) (PYME.LMVis.layers.tracks.TrackRenderLayer method) update_from_file() (PYME.recipes.recipe.Recipe method) update_from_yaml() (PYME.recipes.recipe.Recipe method) update_indices_add() (in module PYME.IO.buffer_helpers) update_indices_add_pc() (in module PYME.IO.buffer_helpers) update_indices_remove() (in module PYME.IO.buffer_helpers) update_indices_remove_pc() (in module PYME.IO.buffer_helpers) update_json() (PYME.Acquire.stackSettings.StackSettings method) update_levels() (PYME.ui.histLimits.HistLimitDialog method) update_list() (PYME.Acquire.htsms.rule_ui.ProtocolRuleFactoryListCtrl method) update_pyramid() (PYME.Analysis.distributed_pyramid.DistributedImagePyramid method) (PYME.Analysis.distributed_pyramid.PartialPyramid method) (PYME.Analysis.tile_pyramid.ImagePyramid method) update_recipe_text() (PYME.recipes.recipeGui.RecipeView method) update_scope_state() (PYME.Acquire.acquire_client.AcquireClient method) (PYME.Acquire.acquire_server.PYMEAcquireServer method) update_settings() (PYME.Acquire.SpoolController.SpoolController method) update_spooler_compression_settings() (PYME.Acquire.ui.HDFSpoolFrame.PanSpool method) update_status() (PYME.Acquire.htsms.tweeter.FakeAPI method) update_trace() (PYME.Acquire.ui.intensity_trace.IntensityTracePanel method) update_ui() (PYME.Acquire.ui.HDFSpoolFrame.PanSpool method) update_version() (in module PYME.update_version) update_version_hg() (in module PYME.update_version) update_yaml_keys() (in module PYME.config) updateBuffers() (PYME.localization.remFitBuf.BufferManager method) UpdateColourFilterChoices() (PYME.LMVis.colourFilterGUI.ColourFilterPane method) UpdateDisp() (PYME.Acquire.ui.seqdialog.seqPanel method) (PYME.DSView.fitInfo.FitInfoPanel method) UpdateFileList() (PYME.DSView.OpenSequenceDialog.SequencePanel method) (PYME.recipes.recipeGui.FileListPanel method) UpdateFreeSpace() (PYME.Acquire.ui.HDFSpoolFrame.PanSpool method) updateMetadata() (PYME.IO.h5rFile.H5RFile method) UpdatePointColourChoices() (PYME.LMVis.pointSettingsPanel.PointSettingsPanel method) UpdateRecipeText() (PYME.recipes.recipeGui.RecipeManager method) UpdateState (class in PYME.Acquire.actions) updateStatus() (in module PYME.cluster.HTTPDataServer) updateTrack() (PYME.Analysis.Tracking.tracking.Tracker method) updateValue() (PYME.localization.MetaDataEdit.BoolFloatParam method) (PYME.localization.MetaDataEdit.BoolParam method) (PYME.localization.MetaDataEdit.ChoiceParam method) (PYME.localization.MetaDataEdit.FilenameParam method) (PYME.localization.MetaDataEdit.FloatListParam method) (PYME.localization.MetaDataEdit.FloatParam method) (PYME.localization.MetaDataEdit.IntParam method) (PYME.localization.MetaDataEdit.RangeParam method) (PYME.localization.MetaDataEdit.StringParam method) updateView() (PYME.Acquire.Utils.fastTiler.fastTiler method) updateVX() (PYME.Deconv.richardsonLucyMVM.MotionCompensatingRichardsonLucy method) upload_directory() (in module PYME.IO.clusterUpload) upload_glob() (in module PYME.IO.clusterUpload) UPRIGHT (PYME.DSView.displayOptions.DisplayOpts attribute) upstream_inputs() (PYME.recipes.recipe.Recipe method) URI (PYME.misc.sqlite_ns.NSInfo property) use() (PYME.LMVis.shader_programs.shader_program.ShaderProgram method) use_cluster (PYME.DSView.modules.LMAnalysis.LMAnalyser2 property) use_oit() (PYME.LMVis.layers.mesh.OITShadedFaceEngine method) UserError UserErrorDialog (class in PYME.ui.progress)

V

V() (in module PYME.Analysis.PSFGen.nijboer_zernike) validate() (PYME.recipes.processing.PSFFile method) (PYME.recipes.traits.FileOrURI method) (PYME.recipes.traits.Input method) (PYME.recipes.traits.Output method) validate_token() (in module PYME.util.authenticate) values (PYME.simulation.pointsets.WRDictEnum property) variance_threshold (PYME.recipes.processing.DarkAndVarianceMap attribute) varnames (PYME.Analysis.Tracking.trackUtils.Clump property) vectDistanceHistogram3D() (in module PYME.Analysis.points.DistHist.distHist) vector_features_3d() (PYME.Analysis.points.features.metal.Backend method) vector_property (PYME.LMVis.layers.quiver.QuiverRenderLayer attribute) VectorfieldAngle (class in PYME.recipes.processing) VectorfieldCurl (class in PYME.recipes.processing) VectorfieldNorm (class in PYME.recipes.processing) vectorial (PYME.DSView.modules.pupilTools.PupilTools attribute) (PYME.recipes.simulation.TheoreticalPSF attribute) velocity_data (PYME.recipes.processing.CaWave property) velocity_image (PYME.recipes.processing.CaWave property) velocity_plot (PYME.recipes.processing.CaWave property) verbose_fix_name() (in module PYME.IO.unifiedIO) Verify() (PYME.Acquire.stackSettings.StackSettings method) verify_cluster_results_filename() (in module PYME.cluster.HTTPRulePusher) (in module PYME.cluster.HTTPTaskPusher) (in module PYME.cluster.rules) vertex_normals (PYME.recipes.pointcloud.Tesselation property) vertexColour (PYME.LMVis.layers.mesh.TriangleRenderLayer attribute) (PYME.LMVis.layers.pointcloud.PointCloudRenderLayer attribute) (PYME.LMVis.layers.tracks.TrackRenderLayer attribute) VibrAnal (class in PYME.Acquire.Utils.vibrationAnalysis) VibrationAnalyser (class in PYME.LMVis.Extras.vibration) VibrationSpecgram() (PYME.LMVis.Extras.vibration.VibrationAnalyser method) VideoFrame (class in PYME.LMVis.Extras.animation)

VideoPanel (class in PYME.LMVis.Extras.animation) VideoView (class in PYME.LMVis.views) View (class in PYME.LMVis.views) View() (in module PYME.misc.mock_traitsui) View3D() (in module PYME.DSView.dsviewer) view_id (PYME.LMVis.views.View property) view_limits (PYME.LMVis.view_clipping_pane.ClippingPanel property) view_number (PYME.recipes.multiview.ExtractMultiviewChannel attribute) view_vector (PYME.LMVis.shader_programs.GouraudShaderProgram.GouraudShaderProgram attribute) ViewClippingPanel (class in PYME.LMVis.view_clipping_pane) ViewIm3D() (in module PYME.DSView.dsviewer) ViewPanel (class in PYME.LMVis.Extras.saved_views) VirtList (class in PYME.Acquire.sampleInformation) VisGUICore (class in PYME.LMVis.visCore) visGuiExtras (class in PYME.DSView.modules.visgui) VisGUIFrame (class in PYME.LMVis.VisGUI) visible (PYME.LMVis.layers.base.BaseLayer attribute) visible_bounds (PYME.DSView.arrayViewPanel.ArrayViewPanel property) Visualiser (class in PYME.DSView.modules.vis3D) vlj() (in module PYME.Analysis.PSFGen.nijboer_zernike) VoronoiRenderer (class in PYME.LMVis.renderers) voxels (PYME.IO.image.ImageStack property) VoxelSize (class in PYME.IO.MetaDataHandler) voxelsize (PYME.DSView.arrayViewPanel.ArrayViewPanel property) (PYME.DSView.modules.composite.CompositeDialog property) (PYME.IO.image.ImageStack property) voxelsize_nm (PYME.IO.image.ImageStack property) (PYME.IO.MetaDataHandler.MDHandlerBase property) (PYME.recipes.surface_fitting.ImageMaskFromSphericalHarmonicShell attribute) voxelsize_x() (in module PYME.Analysis.PSFEst.psfQuality) voxelsize_z_dec() (in module PYME.Analysis.PSFEst.psfQuality) voxelsize_z_loc() (in module PYME.Analysis.PSFEst.psfQuality) VoxelSizeDialog (class in PYME.Acquire.ui.voxelSizeDialog) VoxSizeDialog (class in PYME.DSView.voxSizeDialog)

W

wait_close() (PYME.IO.h5rFile.H5RFile method) wait_for_init() (PYME.Acquire.microscope.microscope method) walk() (in module PYME.IO.clusterIO) Warn() (in module PYME.LMVis.Extras.multiColourAnalysis) (in module PYME.LMVis.Extras.QPobjectSegment) warn() (in module PYME.warnings) warpCorrectRedImage() (in module PYME.Analysis.points.twoColour) watch() (PYME.cluster.rules.Rule method) (PYME.cluster.rules.RuleGroupWatcher method) (PYME.cluster.rules.RuleWatcher method) Watershed (class in PYME.recipes.processing) wavefront_image (PYME.recipes.processing.CaWave property) WavefrontDetection (class in PYME.recipes.processing) WavefrontVelocity (class in PYME.recipes.processing) wavelength (PYME.DSView.modules.psfGeneration.PupilGenerator attribute) (PYME.DSView.modules.pupilTools.PupilTools attribute) (PYME.recipes.simulation.TheoreticalPSF attribute) waveRecipeFileName (PYME.recipes.processing.FindCaWaves attribute) wavetableZScanner (class in PYME.Acquire.zScanner) WeakRef (in module PYME.misc.mock_traits) WebAuth() (PYME.cluster.webdav.DAVRequestHandler method) weightedAverage() (in module PYME.Analysis.points.DeClump.pyDeClump) weightedAverage_() (in module PYME.Analysis.points.DeClump.pyDeClump) WFNodeServer (class in PYME.cluster.rulenodeserver) WFPSFFitFactory (class in PYME.localization.FitFactories.InterpFitWFR) WFRuleServer (class in PYME.cluster.ruleserver) WhiteTophat (class in PYME.recipes.processing) widefield_pupil_and_propagator() (in module PYME.Analysis.PSFGen.fourierHNA) (in module PYME.Analysis.PSFGen.fourierHNA2) widefieldify() (in module PYME.Analysis.widefieldify) WidefieldPupil (class in PYME.DSView.modules.psfGeneration) width() (in module PYME.Analysis.angleFilter) (PYME.IO.image.ImageBounds method) (PYME.LMVis.visHelpersMin.ImageBounds method) width_filter() (in module PYME.Analysis.angleFilter) width_filter_m() (in module PYME.Analysis.angleFilter) width_inches (PYME.LMVis.Extras.snapshot.SnapshotSettings attribute) width_o() (in module PYME.Analysis.angleFilter) width_pixels (PYME.LMVis.Extras.snapshot.SnapshotSettings attribute) widthPixels (PYME.recipes.filters.MaskEdges attribute)

WienerDeconvolver (class in PYME.DSView.modules.deconvolution) wiglyFibre() (in module PYME.simulation.wormlike2) (in module PYME.simulation.wormlike3) WiglyFibreSource (class in PYME.simulation.pointsets) WinDLL (in module PYME.misc.mock_ctypes) window (PYME.recipes.localisations.AutocorrelationDriftCorrection attribute) (PYME.recipes.processing.BackgroundSubtractionMovingAverage attribute) (PYME.recipes.surface_fitting.NthPointIsosurface attribute) WireframeEngine (class in PYME.LMVis.layers.mesh) WireFrameShaderProgram (class in PYME.LMVis.shader_programs.WireFrameShaderProgram) with_constant() (in module PYME.contrib.pad.pad) with_linear_ramp() (in module PYME.contrib.pad.pad) with_maximum() (in module PYME.contrib.pad.pad) with_mean() (in module PYME.contrib.pad.pad) with_median() (in module PYME.contrib.pad.pad) with_minimum() (in module PYME.contrib.pad.pad) with_reflect() (in module PYME.contrib.pad.pad) with_wrap() (in module PYME.contrib.pad.pad) wormlikeChain (class in PYME.simulation.wormlike) (class in PYME.simulation.wormlike2) (class in PYME.simulation.wormlike3) (class in PYME.simulation.wormlike_curled) wormlikeChain2D (class in PYME.simulation.wormlike3) WormlikeSource (class in PYME.simulation.pointsets) Wrap() (in module PYME.IO.dataWrap) WRDictEnum (class in PYME.simulation.pointsets) write() (in module PYME.IO.unifiedIO) (PYME.Acquire.webui.ipy.TTYDummy method) (PYME.cluster.webdav.BufWriter method) (PYME.DSView.logparser.logwriter method) (PYME.IO.MetaDataHandler.SimpleMDHandler method) write_metadata() (PYME.DSView.modules.psfExtraction.PsfExtractor method) write_response() (PYME.util.webframework.HTTPResponse method) writebytes() (in module PYME.contrib.lzw) WriteSimple() (PYME.IO.MetaDataHandler.MDHandlerBase method) writeTiff() (in module PYME.IO.FileUtils.saveTiffStack) writeXML() (PYME.IO.MetaDataHandler.OMEXMLMDHandler method) (PYME.IO.MetaDataHandler.XMLMDHandler method) wsgiref_server() (in module PYME.cluster.dataserver_wsgi) wxThread (class in PYME.misc.wxThread)

X

x (PYME.IO.MetaDataHandler.VoxelSize property) X (PYME.localization.FitFactories.AstigGaussGPUFitFR.GaussianFitFactory attribute) (PYME.localization.FitFactories.ChecksumGPUFR.ChecksumFitFactory attribute) (PYME.localization.FitFactories.ChecksumMultifitSR.ChecksumFitFactory attribute) (PYME.localization.FitFactories.GaussMultifitLinesR.GaussianFitFactory attribute) (PYME.localization.FitFactories.GaussMultifitR.GaussianFitFactory attribute) (PYME.localization.FitFactories.GaussMultifitSR.GaussianFitFactory attribute) (PYME.localization.FitFactories.SplitterMultifitSR.GaussianFitFactory attribute) x (PYME.tileviewer.tileviewer.Location property) (PYME.ui.selection.Point property) x0() (PYME.localization.FitFactories.Gauss3DFitR.GaussFitResult method) (PYME.localization.FitFactories.LatPSFFitR.PSFFitResult method) x_range (PYME.recipes.base.Crop attribute) XC (PYME.DSView.modules.blobMeasure.DataBlock property)

xkey (PYME.recipes.measurement.Plot attribute) XLSOutput (class in PYME.recipes.output) XMLDict_Parser (class in PYME.cluster.webdav) XMLMDHandler (class in PYME.IO.MetaDataHandler) xp (PYME.DSView.displayOptions.DisplayOpts property) XTZCBackgroundSource (class in PYME.IO.DataSources.BGSDataSource) xyBoundsMode (PYME.recipes.localisations.DensityMapping attribute) XYTCDataSource (class in PYME.IO.DataSources.BaseDataSource) XYTCWrapper (class in PYME.IO.DataSources.BaseDataSource) XYZSubvolume (class in PYME.IO.DataSources.BaseDataSource) XYZTCAcquisition (class in PYME.Acquire.xyztc) XYZTCArrayDataSource (class in PYME.IO.DataSources.ArrayDataSource) XYZTCBgsSource (class in PYME.IO.DataSources.BGSDataSource) XYZTCDataSource (class in PYME.IO.DataSources.BaseDataSource) XYZTCWrapper (class in PYME.IO.DataSources.BaseDataSource)

Y

y (PYME.IO.MetaDataHandler.VoxelSize property) Y (PYME.localization.FitFactories.AstigGaussGPUFitFR.GaussianFitFactory attribute) (PYME.localization.FitFactories.ChecksumGPUFR.ChecksumFitFactory attribute) (PYME.localization.FitFactories.ChecksumMultifitSR.ChecksumFitFactory attribute) (PYME.localization.FitFactories.GaussMultifitLinesR.GaussianFitFactory attribute) (PYME.localization.FitFactories.GaussMultifitR.GaussianFitFactory attribute) (PYME.localization.FitFactories.GaussMultifitSR.GaussianFitFactory attribute) (PYME.localization.FitFactories.SplitterMultifitSR.GaussianFitFactory attribute) y (PYME.tileviewer.tileviewer.Location property) (PYME.ui.selection.Point property)

y0() (PYME.localization.FitFactories.Gauss3DFitR.GaussFitResult method) (PYME.localization.FitFactories.LatPSFFitR.PSFFitResult method) y_range (PYME.recipes.base.Crop attribute) YC (PYME.DSView.modules.blobMeasure.DataBlock property) Yellow() (in module PYME.misc.colormaps) yiq_to_rgb() (in module PYME.misc.colorsys) ykey (PYME.recipes.measurement.Plot attribute) yp (PYME.DSView.displayOptions.DisplayOpts property)

Z

z (PYME.IO.MetaDataHandler.VoxelSize property) (PYME.ui.selection.Point property) z() (in module PYME.misc.zernike) z0() (PYME.localization.FitFactories.Gauss3DFitR.GaussFitResult method) (PYME.localization.FitFactories.LatPSFFitR.PSFFitResult method) z_column_name (PYME.recipes.processing.AverageFramesByZStep attribute) z_nm (PYME.LMVis.layers.image_layer.ImageRenderLayer property) z_pos (PYME.LMVis.layers.image_layer.ImageRenderLayer attribute) z_range (PYME.recipes.base.Crop attribute) z_sampling (PYME.recipes.processing.ResampleZ attribute) z_scale (PYME.recipes.localisations.MapAstigZ attribute) zBounds (PYME.recipes.localisations.DensityMapping attribute) zBoundsMode (PYME.recipes.localisations.DensityMapping attribute) ZC (PYME.DSView.modules.blobMeasure.DataBlock property) ZCListener (class in PYME.misc.pyme_zeroconf) ZDEPSHIFT (PYME.Analysis.points.twoColour.lin3zModel attribute) zernike() (in module PYME.misc.zernike)

zernike_modes (PYME.recipes.simulation.TheoreticalPSF attribute) zernikeIm() (in module PYME.misc.zernike) ZernikeMode (class in PYME.DSView.modules.psfGeneration) ZernikePSF (class in PYME.Analysis.PSFGen.fourierHNA) ZernikePSFModel (class in PYME.localization.autopsf.autopsf) ZeroConfNS (class in PYME.misc.pyme_zeroconf) zeros() (in module PYME.util.shmarray.shmarray) ZMX (class in PYME.misc.zemax) Zoom (class in PYME.recipes.filters) zoom (PYME.recipes.filters.Zoom attribute) (PYME.recipes.output.RGBImageOutput attribute) zp (PYME.DSView.displayOptions.DisplayOpts property) zPadding (PYME.recipes.processing.Deconvolve attribute) zScale (PYME.simulation.pointsets.WiglyFibreSource attribute) zScanner (class in PYME.Acquire.zScanner) zSliceThickness (PYME.recipes.localisations.DensityMapping attribute) zSpacing (PYME.DSView.modules.pupilTools.PupilTools attribute) ZStackTaskListProtocol (class in PYME.Acquire.protocol)