Index

_

__init__() (acia.analysis.AreaEx method) (acia.analysis.BoundaryClosenessEx method) (acia.analysis.CircularityEx method) (acia.analysis.DynamicTimeEx method) (acia.analysis.ExtractorExecutor method) (acia.analysis.FluorescenceEx method) (acia.analysis.FrameEx method) (acia.analysis.growth_rate.GrowthRateResult method) (acia.analysis.IdEx method) (acia.analysis.LabelEx method) (acia.analysis.LengthEx method) (acia.analysis.LengthWidthEx method) (acia.analysis.PerimeterEx method) (acia.analysis.PositionEx method) (acia.analysis.PropertyExtractor method) (acia.analysis.stage.StageContext method) (acia.analysis.TimeEx method) (acia.analysis.WidthEx method) (acia.base.ArrayImage method) (acia.base.Contour method) (acia.base.ImageRoISource method) (acia.base.Instance method) (acia.base.Overlay method) (acia.base.RegisteredSequenceSource method) (acia.base.RGBSequenceSource method) (acia.base.RotatedCropSequenceSource method) (acia.base.RotatedCropSpec method) (acia.base.SlicedSequenceSource method) (acia.notebook.FilterExplorer method) (acia.notebook.RegistrationDashboard method) (acia.notebook.ROICropper method) (acia.notebook.SequenceDashboard method) (acia.registration.FeatureRANSACEuclidean method) (acia.registration.FrameTransform method) (acia.registration.GradientECC method) (acia.registration.HoughLineRigidFit method) (acia.registration.MaskedTemplateCorrelation method) (acia.registration.PhaseCorrelationHighpass method) (acia.registration.ReanchoringReference method) (acia.registration_persistence.RegistrationManifest method) (acia.registration_persistence.RegistrationRecord method) (acia.segm.czi_source.CZISequenceSource method) (acia.segm.filter.BoundaryClosenessFilter method) (acia.segm.filter.CellFilter method) (acia.segm.folder_source.FolderSequenceSource method) (acia.segm.local.ImageJRoISource method) (acia.segm.local.InMemorySequenceSource method) (acia.segm.local.LocalImage method) (acia.segm.local.LocalImageSource method) (acia.segm.local.LocalSequenceSource method) (acia.segm.local.SambaSequenceSource method) (acia.segm.local.THWCSequenceSource method) (acia.segm.nd2_source.ND2SequenceSource method) (acia.segm.omero.storer.BlitzConn method) (acia.segm.omero.storer.IngoreWithWrapper method) (acia.segm.omero.storer.OmeroRawSource method) (acia.segm.omero.storer.OmeroRoISource method) (acia.segm.omero.storer.OmeroSequenceSource method) (acia.segm.omero.storer.OmeroSource method) (acia.segm.omero.utils.OmeroScaleBar method) (acia.segm.open.PositionInfo method) (acia.segm.open.SequenceFile method) (acia.segm.open.SequenceMetadata method) (acia.segm.output.DatasetExporter method) (acia.segm.output.MMSegmentationDataset method) (acia.segm.processor.canny.CannySegmentationProcessor method) (acia.segm.processor.cellpose.CellposeSegmenter method) (acia.segm.processor.cellpose_sam.CellposeSAMSegmenter method) (acia.segm.processor.cpn.CPNSegmenter method) (acia.segm.processor.flowpose_rt.FlowposeRTSegmenter method) (acia.segm.processor.offline.OfflineModel method) (acia.segm.processor.offline.PoseModel method) (acia.segm.processor.omnipose.OmniposeSegmenter method) (acia.segm.processor.online.FlexibleOnlineModel method) (acia.segm.processor.online.ModelDescriptor method) (acia.segm.processor.online.OnlineModel method) (acia.segm.processor.yolo.YOLOSegmenter method) (acia.segm.tiff_metadata.TiffCalibration method) (acia.selection.RoiSelection method) (acia.selection.SelectionManifest method) (acia.tracking.output.CellTrackingChallengeDatasetGT method) (acia.tracking.output.CellTrackingDatasetResult method) (acia.tracking.output.CTCTrackingHelper method) (acia.tracking.processor.laptrack.LAPTracker method) (acia.tracking.processor.laptrack.LAPTracker2 method) (acia.tracking.processor.laptrack.LaptrackTracker method) (acia.tracking.processor.pyuat.PyUATTracker method) (acia.tracking.processor.trackastra.TrackastraTracker method) (acia.tracking.processor.ultrack.UltrackTracker method) (acia.tracking.SimpleTrackingSource method) (acia.tracking.TrackingSourceInMemory method) (acia.viz.compose.ComposedSequenceSource method) (acia.viz.VideoExporter method) (acia.viz.VideoExporter2 method)

A

accepts() (acia.segm.filter.CellFilter method) acia.analysis module acia.analysis.doubling_time module acia.analysis.growth_rate module acia.analysis.properties module acia.analysis.stage module acia.analysis.units module acia.attribute module acia.base module acia.colors module acia.config module acia.crop_capture module acia.notebook module acia.registration module acia.registration_persistence module acia.segm.czi_source module acia.segm.filter module acia.segm.folder_source module acia.segm.formats module acia.segm.local module acia.segm.nd2_source module acia.segm.omero.shapeUtils module acia.segm.omero.storer module acia.segm.omero.utils module acia.segm.open module acia.segm.output module acia.segm.processor.canny module acia.segm.processor.cellpose module acia.segm.processor.cellpose_sam module acia.segm.processor.cpn module acia.segm.processor.flowpose_rt module acia.segm.processor.offline module acia.segm.processor.omnipose module acia.segm.processor.online module

acia.segm.processor.predict module acia.segm.processor.yolo module acia.segm.tiff_export module acia.segm.tiff_metadata module acia.segm.utils module acia.selection module acia.timing module acia.tracking module acia.tracking.formats module acia.tracking.output module acia.tracking.processor.laptrack module acia.tracking.processor.pyuat module acia.tracking.processor.trackastra module acia.tracking.processor.ultrack module acia.tracking.processor.utils module acia.tracking.utils module acia.utils module acia.viz module acia.viz.compose module acia.viz.utils module add() (acia.segm.output.DatasetExporter method) (acia.tracking.output.CellTrackingChallengeDatasetGT method) (acia.tracking.output.CellTrackingDatasetResult method) add_contour() (acia.base.Overlay method) add_contours() (acia.base.Overlay method) AggMode (in module acia.analysis.growth_rate) anchor_frame (acia.registration.ReanchoringReference property) (acia.selection.RoiSelection attribute) angle (acia.base.RotatedCropSpec attribute) (acia.notebook.ROICropper attribute) annotate_tracklet_times() (in module acia.tracking) apply() (acia.base.ImageRoISource method) apply_cell_filters() (in module acia.segm.filter) apply_correction() (in module acia.registration) apply_correction_to_spec() (in module acia.registration) apply_parallel() (acia.base.ImageRoISource method) apply_parallel_star() (acia.base.ImageRoISource method) apply_star() (acia.base.ImageRoISource method) area (acia.base.Contour property) (acia.base.Instance property) AreaEx (class in acia.analysis) AreaFilter (class in acia.segm.filter) ArrayImage (class in acia.base) attach_units() (in module acia.analysis.units) attribute_segmentation() (in module acia.attribute) attribute_tracking() (in module acia.attribute) auto_save (acia.notebook.SequenceDashboard attribute)

B

BaseImage (class in acia.base) batch() (in module acia.segm.processor.omnipose) (in module acia.segm.processor.online) batch_apply() (acia.notebook.RegistrationDashboard method) batch_running (acia.notebook.RegistrationDashboard attribute)

bbox_to_rectangle() (in module acia.segm.filter) binary_mask (acia.base.Instance property) BlitzConn (class in acia.segm.omero.storer) BoundaryClosenessEx (class in acia.analysis) BoundaryClosenessFilter (class in acia.segm.filter) build_sample_frame_indices() (in module acia.registration)

C

calibration() (acia.analysis.stage.StageContext method) CALIBRATION_SCHEMA (in module acia.analysis.stage) calibration_source (acia.segm.folder_source.FolderSequenceSource property) (acia.segm.local.LocalSequenceSource property) CannySegmentationProcessor (class in acia.segm.processor.canny) CellFilter (class in acia.segm.filter) CellposeSAMSegmenter (class in acia.segm.processor.cellpose_sam) CellposeSegmenter (class in acia.segm.processor.cellpose) CellTrackingChallengeDatasetGT (class in acia.tracking.output) CellTrackingDatasetResult (class in acia.tracking.output) center (acia.base.Contour property) (acia.base.Instance property) (acia.base.RotatedCropSpec attribute) center_x (acia.notebook.ROICropper attribute) center_y (acia.notebook.ROICropper attribute) channel_names (acia.segm.czi_source.CZISequenceSource property) (acia.segm.nd2_source.ND2SequenceSource property) channels (acia.segm.open.SequenceMetadata attribute) check_stale() (in module acia.analysis.stage) CircularityEx (class in acia.analysis) CircularityFilter (class in acia.segm.filter) clear() (acia.analysis.stage.StageContext method) (acia.segm.omero.storer.OmeroRoIStorer static method) close() (acia.segm.folder_source.FolderSequenceSource method) (acia.segm.local.LocalSequenceSource method) (acia.segm.open.SequenceFile method) (acia.viz.VideoExporter method) (acia.viz.VideoExporter2 method) colorize_instance_mask() (in module acia.viz) compose() (in module acia.registration) compose_sequences() (in module acia.viz.compose) ComposedSequenceSource (class in acia.viz.compose) compute_doubling_times() (in module acia.analysis.doubling_time) compute_indices() (in module acia.segm.utils)

compute_life_cycles() (acia.tracking.output.CTCTrackingHelper static method) compute_lineage_y() (in module acia.viz) compute_trace() (in module acia.tracking.utils) confidence (acia.registration.FrameTransform attribute) configured_filters() (acia.notebook.FilterExplorer method) Contour (class in acia.base) contour_from_mask() (in module acia.segm.processor.predict) contours (acia.notebook.FilterExplorer attribute) convert() (acia.analysis.PropertyExtractor method) convert_array() (acia.analysis.PropertyExtractor method) convert_overlay_to_ctc_mask() (acia.tracking.output.CTCTrackingHelper static method) coordinates (acia.base.Contour property) (acia.base.Instance property) copy() (acia.tracking.TrackingSource method) (acia.tracking.TrackingSourceInMemory method) CPNSegmenter (class in acia.segm.processor.cpn) create_dataset() (in module acia.segm.omero.utils) create_ellipse() (in module acia.segm.omero.shapeUtils) create_life_cycle_lookup() (acia.tracking.output.CTCTrackingHelper static method) create_polygon() (in module acia.segm.omero.shapeUtils) create_project() (in module acia.segm.omero.utils) create_rectangle() (in module acia.segm.omero.shapeUtils) create_roi() (in module acia.segm.omero.storer) create_roi_fast() (in module acia.segm.omero.storer) created (acia.registration_persistence.RegistrationManifest attribute) (acia.selection.SelectionManifest attribute) crop_rotated() (acia.base.ImageSequenceSource method) cropped() (acia.notebook.ROICropper method) croppedContours() (acia.base.Overlay method) ctc_track_graph() (in module acia.tracking) (in module acia.tracking.formats) CTCTrackingHelper (class in acia.tracking.output) CZISequenceSource (class in acia.segm.czi_source)

D

DatasetExporter (class in acia.segm.output) datasetName() (acia.segm.omero.storer.OmeroSequenceSource method) DEFAULT_CI_LEVELS (in module acia.analysis.doubling_time) default_execution_naming() (in module acia.analysis) default_h264() (acia.viz.VideoExporter2 static method) default_h265() (acia.viz.VideoExporter2 static method) DEFAULT_KEY_PATTERN (in module acia.analysis.stage) default_mjpg() (acia.viz.VideoExporter2 static method) DEFAULT_TIME_UNIT (in module acia.analysis.growth_rate) default_vp9() (acia.viz.VideoExporter2 static method) delete_file_annotation() (in module acia.segm.omero.storer) delete_nodes() (in module acia.tracking.utils) doubling_time (acia.analysis.growth_rate.GrowthRateResult attribute) download_file_from_annotation() (in module acia.segm.omero.storer)

download_file_from_object() (in module acia.segm.omero.storer) draw() (acia.base.Contour method) (acia.base.Instance method) (acia.base.Overlay method) (acia.segm.omero.utils.OmeroScaleBar method) (acia.utils.ScaleBar method) draw_scale_bar() (in module acia.viz) draw_time() (in module acia.viz) dtype (acia.segm.czi_source.CZISequenceSource property) (acia.segm.folder_source.FolderSequenceSource property) (acia.segm.nd2_source.ND2SequenceSource property) (acia.segm.open.SequenceMetadata attribute) dx (acia.registration.FrameTransform attribute) dy (acia.registration.FrameTransform attribute) DynamicTimeEx (class in acia.analysis)

E

EllipsoidFilter (class in acia.segm.filter) estimate() (acia.registration.FeatureRANSACEuclidean method) (acia.registration.GradientECC method) (acia.registration.HoughLineRigidFit method) (acia.registration.MaskedTemplateCorrelation method) (acia.registration.PhaseCorrelationHighpass method) (acia.registration.ReanchoringReference method) (acia.registration.RegistrationMethod method) estimate_growth_rate() (in module acia.analysis.growth_rate) execute() (acia.analysis.ExtractorExecutor method) extract() (acia.analysis.AreaEx method) (acia.analysis.BoundaryClosenessEx method) (acia.analysis.CircularityEx method) (acia.analysis.DynamicTimeEx method) (acia.analysis.FluorescenceEx method) (acia.analysis.FrameEx method) (acia.analysis.IdEx method) (acia.analysis.LabelEx method) (acia.analysis.LengthEx method) (acia.analysis.LengthWidthEx method) (acia.analysis.PerimeterEx method) (acia.analysis.PositionEx method) (acia.analysis.PropertyExtractor method) (acia.analysis.TimeEx method) (acia.analysis.WidthEx method)

extract_fluorescence() (acia.analysis.FluorescenceEx static method) extract_growth() (in module acia.analysis) extract_lineage_plotdata() (in module acia.viz) extract_segmentation_stacks() (in module acia.segm.utils) extractor ExtractorExecutor (class in acia.analysis)

F

failed_frames (acia.registration_persistence.RegistrationRecord attribute) fast_mask_rendering() (in module acia.segm.output) fast_mask_rendering_torch() (in module acia.segm.output) fast_vp9() (acia.viz.VideoExporter2 static method) FeatureRANSACEuclidean (class in acia.registration) files (acia.segm.folder_source.FolderSequenceSource property) filter() (acia.segm.filter.EllipsoidFilter static method) (acia.segm.filter.NMSFilter static method) (acia.segm.filter.SizeFilter static method) filter_specs (acia.notebook.FilterExplorer attribute) filtered_overlay() (acia.notebook.FilterExplorer method) FilterExplorer (class in acia.notebook) finish() (acia.analysis.stage.StageContext method) fit_to_points() (acia.notebook.ROICropper method) FlexibleOnlineModel (class in acia.segm.processor.online) FlowposeRTSegmenter (class in acia.segm.processor.flowpose_rt) FluorescenceEx (class in acia.analysis) flush() (acia.analysis.stage.StageContext method)

FolderSequenceSource (class in acia.segm.folder_source) for_image() (acia.analysis.stage.StageContext class method) frame_interval (acia.segm.open.SequenceMetadata attribute) (acia.segm.tiff_metadata.TiffCalibration attribute) frame_list (acia.segm.omero.storer.OmeroSequenceSource property) FrameEx (class in acia.analysis) frames() (acia.base.Overlay method) FrameTransform (class in acia.registration) from_array() (acia.segm.local.LocalImageSource static method) from_dict() (acia.base.RotatedCropSpec class method) (acia.registration.FrameTransform class method) (acia.registration_persistence.RegistrationManifest class method) (acia.registration_persistence.RegistrationRecord class method) (acia.selection.RoiSelection class method) (acia.selection.SelectionManifest class method) from_file() (acia.segm.local.LocalImageSource static method) (acia.tracking.SimpleTrackingSource static method) from_header() (in module acia.analysis.units) from_url() (acia.segm.local.SambaSequenceSource class method)

G

gen_simple_segmentation() (in module acia.segm.formats) gen_simple_tracking() (in module acia.tracking.formats) get_channel() (acia.base.ArrayImage method) (acia.base.BaseImage method) (acia.segm.local.LocalImage method) get_frame() (acia.base.ImageSequenceSource method) (acia.base.RegisteredSequenceSource method) (acia.base.RGBSequenceSource method) (acia.base.RotatedCropSequenceSource method) (acia.base.SlicedSequenceSource method) (acia.notebook.JupyterVisualizationMixin method) (acia.segm.czi_source.CZISequenceSource method) (acia.segm.folder_source.FolderSequenceSource method) (acia.segm.local.InMemorySequenceSource method) (acia.segm.local.LocalImageSource method) (acia.segm.local.LocalSequenceSource method) (acia.segm.local.THWCSequenceSource method) (acia.segm.nd2_source.ND2SequenceSource method) (acia.segm.omero.storer.OmeroRawSource method) (acia.segm.omero.storer.OmeroSequenceSource method) (acia.viz.compose.ComposedSequenceSource method)

get_image_name() (in module acia.segm.omero.utils) get_mask() (in module acia.viz) get_overlay() (acia.segm.omero.storer.OmeroRoISource method) get_project_name() (in module acia.segm.omero.utils) get_user() (in module acia.attribute) getDataset() (in module acia.segm.omero.utils) getImage() (in module acia.segm.omero.utils) getProject() (in module acia.segm.omero.utils) GradientECC (class in acia.registration) growth_rate (acia.analysis.growth_rate.GrowthRateResult attribute) growth_rate_ci (acia.analysis.growth_rate.GrowthRateResult attribute) growth_rate_std_err (acia.analysis.growth_rate.GrowthRateResult attribute) GrowthRateResult (class in acia.analysis.growth_rate)

H

has() (acia.analysis.stage.StageContext method) has_all_tags() (in module acia.segm.omero.utils)

height (acia.notebook.ROICropper attribute) HoughLineRigidFit (class in acia.registration)

I

id (acia.selection.RoiSelection attribute) IdEx (class in acia.analysis) image_b64 (acia.notebook.FilterExplorer attribute) (acia.notebook.ROICropper attribute) image_h (acia.notebook.FilterExplorer attribute) (acia.notebook.ROICropper attribute) image_id (acia.analysis.stage.StageContext attribute) image_iterator() (in module acia.segm.omero.utils) image_w (acia.notebook.FilterExplorer attribute) (acia.notebook.ROICropper attribute) ImageJRoISource (class in acia.segm.local) imageName() (acia.segm.omero.storer.OmeroSequenceSource method)

ImageRoISource (class in acia.base) ImageSequenceSource (class in acia.base) index (acia.segm.open.PositionInfo attribute) inference() (in module acia.segm.processor.predict) IngoreWithWrapper (class in acia.segm.omero.storer) initial_value (acia.analysis.growth_rate.GrowthRateResult attribute) InMemorySequenceSource (class in acia.segm.local) input_path() (acia.analysis.stage.StageContext method) Instance (class in acia.base) IO_SCHEMA (in module acia.analysis.stage) is_fragmented (acia.base.Instance property)

J

JupyterVisualizationMixin (class in acia.notebook)

K

keyed() (acia.analysis.stage.StageContext method)

keys (acia.analysis.stage.StageContext attribute)

L

label (acia.base.Instance property) (acia.selection.RoiSelection attribute) label_sequence() (in module acia.viz.compose) LabelEx (class in acia.analysis) LAPTracker (class in acia.tracking.processor.laptrack) LAPTracker2 (class in acia.tracking.processor.laptrack) LaptrackTracker (class in acia.tracking.processor.laptrack) largest_polygon() (in module acia.utils) lazy view length_and_area() (in module acia.segm.utils) LengthEx (class in acia.analysis) LengthFilter (class in acia.segm.filter) LengthWidthEx (class in acia.analysis) life_cycle_lineage() (in module acia.tracking.utils) list_datasets_in_project() (in module acia.segm.omero.utils) list_file_annotations() (in module acia.segm.omero.storer) list_image_ids_in() (in module acia.segm.omero.utils) list_image_ids_in_dataset() (in module acia.segm.omero.utils) list_images_in_dataset() (in module acia.segm.omero.utils) list_images_in_project() (in module acia.segm.omero.utils) list_projects() (in module acia.segm.omero.utils) list_sequence_sources() (in module acia.segm.local) load() (acia.registration_persistence.RegistrationManifest class method) (acia.segm.local.RoiStorer static method) (acia.segm.omero.storer.OmeroRoIStorer static method) (acia.selection.SelectionManifest class method)

load_crop_spec() (in module acia.crop_capture) load_ctc_format() (acia.tracking.output.CTCTrackingHelper static method) load_ctc_segmentation() (in module acia.segm.formats) load_model() (acia.segm.processor.offline.OfflineModel method) (acia.segm.processor.offline.PoseModel method) load_registration() (in module acia.registration_persistence) load_segmentation() (in module acia.segm.formats) load_selection() (in module acia.selection) load_tracking() (in module acia.tracking.formats) LocalImage (class in acia.segm.local) LocalImageSource (class in acia.segm.local) LocalSequenceSource (class in acia.segm.local) log_artifact() (acia.analysis.stage.StageContext method) log_calibration() (acia.analysis.stage.StageContext method) log_figure() (acia.analysis.stage.StageContext method) log_metrics() (acia.analysis.stage.StageContext method) log_params() (acia.analysis.stage.StageContext method) LOW_CONFIDENCE_POLICIES (in module acia.registration) LowConfidenceWarning lut_mapping() (in module acia.utils)

M

make_connection() (acia.segm.omero.storer.BlitzConn method) make_coordinates() (in module acia.segm.omero.shapeUtils) make_polystr() (in module acia.segm.omero.shapeUtils) make_source_block() (in module acia.selection) manifest (acia.notebook.RegistrationDashboard property) (acia.notebook.SequenceDashboard property) manifest() (acia.analysis.stage.StageContext method) MANIFEST_NAME (in module acia.analysis.stage) manifest_path (acia.analysis.stage.StageContext property) mask (acia.base.Instance property) mask() (acia.segm.filter.CellFilter method) mask_angle (acia.notebook.RegistrationDashboard attribute) mask_center_x (acia.notebook.RegistrationDashboard attribute) mask_center_y (acia.notebook.RegistrationDashboard attribute) mask_height (acia.notebook.RegistrationDashboard attribute) mask_image_b64 (acia.notebook.RegistrationDashboard attribute) mask_image_h (acia.notebook.RegistrationDashboard attribute) mask_image_w (acia.notebook.RegistrationDashboard attribute) mask_nms() (in module acia.segm.processor.predict) mask_points (acia.notebook.RegistrationDashboard attribute) mask_rect (acia.notebook.RegistrationDashboard property) mask_to_polygons() (in module acia.utils) mask_width (acia.notebook.RegistrationDashboard attribute) MaskedTemplateCorrelation (class in acia.registration) materialize() (acia.base.ImageSequenceSource method) merge() (acia.tracking.TrackingSourceInMemory method) merge_cells_to_colonies() (in module acia.segm.utils) merge_incosistent_segmentation() (in module acia.tracking.utils) metadata (acia.notebook.RegistrationDashboard attribute) (acia.notebook.SequenceDashboard attribute) (acia.segm.open.SequenceFile property) method (acia.registration_persistence.RegistrationManifest attribute) (acia.registration_persistence.RegistrationRecord attribute) method_name (acia.notebook.RegistrationDashboard attribute) method_params (acia.registration_persistence.RegistrationManifest attribute) missing_frames (acia.base.RegisteredSequenceSource property) MISSING_POLICIES (acia.base.RegisteredSequenceSource attribute) MMSegmentationDataset (class in acia.segm.output) ModelDescriptor (class in acia.segm.processor.online) MODES (acia.registration.ReanchoringReference attribute) module acia.analysis acia.analysis.doubling_time acia.analysis.growth_rate acia.analysis.properties acia.analysis.stage acia.analysis.units acia.attribute acia.base acia.colors acia.config acia.crop_capture acia.notebook acia.registration acia.registration_persistence acia.segm.czi_source acia.segm.filter acia.segm.folder_source acia.segm.formats acia.segm.local acia.segm.nd2_source acia.segm.omero.shapeUtils acia.segm.omero.storer acia.segm.omero.utils acia.segm.open acia.segm.output acia.segm.processor.canny acia.segm.processor.cellpose acia.segm.processor.cellpose_sam acia.segm.processor.cpn acia.segm.processor.flowpose_rt acia.segm.processor.offline acia.segm.processor.omnipose acia.segm.processor.online acia.segm.processor.predict acia.segm.processor.yolo acia.segm.tiff_export acia.segm.tiff_metadata acia.segm.utils acia.selection acia.timing acia.tracking acia.tracking.formats acia.tracking.output acia.tracking.processor.laptrack acia.tracking.processor.pyuat acia.tracking.processor.trackastra acia.tracking.processor.ultrack acia.tracking.processor.utils acia.tracking.utils acia.utils acia.viz acia.viz.compose acia.viz.utils

multi_mask_to_polygons() (in module acia.utils)

N

n_sample_frames (acia.notebook.RegistrationDashboard attribute) n_scenes (acia.segm.czi_source.CZISequenceSource property) name (acia.segm.filter.AreaFilter attribute) (acia.segm.filter.BoundaryClosenessFilter attribute) (acia.segm.filter.CellFilter attribute) (acia.segm.filter.CircularityFilter attribute) (acia.segm.filter.LengthFilter attribute) (acia.segm.filter.WidthFilter attribute) (acia.segm.open.PositionInfo attribute) natural_key() (in module acia.segm.folder_source) ND2SequenceSource (class in acia.segm.nd2_source) NMSFilter (class in acia.segm.filter) no_crop() (in module acia.segm.output) non_max_supression() (in module acia.segm.processor.predict) normalize_to_uint8() (in module acia.notebook) notes (acia.registration_persistence.RegistrationRecord attribute) (acia.selection.RoiSelection attribute) np_vec_no_jit_iou() (in module acia.segm.processor.predict) num_channels (acia.base.ArrayImage property) (acia.base.BaseImage property) (acia.base.ImageSequenceSource property) (acia.base.RegisteredSequenceSource property) (acia.base.RGBSequenceSource property) (acia.base.RotatedCropSequenceSource property) (acia.base.SlicedSequenceSource property) (acia.segm.czi_source.CZISequenceSource property) (acia.segm.folder_source.FolderSequenceSource property) (acia.segm.local.InMemorySequenceSource property) (acia.segm.local.LocalImage property) (acia.segm.local.LocalImageSource property) (acia.segm.local.LocalSequenceSource property) (acia.segm.local.THWCSequenceSource property) (acia.segm.nd2_source.ND2SequenceSource property) (acia.segm.omero.storer.OmeroRawSource property) (acia.segm.omero.storer.OmeroSequenceSource property) (acia.viz.compose.ComposedSequenceSource property)

num_frames (acia.segm.local.LocalImageSource property) (acia.segm.omero.storer.OmeroSequenceSource property) num_positions (acia.segm.open.SequenceFile property) (acia.segm.open.SequenceMetadata attribute) num_timepoints (acia.segm.open.SequenceMetadata attribute) numFrames() (acia.base.Overlay method)

O

OfflineModel (class in acia.segm.processor.offline) OmeroRawSource (class in acia.segm.omero.storer) OmeroRoISource (class in acia.segm.omero.storer) OmeroRoIStorer (class in acia.segm.omero.storer) OmeroScaleBar (class in acia.segm.omero.utils) OmeroSequenceSource (class in acia.segm.omero.storer) OmeroSource (class in acia.segm.omero.storer) OmniposeSegmenter (class in acia.segm.processor.omnipose) OnlineModel (class in acia.segm.processor.online)

open() (acia.analysis.stage.StageContext method) open_sequence() (in module acia.segm.open) output_dir (acia.analysis.stage.StageContext attribute) output_path() (acia.analysis.stage.StageContext method) Overlay overlay (acia.tracking.TrackingSource property) (acia.tracking.TrackingSourceInMemory property) Overlay (class in acia.base) overlay_from_masks() (in module acia.segm.formats) overlay_to_masks() (in module acia.tracking.processor.utils)

P

p_value (acia.analysis.growth_rate.GrowthRateResult attribute) pairwise_distances() (in module acia.utils) params (acia.notebook.FilterExplorer property) parse_simple_segmentation() (in module acia.segm.formats) parse_simple_tracking() (in module acia.tracking.formats) parseContours() (acia.segm.processor.online.FlexibleOnlineModel static method) (acia.segm.processor.online.OnlineModel static method) path() (acia.analysis.stage.StageContext method) PerimeterEx (class in acia.analysis) PhaseCorrelationHighpass (class in acia.registration) pixel size / frame interval pixel_input_unit() (in module acia.timing) pixel_size (acia.base.ImageSequenceSource property) (acia.base.RegisteredSequenceSource property) (acia.base.RGBSequenceSource property) (acia.base.RotatedCropSequenceSource property) (acia.base.SlicedSequenceSource property) (acia.segm.czi_source.CZISequenceSource property) (acia.segm.folder_source.FolderSequenceSource property) (acia.segm.local.LocalSequenceSource property) (acia.segm.nd2_source.ND2SequenceSource property) (acia.segm.omero.storer.OmeroRawSource property) (acia.segm.omero.storer.OmeroSequenceSource property) (acia.segm.omero.storer.OmeroSource property) (acia.segm.open.SequenceMetadata attribute) (acia.segm.tiff_metadata.TiffCalibration attribute) pixelSize (acia.segm.omero.storer.OmeroSource property) pixelWidth (acia.utils.ScaleBar attribute) plot_cell_lineage() (in module acia.viz) plot_doubling_time_hose() (in module acia.analysis.doubling_time) plot_property_histograms() (in module acia.analysis.properties) plot_tracklet_lineage() (in module acia.viz) plotly_cell_lineage() (in module acia.viz) points (acia.notebook.ROICropper attribute)

polygon (acia.base.Contour property) (acia.base.Instance property) polygon_to_mask() (in module acia.utils) population_id (acia.analysis.stage.StageContext attribute) population_id_of() (in module acia.analysis.stage) PoseModel (class in acia.segm.processor.offline) position (acia.registration_persistence.RegistrationRecord attribute) (acia.selection.RoiSelection attribute) position() (acia.segm.open.SequenceFile method) PositionEx (class in acia.analysis) PositionInfo (class in acia.segm.open) positions (acia.notebook.RegistrationDashboard attribute) (acia.notebook.SequenceDashboard attribute) (acia.segm.open.SequenceFile property) postprocess() (in module acia.segm.processor.predict) predict() (acia.segm.processor.offline.OfflineModel method) (acia.segm.processor.offline.PoseModel method) (acia.segm.processor.omnipose.OmniposeSegmenter method) (acia.segm.processor.online.FlexibleOnlineModel method) (acia.segm.processor.online.OnlineModel method) predict_batch() (acia.segm.processor.online.FlexibleOnlineModel method) predict_single() (acia.segm.processor.online.FlexibleOnlineModel method) prediction() (in module acia.segm.processor.predict) prepare_contours() (in module acia.segm.processor.predict) prepare_image() (in module acia.segm.local) preview (acia.selection.RoiSelection attribute) preview_frame (acia.notebook.SequenceDashboard attribute) print_file_annotations() (in module acia.segm.omero.storer) printPixelSize() (acia.segm.omero.storer.OmeroSource method) Processor (class in acia.base) projectName() (acia.segm.omero.storer.OmeroSequenceSource method) PropertyExtractor (class in acia.analysis) PyUATTracker (class in acia.tracking.processor.pyuat)

R

r_squared (acia.analysis.growth_rate.GrowthRateResult attribute) range (acia.segm.filter.CellFilter property) raw (acia.base.ArrayImage property) (acia.base.BaseImage property) (acia.segm.local.LocalImage property) rawPixelSize (acia.segm.omero.storer.OmeroSource property) read_ctc_segmentation_native() (in module acia.segm.formats) read_ctc_tracking() (in module acia.tracking.formats) read_ctc_tracklet_graph() (in module acia.tracking.formats) read_manifest() (in module acia.analysis.stage) read_tiff_calibration() (in module acia.segm.tiff_metadata) read_units_csv() (in module acia.analysis.units) ReanchoringReference (class in acia.registration) record() (acia.analysis.stage.StageContext method) records (acia.registration_persistence.RegistrationManifest attribute) reference_frame (acia.registration_persistence.RegistrationRecord attribute) reference_frames (acia.registration_persistence.RegistrationRecord attribute) reference_mode (acia.registration_persistence.RegistrationRecord attribute) register() (acia.base.ImageSequenceSource method) RegisteredSequenceSource (class in acia.base) RegistrationDashboard (class in acia.notebook) RegistrationError RegistrationManifest (class in acia.registration_persistence) RegistrationMethod (class in acia.registration) RegistrationRecord (class in acia.registration_persistence) render_cell_centers() (in module acia.viz) render_overlay_frame() (in module acia.viz)

render_scalebar() (in module acia.viz) render_segmentation() (in module acia.viz) render_segmentation_mask() (in module acia.viz) render_time() (in module acia.viz) render_tracking() (in module acia.viz) render_tracking_mask() (in module acia.viz) render_video() (in module acia.viz) renderVideo() (in module acia.segm.output) replace_file_annotation() (in module acia.segm.omero.storer) require() (acia.analysis.stage.StageContext method) resolve_channel_color() (in module acia.colors) resolve_layout() (in module acia.segm.folder_source) resolve_storage_options() (in module acia.config) resolve_timepoints() (in module acia.timing) resume() (acia.notebook.SequenceDashboard class method) rgba_to_int() (in module acia.segm.omero.shapeUtils) RGBSequenceSource (class in acia.base) roi (acia.selection.RoiSelection attribute) roi_mode (acia.notebook.SequenceDashboard attribute) (acia.selection.SelectionManifest attribute) ROICropper (class in acia.notebook) RoiSelection (class in acia.selection) RoISource (class in acia.base) RoiStorer (class in acia.segm.local) RotatedCropSequenceSource (class in acia.base) RotatedCropSpec (class in acia.base) run_comparison() (in module acia.registration)

S

SambaSequenceSource (class in acia.segm.local) save() (acia.notebook.FilterExplorer method) (acia.notebook.RegistrationDashboard method) (acia.notebook.ROICropper method) (acia.notebook.SequenceDashboard method) (acia.registration_persistence.RegistrationManifest method) (acia.selection.SelectionManifest method) save_crop_capture() (in module acia.crop_capture) save_registration() (in module acia.registration_persistence) save_segmentation() (in module acia.segm.formats) save_selection() (in module acia.selection) save_tiff_stack() (in module acia.segm.tiff_export) save_tracking() (in module acia.tracking.formats) scale() (acia.base.Contour method) (acia.base.Overlay method) (in module acia.analysis) ScaleBar (class in acia.utils) scene_names (acia.segm.czi_source.CZISequenceSource property) schema (acia.registration_persistence.RegistrationManifest attribute) (acia.selection.SelectionManifest attribute) seed() (acia.registration.ReanchoringReference method) selection (acia.notebook.FilterExplorer attribute) SelectionManifest (class in acia.selection) selections (acia.notebook.SequenceDashboard attribute) (acia.selection.SelectionManifest attribute) SequenceDashboard (class in acia.notebook) SequenceFile (class in acia.segm.open) SequenceMetadata (class in acia.segm.open) SimpleTrackingSource (class in acia.tracking) size (acia.base.RotatedCropSpec attribute) size_c (acia.base.ImageSequenceSource property) (acia.base.RegisteredSequenceSource property) (acia.base.RGBSequenceSource property) (acia.base.RotatedCropSequenceSource property) (acia.base.SlicedSequenceSource property) (acia.segm.czi_source.CZISequenceSource property) (acia.segm.folder_source.FolderSequenceSource property) (acia.segm.local.THWCSequenceSource property) (acia.segm.nd2_source.ND2SequenceSource property) (acia.segm.omero.storer.OmeroRawSource property) (acia.segm.omero.storer.OmeroSequenceSource property) (acia.viz.compose.ComposedSequenceSource property) size_h (acia.base.ImageSequenceSource property) (acia.base.RegisteredSequenceSource property) (acia.base.RGBSequenceSource property) (acia.base.RotatedCropSequenceSource property) (acia.base.SlicedSequenceSource property) (acia.segm.czi_source.CZISequenceSource property) (acia.segm.folder_source.FolderSequenceSource property) (acia.segm.local.THWCSequenceSource property) (acia.segm.nd2_source.ND2SequenceSource property) (acia.segm.omero.storer.OmeroRawSource property) (acia.segm.omero.storer.OmeroSequenceSource property) (acia.viz.compose.ComposedSequenceSource property) size_t (acia.base.ImageSequenceSource property) (acia.base.RegisteredSequenceSource property) (acia.base.RGBSequenceSource property) (acia.base.RotatedCropSequenceSource property) (acia.base.SlicedSequenceSource property) (acia.segm.czi_source.CZISequenceSource property) (acia.segm.folder_source.FolderSequenceSource property) (acia.segm.local.InMemorySequenceSource property) (acia.segm.local.LocalImageSource property) (acia.segm.local.LocalSequenceSource property) (acia.segm.local.THWCSequenceSource property) (acia.segm.nd2_source.ND2SequenceSource property) (acia.segm.omero.storer.OmeroRawSource property) (acia.segm.omero.storer.OmeroSequenceSource property) (acia.viz.compose.ComposedSequenceSource property)

size_w (acia.base.ImageSequenceSource property) (acia.base.RegisteredSequenceSource property) (acia.base.RGBSequenceSource property) (acia.base.RotatedCropSequenceSource property) (acia.base.SlicedSequenceSource property) (acia.segm.czi_source.CZISequenceSource property) (acia.segm.folder_source.FolderSequenceSource property) (acia.segm.local.THWCSequenceSource property) (acia.segm.nd2_source.ND2SequenceSource property) (acia.segm.omero.storer.OmeroRawSource property) (acia.segm.omero.storer.OmeroSequenceSource property) (acia.viz.compose.ComposedSequenceSource property) SizeFilter (class in acia.segm.filter) sizes (acia.segm.czi_source.CZISequenceSource property) (acia.segm.nd2_source.ND2SequenceSource property) (acia.segm.open.SequenceMetadata attribute) slice() (acia.segm.local.LocalSequenceSource method) SlicedSequenceSource (class in acia.base) source (acia.registration_persistence.RegistrationManifest attribute) (acia.segm.tiff_metadata.TiffCalibration attribute) (acia.selection.SelectionManifest attribute) source_path (acia.registration_persistence.RegistrationManifest property) (acia.selection.SelectionManifest property) spec (acia.notebook.ROICropper property) (acia.selection.RoiSelection property) stage() (acia.analysis.stage.StageContext method) stage_graph() (in module acia.analysis.stage) stage_name (acia.analysis.stage.StageContext attribute) STAGE_SCHEMA (in module acia.analysis.stage) stage_table() (in module acia.analysis.stage) stage_xy (acia.segm.open.PositionInfo attribute) StageContext (class in acia.analysis.stage) stages_run() (in module acia.analysis.stage) store() (acia.segm.local.RoiStorer static method) (acia.segm.omero.storer.OmeroRoIStorer static method) (acia.tracking.SimpleTrackingSource method) storeWithConn() (acia.segm.omero.storer.OmeroRoIStorer static method) strfdelta() (in module acia.viz.utils) strip_units() (in module acia.analysis.units) subsample_lineage() (in module acia.tracking.utils) subsample_tracking() (in module acia.tracking) summary() (acia.analysis.stage.StageContext method)

T

theta (acia.registration.FrameTransform attribute) thumbnail() (acia.segm.open.SequenceFile method) thumbnail_png() (acia.segm.open.SequenceFile method) THWC THWCSequenceSource (class in acia.segm.local) TiffCalibration (class in acia.segm.tiff_metadata) tile_touch_filter() (in module acia.segm.processor.predict) tiled_inference() (in module acia.segm.processor.predict) time_iterator() (acia.base.Overlay method) TimeEx (class in acia.analysis) timeIterator() (acia.base.Overlay method) timepoints (acia.base.ImageSequenceSource property) (acia.base.Overlay property) (acia.base.RegisteredSequenceSource property) (acia.base.RGBSequenceSource property) (acia.base.RotatedCropSequenceSource property) (acia.base.SlicedSequenceSource property) (acia.segm.czi_source.CZISequenceSource property) (acia.segm.folder_source.FolderSequenceSource property) (acia.segm.local.LocalSequenceSource property) (acia.segm.nd2_source.ND2SequenceSource property) (acia.segm.tiff_metadata.TiffCalibration attribute) timestamps (acia.base.Overlay property) to_channel() (acia.base.ImageSequenceSource method) (acia.segm.local.THWCSequenceSource method) to_ctc_format() (acia.tracking.output.CTCTrackingHelper method) to_dict() (acia.base.RotatedCropSpec method) (acia.registration.FrameTransform method) (acia.registration_persistence.RegistrationManifest method) (acia.registration_persistence.RegistrationRecord method) (acia.segm.open.SequenceMetadata method) (acia.selection.RoiSelection method) (acia.selection.SelectionManifest method)

to_quantity() (in module acia.timing) to_rgb() (acia.base.ImageSequenceSource method) toMask() (acia.base.Contour method) (acia.base.Instance method) toMasks() (acia.base.Overlay method) torch_mask_nms() (in module acia.segm.processor.predict) torch_vec_no_jit_iou() (in module acia.segm.processor.predict) toTHWC() (acia.segm.omero.storer.OmeroRawSource method) (acia.segm.omero.storer.OmeroSequenceSource method) track() (acia.analysis.stage.StageContext method) TrackastraTracker (class in acia.tracking.processor.trackastra) tracking graph tracking_graph (acia.tracking.TrackingSource property) (acia.tracking.TrackingSourceInMemory property) tracking_to_graph() (in module acia.tracking.formats) TrackingSource (class in acia.tracking) TrackingSourceInMemory (class in acia.tracking) tracklet graph tracklet_graph_to_segments() (in module acia.viz) tracklet_to_tracking() (in module acia.tracking.utils) transforms (acia.registration_persistence.RegistrationRecord attribute) txt_format() (acia.tracking.output.CTCTrackingHelper static method)

U

UltrackTracker (class in acia.tracking.processor.ultrack) UNIT_ATTR (in module acia.analysis.units)

units_in_header() (in module acia.analysis.units) unpack() (in module acia.base) upload_file() (in module acia.segm.omero.storer)

V

value() (acia.segm.filter.BoundaryClosenessFilter method) (acia.segm.filter.CellFilter method) (acia.segm.filter.CircularityFilter method)

VideoExporter (class in acia.viz) VideoExporter2 (class in acia.viz) view_size (acia.notebook.SequenceDashboard attribute)

W

width (acia.notebook.ROICropper attribute) WidthEx (class in acia.analysis) WidthFilter (class in acia.segm.filter) with_frame_interval() (acia.base.ImageSequenceSource method) (acia.base.Overlay method) (acia.segm.folder_source.FolderSequenceSource method) with_pixel_size() (acia.base.ImageSequenceSource method) (acia.segm.folder_source.FolderSequenceSource method) with_timepoints() (acia.base.ImageSequenceSource method) (acia.base.Overlay method) (acia.segm.folder_source.FolderSequenceSource method)

write() (acia.segm.output.MMSegmentationDataset method) (acia.tracking.output.CellTrackingChallengeDatasetGT method) (acia.tracking.output.CellTrackingDatasetResult method) (acia.viz.VideoExporter method) (acia.viz.VideoExporter2 method) write_ctc_tracking() (in module acia.tracking.formats) write_units_csv() (in module acia.analysis.units)

Y

YOLOSegmenter (class in acia.segm.processor.yolo)