Index

_

_cancelled (pycroglia.core.compute.mp_pool.CancelFlag attribute)

A

all_cells_to_2d() (pycroglia.core.labeled_cells.LabeledCells method) all_finished (pycroglia.core.compute.mp_pool.MPPool attribute) (pycroglia.core.compute.qt_pool.QPool attribute), [1] AnalysisSummary (class in pycroglia.core.io.output) AnalysisSummaryConfig (class in pycroglia.core.io.output) apply_binary_erosion() (in module pycroglia.core.erosion) arclength (pycroglia.core.arclength.Result attribute), [1] arclength() (in module pycroglia.core.arclength)

ARRAY_ELEMENTS_TYPE (pycroglia.core.labeled_cells.LabeledCells attribute), [1] (pycroglia.core.labeled_cells.LabelingStrategy attribute), [1] as_dict() (pycroglia.ui.widgets.imagefilters.results.FilterResults method) (pycroglia.ui.widgets.segmentation.results.SegmentationResults method) avg_branch_length (pycroglia.core.io.output.CellAnalysis attribute), [1] avg_branch_length_txt (pycroglia.core.io.output.CellAnalysisConfig attribute), [1] avg_centroid_distance (pycroglia.core.io.output.AnalysisSummary attribute), [1] avg_centroid_distance_txt (pycroglia.core.io.output.AnalysisSummaryConfig attribute), [1]

B

Backend (class in pycroglia.core.compute.backend) backend (pycroglia.core.compute.pool.Pool attribute) Ball3DFootprint (class in pycroglia.core.erosion) bottom (pycroglia.core.bounding_box.ComputeResult attribute)

bounded_img (pycroglia.core.bounding_box.ComputeResult attribute) bounds_check() (in module pycroglia.core.skeletonize.msfm) branch_analysis (pycroglia.core.io.output.CellAnalysis attribute) BranchAnalysis (class in pycroglia.core.branch_analysis) BranchpointsCellPlot (class in pycroglia.core.plot.branch)

C

calculate() (pycroglia.core.skeletonize.shortest_path.ShortestPath method) calculate_derivative() (pycroglia.core.skeletonize.msfm.FirstOrderStencil method) (pycroglia.core.skeletonize.msfm.SecondOrderStencil method) calculate_otsu_threshold() (in module pycroglia.core.filters) cancel() (pycroglia.core.compute.backend.Backend method) (pycroglia.core.compute.mp_pool.MPPool method) (pycroglia.core.compute.pool.Pool method) (pycroglia.core.compute.qt_pool.QPool method) cancel_flag (pycroglia.core.compute.mp_pool.MPTask attribute) CancelFlag (class in pycroglia.core.compute.mp_pool) (class in pycroglia.core.compute.qt_pool) cancelled (pycroglia.core.compute.qt_pool.CancelFlag attribute) cell (pycroglia.core.branch_analysis.BranchAnalysis attribute) cell_territory_volume (pycroglia.core.io.output.CellAnalysis attribute), [1] cell_territory_volume_txt (pycroglia.core.io.output.CellAnalysisConfig attribute), [1] cell_to_2d() (pycroglia.core.labeled_cells.LabeledCells method) cell_volume (pycroglia.core.io.output.CellAnalysis attribute), [1] cell_volume_txt (pycroglia.core.io.output.CellAnalysisConfig attribute), [1] CellAnalysis (class in pycroglia.core.io.output) CellAnalysisConfig (class in pycroglia.core.io.output) cells (pycroglia.core.io.output.FullAnalysis attribute), [1] cells_masks (pycroglia.ui.widgets.common.results.ImgWithPathResults attribute) center_of_mass (pycroglia.core.slimskel3d.skel2graph.Node attribute), [1] CenterOfMass (class in pycroglia.core.slimskel3d.skel2graph)

centroid (pycroglia.core.branch_analysis.BranchAnalysis attribute) Centroids (class in pycroglia.core.centroid) centroids (pycroglia.core.centroid.Centroids attribute) cmap (pycroglia.core.plot.original_cell.OriginalCellPlot attribute) Computable (class in pycroglia.core.compute.computable) computable (pycroglia.core.compute.mp_pool.MPTask attribute) (pycroglia.core.compute.qt_pool.QTask attribute) compute() (in module pycroglia.core.bounding_box) (in module pycroglia.core.nearest_pixel) (pycroglia.core.branch_analysis.BranchAnalysis method) (pycroglia.core.centroid.Centroids method) (pycroglia.core.compute.computable.Computable method) (pycroglia.core.compute.tests.unit.test_mp_pool.DummyComputable method) (pycroglia.core.compute.tests.unit.test_qt_pool.DummyComputable method) (pycroglia.core.full_cell_analysis.FullCellAnalysis method) (pycroglia.core.territorial_volume.TerritorialVolume method) ComputeResult (class in pycroglia.core.bounding_box) connect_points_along_path() (in module pycroglia.core.connection) connections (pycroglia.core.slimskel3d.skel2graph.Node attribute), [1] connectivity (pycroglia.core.labeled_cells.SkimageImgLabeling attribute) (pycroglia.core.segmentation.SegmentationConfig attribute), [1] Coordinates (class in pycroglia.core.nearest_pixel) CORNERS (pycroglia.core.enums.SkimageCellConnectivity attribute), [1] create_channeled_reader() (in module pycroglia.core.io.readers) cut_off_size (pycroglia.core.segmentation.SegmentationConfig attribute), [1]

D

default() (pycroglia.core.io.output.AnalysisSummaryConfig class method) (pycroglia.core.io.output.CellAnalysisConfig class method) DEFAULT_FILE_EXTENSION (pycroglia.core.io.output.ExcelOutput attribute) (pycroglia.core.io.output.JSONOutput attribute) DEFAULT_GMM_N_INIT (pycroglia.core.segmentation.SegmentationConfig attribute), [1] DEFAULT_MIN_NUCLEUS_FRACTION (pycroglia.core.segmentation.SegmentationConfig attribute), [1] DEFAULT_NAME (pycroglia.core.io.output.ExcelOutput attribute) (pycroglia.core.io.output.JSONOutput attribute)

DEFAULT_PER_CELL_SHEET_TITLE (pycroglia.core.io.output.ExcelOutput attribute) DEFAULT_SUMMARY_SHEET_TITLE (pycroglia.core.io.output.ExcelOutput attribute) DerivativeResult (class in pycroglia.core.skeletonize.msfm) Diamond2DFootprint (class in pycroglia.core.erosion) Disk2DFootprint (class in pycroglia.core.erosion) distance_map (pycroglia.core.skeletonize.raytracing.simple.Simple attribute) DummyComputable (class in pycroglia.core.compute.tests.unit.test_mp_pool) (class in pycroglia.core.compute.tests.unit.test_qt_pool)

E

EDGES (pycroglia.core.enums.SkimageCellConnectivity attribute), [1] EmptySkeleton end (pycroglia.core.slimskel3d.skel2graph.Link attribute), [1] EndpointsCellPlot (class in pycroglia.core.plot.endpoints) error (pycroglia.core.compute.qt_pool.QTaskSignal attribute), [1]

Euler (class in pycroglia.core.skeletonize.raytracing.euler) (pycroglia.core.skeletonize.raytracing.factory.StepperType attribute), [1] ExcelOutput (class in pycroglia.core.io.output) EXTENSION_ERROR_CODE (pycroglia.core.io.readers.LsmReader attribute), [1] (pycroglia.core.io.readers.TiffReader attribute), [1]

F

FACES (pycroglia.core.enums.SkimageCellConnectivity attribute), [1] file (pycroglia.core.io.output.AnalysisSummary attribute), [1] file_path (pycroglia.ui.widgets.common.results.ImgWithPathResults attribute), [1] (pycroglia.ui.widgets.segmentation.results.SegmentationResults attribute), [1] file_txt (pycroglia.core.io.output.AnalysisSummaryConfig attribute), [1] FilterResults (class in pycroglia.ui.widgets.imagefilters.results)

finished (pycroglia.core.compute.qt_pool.QTaskSignal attribute), [1] FirstOrderStencil (class in pycroglia.core.skeletonize.msfm) FootprintShape (class in pycroglia.core.erosion) full_cell_analysis (pycroglia.core.io.output.CellAnalysis attribute) FullAnalysis (class in pycroglia.core.io.output) FullCellAnalysis (class in pycroglia.core.full_cell_analysis) FullCellAnalysisPlot (class in pycroglia.core.plot.full_cell_analysis)

G

gaussian_mixture_predict() (in module pycroglia.core.clustering) get_border_cells() (pycroglia.core.labeled_cells.LabeledCells method) get_cell() (pycroglia.core.labeled_cells.LabeledCells method) get_cell_size() (pycroglia.core.labeled_cells.LabeledCells method) get_cells_list() (pycroglia.core.labeled_cells.LabeledCells method) get_empty_branch_analysis() (in module pycroglia.core.branch_analysis) get_name() (pycroglia.core.io.output.ExcelOutput class method) (pycroglia.core.io.output.JSONOutput class method) (pycroglia.core.io.output.OutputWriter class method) get_number_of_nuclei() (in module pycroglia.core.clustering) get_shape() (pycroglia.core.erosion.Ball3DFootprint method) (pycroglia.core.erosion.Diamond2DFootprint method) (pycroglia.core.erosion.Disk2DFootprint method) (pycroglia.core.erosion.FootprintShape method) (pycroglia.core.erosion.Octahedron3DFootprint method) (pycroglia.core.erosion.Rectangle2DFootprint method) (pycroglia.core.erosion.Rectangle3DFootprint method)

get_writers() (pycroglia.core.io.output.OutputWriter class method) gmm_n_init (pycroglia.core.segmentation.SegmentationConfig attribute), [1] gradient_volume (pycroglia.core.skeletonize.raytracing.euler.Euler attribute) (pycroglia.core.skeletonize.raytracing.rk4.RK4 attribute) graph2skel() (in module pycroglia.core.slimskel3d.graph2skel)

I

id (pycroglia.core.slimskel3d.skel2graph.Node attribute), [1] img (pycroglia.ui.widgets.common.results.ImgWithPathResults attribute), [1] (pycroglia.ui.widgets.segmentation.results.SegmentationResults attribute), [1] ImgWithPathResults (class in pycroglia.ui.widgets.common.results) indices (pycroglia.core.slimskel3d.skel2graph.Node attribute), [1] indices_to_mask() (in module pycroglia.core.tests.unit.test_branch_analysis)

init_kernel() (in module pycroglia.core.branch_analysis) InterpolationMethod (class in pycroglia.core.arclength) is_endpoint (pycroglia.core.slimskel3d.skel2graph.Node attribute), [1] is_frozen2d() (in module pycroglia.core.skeletonize.msfm) is_set() (pycroglia.core.compute.mp_pool.CancelFlag method) (pycroglia.core.compute.qt_pool.CancelFlag method)

J

join() (pycroglia.core.compute.backend.Backend method) (pycroglia.core.compute.mp_pool.MPPool method) (pycroglia.core.compute.pool.Pool method) (pycroglia.core.compute.qt_pool.QPool method)

JSONOutput (class in pycroglia.core.io.output)

L

label (pycroglia.core.slimskel3d.skel2graph.Link attribute), [1] (pycroglia.core.slimskel3d.skel2graph.Node attribute), [1] label() (pycroglia.core.labeled_cells.LabelingStrategy method) (pycroglia.core.labeled_cells.MaskListLabeling method) (pycroglia.core.labeled_cells.SkimageImgLabeling method) LabeledCells (class in pycroglia.core.labeled_cells) LabelingStrategy (class in pycroglia.core.labeled_cells)

labels (pycroglia.core.labeled_cells.LabeledCells attribute) labels_to_2d() (pycroglia.core.labeled_cells.LabeledCells method) left (pycroglia.core.bounding_box.ComputeResult attribute) len() (pycroglia.core.labeled_cells.LabeledCells method) LINEAR (pycroglia.core.arclength.InterpolationMethod attribute), [1] Link (class in pycroglia.core.slimskel3d.skel2graph) links (pycroglia.core.slimskel3d.skel2graph.Node attribute), [1] LsmReader (class in pycroglia.core.io.readers)

M

make_stepper() (in module pycroglia.core.skeletonize.raytracing.factory) MaskListLabeling (class in pycroglia.core.labeled_cells) masks (pycroglia.core.full_cell_analysis.FullCellAnalysis attribute) (pycroglia.core.territorial_volume.TerritorialVolume attribute) max_branch_length (pycroglia.core.io.output.CellAnalysis attribute), [1] max_branch_length_txt (pycroglia.core.io.output.CellAnalysisConfig attribute), [1] min_branch_length (pycroglia.core.io.output.CellAnalysis attribute), [1] min_branch_length_txt (pycroglia.core.io.output.CellAnalysisConfig attribute), [1] min_nucleus_fraction (pycroglia.core.segmentation.SegmentationConfig attribute), [1] min_size (pycroglia.core.segmentation.SegmentationConfig attribute), [1] module pycroglia pycroglia.core pycroglia.core.arclength pycroglia.core.bounding_box pycroglia.core.branch_analysis pycroglia.core.centroid pycroglia.core.clustering pycroglia.core.compute pycroglia.core.compute.backend pycroglia.core.compute.computable pycroglia.core.compute.mp_pool pycroglia.core.compute.pool pycroglia.core.compute.qt_pool pycroglia.core.compute.tests pycroglia.core.compute.tests.unit pycroglia.core.compute.tests.unit.test_mp_pool pycroglia.core.compute.tests.unit.test_qt_pool pycroglia.core.connection pycroglia.core.enums pycroglia.core.erosion pycroglia.core.errors pycroglia.core.errors.errors pycroglia.core.filters pycroglia.core.full_cell_analysis pycroglia.core.io pycroglia.core.io.output pycroglia.core.io.readers pycroglia.core.io.tests pycroglia.core.io.tests.unit pycroglia.core.labeled_cells pycroglia.core.nearest_pixel pycroglia.core.plot pycroglia.core.plot.branch pycroglia.core.plot.endpoints pycroglia.core.plot.full_cell_analysis pycroglia.core.plot.original_cell pycroglia.core.plot.skeleton pycroglia.core.reorder pycroglia.core.segmentation pycroglia.core.skeletonize pycroglia.core.skeletonize.msfm pycroglia.core.skeletonize.raytracing pycroglia.core.skeletonize.raytracing.euler pycroglia.core.skeletonize.raytracing.factory pycroglia.core.skeletonize.raytracing.rk4 pycroglia.core.skeletonize.raytracing.simple pycroglia.core.skeletonize.raytracing.stepper pycroglia.core.skeletonize.shortest_path pycroglia.core.skeletonize.skeleton pycroglia.core.skeletonize.tests pycroglia.core.skeletonize.tests.unit pycroglia.core.skeletonize.tests.unit.test_rt pycroglia.core.skeletonize.tests.unit.test_skeleton pycroglia.core.slimskel3d pycroglia.core.slimskel3d.graph2skel pycroglia.core.slimskel3d.skel2graph pycroglia.core.slimskel3d.skeleton3D pycroglia.core.slimskel3d.slimskel3d pycroglia.core.slimskel3d.tests pycroglia.core.slimskel3d.tests.unit pycroglia.core.slimskel3d.tests.unit.test_graph2skel pycroglia.core.slimskel3d.tests.unit.test_skel2graph pycroglia.core.slimskel3d.tests.unit.test_skeleton3D pycroglia.core.slimskel3d.tests.unit.test_slimskel3d pycroglia.core.territorial_volume pycroglia.core.tests pycroglia.core.tests.integration pycroglia.core.tests.unit pycroglia.core.tests.unit.test_arclength pycroglia.core.tests.unit.test_bounding_box pycroglia.core.tests.unit.test_branch_analysis pycroglia.core.tests.unit.test_centroid pycroglia.core.tests.unit.test_full_cell_analysis pycroglia.core.tests.unit.test_nearest_pixel pycroglia.core.tests.unit.test_reorder pycroglia.core.tests.unit.test_segmentation pycroglia.core.tests.unit.test_territorial_volume pycroglia.ui pycroglia.ui.controllers pycroglia.ui.controllers.tests pycroglia.ui.widgets pycroglia.ui.widgets.analysis pycroglia.ui.widgets.analysis.tests pycroglia.ui.widgets.cells pycroglia.ui.widgets.cells.tests pycroglia.ui.widgets.common pycroglia.ui.widgets.common.results pycroglia.ui.widgets.common.tests pycroglia.ui.widgets.imagefilters pycroglia.ui.widgets.imagefilters.results pycroglia.ui.widgets.imagefilters.tests pycroglia.ui.widgets.imagefilters.tests.test_results pycroglia.ui.widgets.io pycroglia.ui.widgets.io.tests pycroglia.ui.widgets.results pycroglia.ui.widgets.segmentation pycroglia.ui.widgets.segmentation.results pycroglia.ui.widgets.segmentation.tests pycroglia.ui.widgets.wizard pycroglia.ui.widgets.wizard.tests

MPPool (class in pycroglia.core.compute.mp_pool) MPTask (class in pycroglia.core.compute.mp_pool) msfm2d() (in module pycroglia.core.skeletonize.msfm) MultiChReader (class in pycroglia.core.io.readers)

N

Node (class in pycroglia.core.slimskel3d.skel2graph) number_of_branches (pycroglia.core.io.output.CellAnalysis attribute), [1]

number_of_branches_txt (pycroglia.core.io.output.CellAnalysisConfig attribute), [1] number_of_endpoints (pycroglia.core.io.output.CellAnalysis attribute), [1] number_of_endpoints_txt (pycroglia.core.io.output.CellAnalysisConfig attribute), [1]

O

Octahedron3DFootprint (class in pycroglia.core.erosion) opacity (pycroglia.core.plot.original_cell.OriginalCellPlot attribute)

order (pycroglia.core.skeletonize.msfm.DerivativeResult attribute) OriginalCellPlot (class in pycroglia.core.plot.original_cell) OutputWriter (class in pycroglia.core.io.output)

P

path (pycroglia.core.io.readers.LsmReader attribute) (pycroglia.core.io.readers.TiffReader attribute) PCHIP (pycroglia.core.arclength.InterpolationMethod attribute), [1] percent_occupied_volume (pycroglia.core.io.output.AnalysisSummary attribute), [1] percent_occupied_volume_txt (pycroglia.core.io.output.AnalysisSummaryConfig attribute), [1] plots (pycroglia.core.plot.original_cell.OriginalCellPlot attribute) plotters (pycroglia.core.plot.full_cell_analysis.FullCellAnalysisPlot attribute) Point (class in pycroglia.core.connection) points (pycroglia.core.slimskel3d.skel2graph.Link attribute), [1] Pool (class in pycroglia.core.compute.pool) pycroglia module pycroglia.core module pycroglia.core.arclength module pycroglia.core.bounding_box module pycroglia.core.branch_analysis module pycroglia.core.centroid module pycroglia.core.clustering module pycroglia.core.compute module pycroglia.core.compute.backend module pycroglia.core.compute.computable module pycroglia.core.compute.mp_pool module pycroglia.core.compute.pool module pycroglia.core.compute.qt_pool module pycroglia.core.compute.tests module pycroglia.core.compute.tests.unit module pycroglia.core.compute.tests.unit.test_mp_pool module pycroglia.core.compute.tests.unit.test_qt_pool module pycroglia.core.connection module pycroglia.core.enums module pycroglia.core.erosion module pycroglia.core.errors module pycroglia.core.errors.errors module pycroglia.core.filters module pycroglia.core.full_cell_analysis module pycroglia.core.io module pycroglia.core.io.output module pycroglia.core.io.readers module pycroglia.core.io.tests module pycroglia.core.io.tests.unit module pycroglia.core.labeled_cells module pycroglia.core.nearest_pixel module pycroglia.core.plot module pycroglia.core.plot.branch module pycroglia.core.plot.endpoints module pycroglia.core.plot.full_cell_analysis module pycroglia.core.plot.original_cell module pycroglia.core.plot.skeleton module pycroglia.core.reorder module pycroglia.core.segmentation module pycroglia.core.skeletonize module pycroglia.core.skeletonize.msfm module pycroglia.core.skeletonize.raytracing module pycroglia.core.skeletonize.raytracing.euler module pycroglia.core.skeletonize.raytracing.factory module pycroglia.core.skeletonize.raytracing.rk4 module pycroglia.core.skeletonize.raytracing.simple module pycroglia.core.skeletonize.raytracing.stepper module pycroglia.core.skeletonize.shortest_path module

pycroglia.core.skeletonize.skeleton module pycroglia.core.skeletonize.tests module pycroglia.core.skeletonize.tests.unit module pycroglia.core.skeletonize.tests.unit.test_rt module pycroglia.core.skeletonize.tests.unit.test_skeleton module pycroglia.core.slimskel3d module pycroglia.core.slimskel3d.graph2skel module pycroglia.core.slimskel3d.skel2graph module pycroglia.core.slimskel3d.skeleton3D module pycroglia.core.slimskel3d.slimskel3d module pycroglia.core.slimskel3d.tests module pycroglia.core.slimskel3d.tests.unit module pycroglia.core.slimskel3d.tests.unit.test_graph2skel module pycroglia.core.slimskel3d.tests.unit.test_skel2graph module pycroglia.core.slimskel3d.tests.unit.test_skeleton3D module pycroglia.core.slimskel3d.tests.unit.test_slimskel3d module pycroglia.core.territorial_volume module pycroglia.core.tests module pycroglia.core.tests.integration module pycroglia.core.tests.unit module pycroglia.core.tests.unit.test_arclength module pycroglia.core.tests.unit.test_bounding_box module pycroglia.core.tests.unit.test_branch_analysis module pycroglia.core.tests.unit.test_centroid module pycroglia.core.tests.unit.test_full_cell_analysis module pycroglia.core.tests.unit.test_nearest_pixel module pycroglia.core.tests.unit.test_reorder module pycroglia.core.tests.unit.test_segmentation module pycroglia.core.tests.unit.test_territorial_volume module pycroglia.ui module pycroglia.ui.controllers module pycroglia.ui.controllers.tests module pycroglia.ui.widgets module pycroglia.ui.widgets.analysis module pycroglia.ui.widgets.analysis.tests module pycroglia.ui.widgets.cells module pycroglia.ui.widgets.cells.tests module pycroglia.ui.widgets.common module pycroglia.ui.widgets.common.results module pycroglia.ui.widgets.common.tests module pycroglia.ui.widgets.imagefilters module pycroglia.ui.widgets.imagefilters.results module pycroglia.ui.widgets.imagefilters.tests module pycroglia.ui.widgets.imagefilters.tests.test_results module pycroglia.ui.widgets.io module pycroglia.ui.widgets.io.tests module pycroglia.ui.widgets.results module pycroglia.ui.widgets.segmentation module pycroglia.ui.widgets.segmentation.results module pycroglia.ui.widgets.segmentation.tests module pycroglia.ui.widgets.wizard module pycroglia.ui.widgets.wizard.tests module PycrogliaException

Q

QPool (class in pycroglia.core.compute.qt_pool)

QTask (class in pycroglia.core.compute.qt_pool) QTaskSignal (class in pycroglia.core.compute.qt_pool)

R

ramification_index (pycroglia.core.io.output.CellAnalysis attribute), [1] ramification_index_txt (pycroglia.core.io.output.CellAnalysisConfig attribute), [1] read() (pycroglia.core.io.readers.LsmReader method) (pycroglia.core.io.readers.MultiChReader method) (pycroglia.core.io.readers.TiffReader method) Rectangle2DFootprint (class in pycroglia.core.erosion) Rectangle3DFootprint (class in pycroglia.core.erosion) remove_small_objects() (in module pycroglia.core.filters) reorder_pixel_list() (in module pycroglia.core.reorder) Result (class in pycroglia.core.arclength) result (pycroglia.core.compute.qt_pool.QTaskSignal attribute), [1]

right (pycroglia.core.bounding_box.ComputeResult attribute) RK4 (class in pycroglia.core.skeletonize.raytracing.rk4) (pycroglia.core.skeletonize.raytracing.factory.StepperType attribute), [1] roots() (in module pycroglia.core.skeletonize.msfm) run() (pycroglia.core.compute.backend.Backend method) (pycroglia.core.compute.backend.Task method) (pycroglia.core.compute.mp_pool.MPPool method) (pycroglia.core.compute.mp_pool.MPTask method) (pycroglia.core.compute.pool.Pool method) (pycroglia.core.compute.qt_pool.QPool method) (pycroglia.core.compute.qt_pool.QTask method)

S

scale (pycroglia.core.branch_analysis.BranchAnalysis attribute) (pycroglia.core.centroid.Centroids attribute) (pycroglia.core.plot.original_cell.OriginalCellPlot attribute) SecondOrderStencil (class in pycroglia.core.skeletonize.msfm) segment_cell() (in module pycroglia.core.segmentation) segment_lengths (pycroglia.core.arclength.Result attribute), [1] segment_single_cell() (in module pycroglia.core.segmentation) SegmentationConfig (class in pycroglia.core.segmentation) SegmentationResults (class in pycroglia.ui.widgets.segmentation.results) selected_cells_mask() (pycroglia.core.labeled_cells.LabeledCells method) set() (pycroglia.core.compute.mp_pool.CancelFlag method) (pycroglia.core.compute.qt_pool.CancelFlag method) ShortestPath (class in pycroglia.core.skeletonize.shortest_path) show_all() (pycroglia.core.plot.branch.BranchpointsCellPlot method) (pycroglia.core.plot.endpoints.EndpointsCellPlot method) (pycroglia.core.plot.full_cell_analysis.FullCellAnalysisPlot method) (pycroglia.core.plot.original_cell.OriginalCellPlot method) (pycroglia.core.plot.skeleton.SkeletonCellPlot method) signals (pycroglia.core.compute.qt_pool.QTask attribute) Simple (class in pycroglia.core.skeletonize.raytracing.simple) (pycroglia.core.skeletonize.raytracing.factory.StepperType attribute), [1] simple_cells_img() (in module pycroglia.core.tests.unit.test_segmentation)

skel2graph() (in module pycroglia.core.slimskel3d.skel2graph) skeleton() (in module pycroglia.core.skeletonize.skeleton) skeleton3D() (in module pycroglia.core.slimskel3d.skeleton3D) SkeletonCellPlot (class in pycroglia.core.plot.skeleton) SkimageCellConnectivity (class in pycroglia.core.enums) SkimageImgLabeling (class in pycroglia.core.labeled_cells) slimskel3d() (in module pycroglia.core.slimskel3d.slimskel3d) SPLINE (pycroglia.core.arclength.InterpolationMethod attribute), [1] start (pycroglia.core.slimskel3d.skel2graph.Link attribute), [1] step() (pycroglia.core.skeletonize.raytracing.euler.Euler method) (pycroglia.core.skeletonize.raytracing.rk4.RK4 method) (pycroglia.core.skeletonize.raytracing.simple.Simple method) (pycroglia.core.skeletonize.raytracing.stepper.Stepper method) step_size (pycroglia.core.skeletonize.raytracing.euler.Euler attribute) (pycroglia.core.skeletonize.raytracing.rk4.RK4 attribute) (pycroglia.core.skeletonize.shortest_path.ShortestPath attribute) Stepper (class in pycroglia.core.skeletonize.raytracing.stepper) StepperType (class in pycroglia.core.skeletonize.raytracing.factory) submit() (pycroglia.core.compute.backend.Backend method) (pycroglia.core.compute.mp_pool.MPPool method) (pycroglia.core.compute.pool.Pool method) (pycroglia.core.compute.qt_pool.QPool method) summary (pycroglia.core.io.output.FullAnalysis attribute), [1]

T

Task (class in pycroglia.core.compute.backend) task_id (pycroglia.core.compute.mp_pool.MPTask attribute) (pycroglia.core.compute.qt_pool.QTask attribute) TerritorialVolume (class in pycroglia.core.territorial_volume) test_all_finished_emitted_once() (in module pycroglia.core.compute.tests.unit.test_mp_pool) (in module pycroglia.core.compute.tests.unit.test_qt_pool) test_bounding_box_of_cell() (in module pycroglia.core.tests.unit.test_bounding_box) test_branch_analysis_equivalence() (in module pycroglia.core.tests.unit.test_branch_analysis) test_circle_linear() (in module pycroglia.core.tests.unit.test_arclength) test_circle_pchip() (in module pycroglia.core.tests.unit.test_arclength) test_circle_spline() (in module pycroglia.core.tests.unit.test_arclength) test_compute_average_centroid_distance() (in module pycroglia.core.tests.unit.test_centroid) test_compute_metrics() (in module pycroglia.core.tests.unit.test_territorial_volume) test_compute_territorial_volume() (in module pycroglia.core.tests.unit.test_territorial_volume) test_diagonal_path() (in module pycroglia.core.tests.unit.test_reorder) test_euler() (in module pycroglia.core.skeletonize.tests.unit.test_rt) test_filter_results_as_dict() (in module pycroglia.ui.widgets.imagefilters.tests.test_results) test_full_cell_analysis() (in module pycroglia.core.tests.unit.test_full_cell_analysis) test_get_centroids() (in module pycroglia.core.tests.unit.test_centroid) test_graph2skel() (in module pycroglia.core.slimskel3d.tests.unit.test_graph2skel) test_multiple_tasks_success() (in module pycroglia.core.compute.tests.unit.test_mp_pool) (in module pycroglia.core.compute.tests.unit.test_qt_pool) test_nearest_pixel() (in module pycroglia.core.tests.unit.test_nearest_pixel) test_pool_cancellation() (in module pycroglia.core.compute.tests.unit.test_mp_pool) (in module pycroglia.core.compute.tests.unit.test_qt_pool)

test_rk4() (in module pycroglia.core.skeletonize.tests.unit.test_rt) test_segment_cell_basic() (in module pycroglia.core.tests.unit.test_segmentation) test_segment_cell_small_cell_not_split() (in module pycroglia.core.tests.unit.test_segmentation) test_segment_single_cell_split() (in module pycroglia.core.tests.unit.test_segmentation) test_segmentation_config_defaults() (in module pycroglia.core.tests.unit.test_segmentation) test_simple() (in module pycroglia.core.skeletonize.tests.unit.test_rt) test_simple_line_path() (in module pycroglia.core.tests.unit.test_reorder) test_single_task_success() (in module pycroglia.core.compute.tests.unit.test_mp_pool) (in module pycroglia.core.compute.tests.unit.test_qt_pool) test_skel2graph() (in module pycroglia.core.slimskel3d.tests.unit.test_skel2graph) test_skeleton() (in module pycroglia.core.skeletonize.tests.unit.test_skeleton) test_skeleton3D() (in module pycroglia.core.slimskel3d.tests.unit.test_skeleton3D) test_slimskel3d() (in module pycroglia.core.slimskel3d.tests.unit.test_slimskel3d) test_task_failure_triggers_error() (in module pycroglia.core.compute.tests.unit.test_mp_pool) (in module pycroglia.core.compute.tests.unit.test_qt_pool) TiffReader (class in pycroglia.core.io.readers) tm (pycroglia.core.skeletonize.msfm.DerivativeResult attribute) top (pycroglia.core.bounding_box.ComputeResult attribute) total_territorial_volume (pycroglia.core.io.output.AnalysisSummary attribute), [1] total_territorial_volume_txt (pycroglia.core.io.output.AnalysisSummaryConfig attribute), [1] total_unoccupied_volume (pycroglia.core.io.output.AnalysisSummary attribute), [1] total_unoccupied_volume_txt (pycroglia.core.io.output.AnalysisSummaryConfig attribute), [1] type (pycroglia.core.skeletonize.shortest_path.ShortestPath attribute)

V

VALID_EXTENSIONS (pycroglia.core.io.readers.LsmReader attribute), [1] (pycroglia.core.io.readers.TiffReader attribute), [1] validate_channels() (pycroglia.core.io.readers.LsmReader method) (pycroglia.core.io.readers.TiffReader method)

validate_path() (pycroglia.core.io.readers.LsmReader method) (pycroglia.core.io.readers.TiffReader method) voxscale (pycroglia.core.full_cell_analysis.FullCellAnalysis attribute) (pycroglia.core.territorial_volume.TerritorialVolume attribute)

W

write() (pycroglia.core.io.output.ExcelOutput method) (pycroglia.core.io.output.JSONOutput method) (pycroglia.core.io.output.OutputWriter method)

X

x (pycroglia.core.connection.Point attribute) (pycroglia.core.erosion.Rectangle3DFootprint attribute) (pycroglia.core.labeled_cells.LabeledCells attribute) (pycroglia.core.nearest_pixel.Coordinates attribute) (pycroglia.core.slimskel3d.skel2graph.CenterOfMass attribute), [1]

Y

y (pycroglia.core.connection.Point attribute) (pycroglia.core.erosion.Rectangle3DFootprint attribute) (pycroglia.core.labeled_cells.LabeledCells attribute) (pycroglia.core.nearest_pixel.Coordinates attribute) (pycroglia.core.slimskel3d.skel2graph.CenterOfMass attribute), [1]

Z

z (pycroglia.core.connection.Point attribute) (pycroglia.core.erosion.Rectangle3DFootprint attribute) (pycroglia.core.labeled_cells.LabeledCells attribute) (pycroglia.core.nearest_pixel.Coordinates attribute) (pycroglia.core.slimskel3d.skel2graph.CenterOfMass attribute), [1]

zscale (pycroglia.core.branch_analysis.BranchAnalysis attribute) (pycroglia.core.centroid.Centroids attribute) (pycroglia.core.plot.original_cell.OriginalCellPlot attribute) zslices (pycroglia.core.branch_analysis.BranchAnalysis attribute)