Index

A

add_hide_element() (PartSeg.common_gui.collapse_checkbox.CollapseCheckbox method) add_labels() (in module PartSegCore.color_image) add_note() (PartSegImage.TiffFileException method) AdditionalLayerDescription (class in PartSegCore.project_info) AddRegisterMeta (class in PartSegCore.algorithm_describe_base) algorithm (PartSegCore.algorithm_describe_base.ROIExtractionProfile attribute) algorithm() (PartSegCore.algorithm_describe_base.AlgorithmSelection method) (PartSegCore.segmentation.watershed.WatershedSelection method) AlgorithmDescribeBase (class in PartSegCore.algorithm_describe_base)

AlgorithmDescribeBaseMeta (class in PartSegCore.algorithm_describe_base) AlgorithmDescribeNotFound AlgorithmProperty (class in PartSegCore.algorithm_describe_base) always_report (in module PartSeg.state_store) annotations (PartSegCore.project_info.HistoryElement attribute) apply_filter() (in module PartSegCore.image_operations) apply_mask (PartSegCore.segmentation.threshold.SimpleITKThresholdParams128 attribute) (PartSegCore.segmentation.threshold.SimpleITKThresholdParams256 attribute) arrays (PartSegCore.project_info.HistoryElement attribute) auto_report (in module PartSeg.state_store)

B

base_class_dict (in module PartSegCore.project_info) base_model_to_algorithm_property() (in module PartSegCore.algorithm_describe_base) base_model_to_algorithm_property_pydantic_1() (in module PartSegCore.algorithm_describe_base) base_model_to_algorithm_property_pydantic_2() (in module PartSegCore.algorithm_describe_base) base_threshold (PartSegCore.segmentation.threshold.DoubleThresholdParams attribute) (PartSegCore.segmentation.threshold.RangeThresholdParams attribute) BaseImageReader (class in PartSegImage.image_reader) BaseImageReaderBuffer (class in PartSegImage.image_reader) BaseImageWriter (class in PartSegImage) BaseMultiScaleOpening (class in PartSegCore.segmentation.restartable_segmentation_algorithms) BaseThreshold (class in PartSegCore.segmentation) (class in PartSegCore.segmentation.threshold) BaseThresholdFlowAlgorithm (class in PartSegCore.segmentation.restartable_segmentation_algorithms)

BaseWatershed (class in PartSegCore.segmentation) (class in PartSegCore.segmentation.watershed) bilateral() (in module PartSegCore.image_operations) bins (PartSegCore.segmentation.threshold.DoubleOtsuParams attribute) (PartSegCore.segmentation.threshold.MultipleOtsuDoubleThresholdParams attribute) (PartSegCore.segmentation.threshold.MultipleOtsuThresholdParams attribute) (PartSegCore.segmentation.threshold.SimpleITKThresholdParams128 attribute) (PartSegCore.segmentation.threshold.SimpleITKThresholdParams256 attribute) border_component (PartSegCore.segmentation.threshold.MultipleOtsuThresholdParams attribute) border_mask() (PartSegCore.mask_partition_utils.BorderRim static method) BorderRim (class in PartSegCore.mask_partition_utils) (class in PartSegCore.segmentation.restartable_segmentation_algorithms) BoundInfo (class in PartSegCore.roi_info) box_size() (PartSegCore.roi_info.BoundInfo method)

C

calc_bounds() (PartSegCore.roi_info.ROIInfo static method) calc_index_to_frame() (PartSegImage.Image static method) calculate_borders() (in module PartSegCore.color_image) calculate_distances_array() (in module PartSegCore.segmentation.watershed) calculate_mask() (in module PartSegCore.mask_create) calculate_mask_from_project() (in module PartSegCore.project_info) calculation_run() (PartSegCore.segmentation.restartable_segmentation_algorithms.BaseMultiScaleOpening method) (PartSegCore.segmentation.restartable_segmentation_algorithms.BaseThresholdFlowAlgorithm method) (PartSegCore.segmentation.restartable_segmentation_algorithms.BorderRim method) (PartSegCore.segmentation.restartable_segmentation_algorithms.MaskDistanceSplit method) (PartSegCore.segmentation.restartable_segmentation_algorithms.OtsuSegment method) (PartSegCore.segmentation.restartable_segmentation_algorithms.RestartableAlgorithm method) (PartSegCore.segmentation.restartable_segmentation_algorithms.ThresholdBaseAlgorithm method) (PartSegCore.segmentation.RestartableAlgorithm method) Channel (class in PartSegImage) channel (PartSegCore.segmentation.restartable_segmentation_algorithms.OtsuSegmentParameters attribute) (PartSegCore.segmentation.restartable_segmentation_algorithms.ThresholdBaseAlgorithmParameters attribute) channel_pos (PartSegImage.Image property) channels (PartSegImage.Image property) check_for_updates (in module PartSeg.state_store) check_name() (PartSegCore.algorithm_describe_base.AlgorithmSelection class method) (PartSegCore.segmentation.watershed.WatershedSelection class method) class_path (PartSegCore.algorithm_describe_base.AlgorithmSelection attribute) (PartSegCore.segmentation.threshold.DoubleThresholdSelection attribute) (PartSegCore.segmentation.threshold.RangeThresholdSelection attribute) (PartSegCore.segmentation.threshold.ThresholdSelection attribute) (PartSegCore.segmentation.watershed.WatershedSelection attribute)

clean() (PartSeg.common_backend.segmentation_thread.SegmentationThread method) clip_array() (PartSegImage.Image method) clip_to_mask (PartSegCore.mask_create.MaskProperty attribute) CollapseCheckbox (class in PartSeg.common_gui.collapse_checkbox) color_grayscale() (in module PartSegCore.color_image) components (PartSegCore.segmentation.restartable_segmentation_algorithms.OtsuSegmentParameters attribute) (PartSegCore.segmentation.threshold.MultipleOtsuDoubleThresholdParams attribute) (PartSegCore.segmentation.threshold.MultipleOtsuThresholdParams attribute) const_item_dict (PartSeg.common_backend.partially_const_dict.PartiallyConstDict attribute) construct() (PartSegCore.segmentation.watershed.MSOWatershedParams class method) (PartSegCore.segmentation.watershed.WatershedSelection class method) convert_colormap_to_image() (in module PartSeg.common_gui.numpy_qimage) copy() (PartSegCore.segmentation.watershed.MSOWatershedParams method) (PartSegCore.segmentation.watershed.WatershedSelection method) core_threshold (PartSegCore.segmentation.threshold.DoubleThresholdParams attribute) (PartSegCore.segmentation.threshold.RangeThresholdParams attribute) create() (PartSegCore.project_info.HistoryElement class method) create_colormap_image() (in module PartSeg.common_gui.numpy_qimage) create_issue() (PartSeg.common_gui.error_report.ErrorDialog method) critical() (PartSeg.common_gui.error_report.QMessageFromException class method) custom_plugin_load (in module PartSeg.state_store) cut_image() (PartSegImage.Image method) CziImageReader (class in PartSegImage) (class in PartSegImage.image_reader)

D

DataImportErrorDialog (class in PartSeg.common_gui.error_report) decode_int() (PartSegImage.image_reader.TiffImageReader static method) (PartSegImage.TiffImageReader static method) default_colormap_dict (in module PartSegCore.color_image) develop (in module PartSeg.state_store) dict() (PartSegCore.segmentation.watershed.MSOWatershedParams method) (PartSegCore.segmentation.watershed.WatershedSelection method) dilate (PartSegCore.mask_create.MaskProperty attribute)

dilate() (in module PartSegCore.image_operations) dilate_radius (PartSegCore.mask_create.MaskProperty attribute) (PartSegCore.segmentation.threshold.MaximumDistanceWatershedParams attribute) distance (PartSegCore.mask_partition_utils.BorderRimParameters attribute) (PartSegCore.segmentation.restartable_segmentation_algorithms.BorderRimParameters attribute) DistanceWatershed (class in PartSegCore.segmentation.watershed) DoubleOtsu (class in PartSegCore.segmentation.threshold) DoubleThreshold (class in PartSegCore.segmentation.threshold) dtype (PartSegImage.Image property)

E

empty_fun() (in module PartSegCore.mask.io_functions) equal_volume (PartSegCore.mask_partition_utils.MaskDistanceSplitParameters attribute) (PartSegCore.segmentation.restartable_segmentation_algorithms.MaskDistanceSplitParameters attribute) erode() (in module PartSegCore.image_operations) error_signal (PartSeg.common_backend.progress_thread.ProgressTread attribute) ErrorDialog (class in PartSeg.common_gui.error_report)

exception_occurred (PartSeg.common_backend.segmentation_thread.SegmentationThread attribute) ExceptionList (class in PartSeg.common_gui.error_report) ExceptionListItem (class in PartSeg.common_gui.error_report) exec() (PartSeg.common_gui.error_report.ErrorDialog method) exec_() (PartSeg.common_gui.error_report.ErrorDialog method) ExecuteFunctionThread (class in PartSeg.common_backend.progress_thread) execution_done (PartSeg.common_backend.segmentation_thread.SegmentationThread attribute)

F

FDTWatershed (class in PartSegCore.segmentation.watershed) file_path (PartSegCore.io_utils.PointsInfo attribute) fill_2d_holes_in_mask() (in module PartSegCore.mask_create) fill_holes (PartSegCore.mask_create.MaskProperty attribute) fill_holes_in_mask() (in module PartSegCore.mask_create) find_problematic_entries() (in module PartSegCore.io_utils) find_problematic_leafs() (in module PartSegCore.io_utils) finished_task() (PartSeg.common_backend.segmentation_thread.SegmentationThread method)

fit_array_to_image() (PartSegImage.Image method) fit_mask_to_image() (PartSegImage.Image method) flow_type (PartSegCore.segmentation.restartable_segmentation_algorithms.BaseThresholdFlowAlgorithmParameters attribute) FlowMethodSelection (in module PartSegCore.segmentation.watershed) frame (PartSegCore.mask.io_functions.SaveComponentsOptions attribute) frame_thickness (PartSegCore.mask.io_functions.SaveROIOptions attribute) from_orm() (PartSegCore.segmentation.watershed.MSOWatershedParams class method) (PartSegCore.segmentation.watershed.WatershedSelection class method)

G

gaussian() (in module PartSegCore.image_operations) GenericImageReader (class in PartSegImage) (class in PartSegImage.image_reader) get_additional_layers() (PartSegCore.segmentation.restartable_segmentation_algorithms.ThresholdBaseAlgorithm method) get_array_axis_positions() (PartSegImage.Image class method) get_axis_positions() (PartSegImage.Image class method) get_channel() (PartSegImage.Image method) get_data_by_axis() (PartSegImage.Image method) get_default() (PartSegCore.algorithm_describe_base.AlgorithmSelection class method) (PartSegCore.algorithm_describe_base.Register method) (PartSegCore.segmentation.watershed.WatershedSelection class method) get_dimension_letters() (PartSegImage.Image method) get_dimension_number() (PartSegImage.Image method) get_fields() (PartSegCore.algorithm_describe_base.AlgorithmDescribeBase class method) (PartSegCore.io_utils.LoadBase class method) (PartSegCore.io_utils.LoadPoints class method) (PartSegCore.io_utils.SaveMaskAsTiff class method) (PartSegCore.io_utils.SaveROIAsNumpy class method) (PartSegCore.io_utils.SaveROIAsTIFF class method) (PartSegCore.io_utils.SaveScreenshot class method) (PartSegCore.mask.io_functions.SaveParametersJSON class method) (PartSegCore.segmentation.BaseThreshold class method) (PartSegCore.segmentation.BaseWatershed class method) (PartSegCore.segmentation.NoiseFilteringBase class method) (PartSegCore.segmentation.RestartableAlgorithm class method) (PartSegCore.segmentation.ROIExtractionAlgorithm class method) (PartSegCore.segmentation.StackAlgorithm class method) (PartSegCore.segmentation.watershed.BaseWatershed class method) (PartSegCore.segmentation.watershed.DistanceWatershed class method) (PartSegCore.segmentation.watershed.FDTWatershed class method) (PartSegCore.segmentation.watershed.MSOWatershed class method) (PartSegCore.segmentation.watershed.PathDistanceWatershed class method) (PartSegCore.segmentation.watershed.PathWatershed class method) get_image_for_save() (PartSegImage.Image method) get_info_text() (PartSeg.common_backend.segmentation_thread.SegmentationThread method) get_layer() (PartSegImage.Image method) get_mask_for_save() (PartSegImage.Image method) get_name() (PartSegCore.algorithm_describe_base.AlgorithmDescribeBase class method) (PartSegCore.io_utils.LoadPlanExcel class method) (PartSegCore.io_utils.LoadPlanJson class method) (PartSegCore.io_utils.LoadPoints class method) (PartSegCore.io_utils.SaveMaskAsTiff class method) (PartSegCore.io_utils.SaveROIAsNumpy class method) (PartSegCore.io_utils.SaveROIAsTIFF class method) (PartSegCore.io_utils.SaveScreenshot class method) (PartSegCore.mask.io_functions.LoadROI class method) (PartSegCore.mask.io_functions.LoadROIFromTIFF class method) (PartSegCore.mask.io_functions.LoadROIImage class method) (PartSegCore.mask.io_functions.LoadROIParameters class method) (PartSegCore.mask.io_functions.LoadStackImage class method) (PartSegCore.mask.io_functions.LoadStackImageWithMask class method) (PartSegCore.mask.io_functions.SaveComponents class method) (PartSegCore.mask.io_functions.SaveComponentsImagej class method) (PartSegCore.mask.io_functions.SaveParametersJSON class method) (PartSegCore.mask.io_functions.SaveROI class method) (PartSegCore.mask_partition_utils.BorderRim class method) (PartSegCore.mask_partition_utils.MaskDistanceSplit class method) (PartSegCore.segmentation.BaseThreshold class method) (PartSegCore.segmentation.BaseWatershed class method) (PartSegCore.segmentation.NoiseFilteringBase class method) (PartSegCore.segmentation.restartable_segmentation_algorithms.BorderRim class method) (PartSegCore.segmentation.restartable_segmentation_algorithms.LowerThresholdAlgorithm class method) (PartSegCore.segmentation.restartable_segmentation_algorithms.LowerThresholdFlowAlgorithm class method) (PartSegCore.segmentation.restartable_segmentation_algorithms.LowerThresholdMultiScaleOpening class method) (PartSegCore.segmentation.restartable_segmentation_algorithms.MaskDistanceSplit class method) (PartSegCore.segmentation.restartable_segmentation_algorithms.OtsuSegment class method) (PartSegCore.segmentation.restartable_segmentation_algorithms.RangeThresholdAlgorithm class method) (PartSegCore.segmentation.restartable_segmentation_algorithms.UpperThresholdAlgorithm class method) (PartSegCore.segmentation.restartable_segmentation_algorithms.UpperThresholdFlowAlgorithm class method) (PartSegCore.segmentation.restartable_segmentation_algorithms.UpperThresholdMultiScaleOpening class method) (PartSegCore.segmentation.RestartableAlgorithm class method) (PartSegCore.segmentation.ROIExtractionAlgorithm class method) (PartSegCore.segmentation.StackAlgorithm class method) (PartSegCore.segmentation.threshold.DoubleOtsu class method) (PartSegCore.segmentation.threshold.DoubleThreshold class method) (PartSegCore.segmentation.threshold.HuangThreshold class method) (PartSegCore.segmentation.threshold.IntermodesThreshold class method) (PartSegCore.segmentation.threshold.IsoDataThreshold class method) (PartSegCore.segmentation.threshold.KittlerIllingworthThreshold class method) (PartSegCore.segmentation.threshold.LiThreshold class method) (PartSegCore.segmentation.threshold.ManualThreshold class method) (PartSegCore.segmentation.threshold.MaximumDistanceCore class method) (PartSegCore.segmentation.threshold.MaximumEntropyThreshold class method) (PartSegCore.segmentation.threshold.MomentsThreshold class method) (PartSegCore.segmentation.threshold.MultipleOtsu class method) (PartSegCore.segmentation.threshold.MultipleOtsuThreshold class method) (PartSegCore.segmentation.threshold.OtsuThreshold class method) (PartSegCore.segmentation.threshold.RangeThreshold class method) (PartSegCore.segmentation.threshold.RenyiEntropyThreshold class method) (PartSegCore.segmentation.threshold.ShanbhagThreshold class method) (PartSegCore.segmentation.threshold.TriangleThreshold class method) (PartSegCore.segmentation.threshold.YenThreshold class method) (PartSegCore.segmentation.watershed.BaseWatershed class method) (PartSegCore.segmentation.watershed.DistanceWatershed class method) (PartSegCore.segmentation.watershed.FDTWatershed class method) (PartSegCore.segmentation.watershed.MSOWatershed class method) (PartSegCore.segmentation.watershed.PathDistanceWatershed class method) (PartSegCore.segmentation.watershed.PathWatershed class method)

get_position() (PartSeg.common_backend.partially_const_dict.PartiallyConstDict method) get_ranges() (PartSegImage.Image method) get_raw_copy() (PartSegCore.mask.io_functions.MaskProjectTuple method) (PartSegCore.project_info.ProjectInfoBase method) get_roi_info_and_mask() (PartSegCore.project_info.HistoryElement method) get_steps_num() (PartSegCore.segmentation.RestartableAlgorithm static method) (PartSegCore.segmentation.ROIExtractionAlgorithm static method) (PartSegCore.segmentation.StackAlgorithm static method) get_um_shift() (PartSegImage.Image method) get_um_spacing() (PartSegImage.Image method) get_user() (in module PartSeg.common_gui.error_report)

H

has_mask (PartSegImage.Image property) header() (PartSegCore.segmentation.restartable_segmentation_algorithms.BorderRimParameters static method) (PartSegCore.segmentation.restartable_segmentation_algorithms.MaskDistanceSplitParameters static method)

hist_num (PartSegCore.segmentation.restartable_segmentation_algorithms.OtsuSegmentParameters attribute) HistoryElement.Config (class in PartSegCore.project_info) HistoryProblem HuangThreshold (class in PartSegCore.segmentation.threshold)

I

Image (class in PartSegImage) image_class (PartSegImage.CziImageReader attribute) (PartSegImage.GenericImageReader attribute) (PartSegImage.image_reader.BaseImageReader attribute) (PartSegImage.ObsepImageReader attribute) (PartSegImage.OifImagReader attribute) (PartSegImage.TiffImageReader attribute) IMAGEJImageWriter (class in PartSegImage) ImageWriter (class in PartSegImage)

info_function() (PartSeg.common_backend.progress_thread.ProgressTread method) information() (PartSeg.common_gui.error_report.QMessageFromException class method) IntermodesThreshold (class in PartSegCore.segmentation.threshold) is_2d (PartSegImage.Image property) is_stack (PartSegImage.Image property) is_time (PartSegImage.Image property) IsoDataThreshold (class in PartSegCore.segmentation.threshold) item_added (PartSeg.common_backend.partially_const_dict.PartiallyConstDict attribute) item_double_clicked() (PartSeg.common_gui.error_report.ExceptionList static method) item_removed (PartSeg.common_backend.partially_const_dict.PartiallyConstDict attribute)

J

json() (PartSegCore.segmentation.watershed.MSOWatershedParams method) (PartSegCore.segmentation.watershed.WatershedSelection method)

K

KittlerIllingworthThreshold (class in PartSegCore.segmentation.threshold)

L

layers (PartSegImage.Image property) LiThreshold (class in PartSegCore.segmentation.threshold) load() (PartSegCore.io_utils.LoadBase class method) (PartSegCore.io_utils.LoadPlanExcel class method) (PartSegCore.io_utils.LoadPlanJson class method) (PartSegCore.io_utils.LoadPoints class method) (PartSegCore.mask.io_functions.LoadROI class method) (PartSegCore.mask.io_functions.LoadROIFromTIFF class method) (PartSegCore.mask.io_functions.LoadROIImage class method) (PartSegCore.mask.io_functions.LoadROIParameters class method) (PartSegCore.mask.io_functions.LoadStackImage class method) (PartSegCore.mask.io_functions.LoadStackImageWithMask class method) load_matadata_part() (in module PartSegCore.io_utils) load_metadata() (in module PartSegCore.mask.io_functions) load_metadata_part() (in module PartSegCore.io_utils)

LoadBase (class in PartSegCore.io_utils) LoadPlanExcel (class in PartSegCore.io_utils) LoadPlanJson (class in PartSegCore.io_utils) LoadPoints (class in PartSegCore.io_utils) LoadROI (class in PartSegCore.mask.io_functions) LoadROIFromTIFF (class in PartSegCore.mask.io_functions) LoadROIImage (class in PartSegCore.mask.io_functions) LoadROIParameters (class in PartSegCore.mask.io_functions) LoadStackImage (class in PartSegCore.mask.io_functions) LoadStackImageWithMask (class in PartSegCore.mask.io_functions) lower (PartSegCore.roi_info.BoundInfo attribute) lower_component (PartSegCore.segmentation.threshold.MultipleOtsuDoubleThresholdParams attribute) lower_threshold (PartSegCore.segmentation.restartable_segmentation_algorithms.TwoThreshold attribute) LowerThresholdAlgorithm (class in PartSegCore.segmentation.restartable_segmentation_algorithms) LowerThresholdFlowAlgorithm (class in PartSegCore.segmentation.restartable_segmentation_algorithms) LowerThresholdMultiScaleOpening (class in PartSegCore.segmentation.restartable_segmentation_algorithms)

M

ManualThreshold (class in PartSegCore.segmentation.threshold) mask_data (PartSegCore.mask.io_functions.SaveComponentsOptions attribute) (PartSegCore.mask.io_functions.SaveROIOptions attribute) mask_property (PartSegCore.project_info.HistoryElement attribute) MaskDistanceSplit (class in PartSegCore.mask_partition_utils) (class in PartSegCore.segmentation.restartable_segmentation_algorithms) MaskProjectTuple (class in PartSegCore.mask.io_functions) max_holes_size (PartSegCore.mask_create.MaskProperty attribute) MaximumDistanceCore (class in PartSegCore.segmentation.threshold) MaximumEntropyThreshold (class in PartSegCore.segmentation.threshold) median() (in module PartSegCore.image_operations) merge() (PartSegImage.Image method) minimum_border_distance (PartSegCore.segmentation.threshold.MaximumDistanceWatershedParams attribute) minimum_size (PartSegCore.segmentation.restartable_segmentation_algorithms.BaseThresholdFlowAlgorithmParameters attribute) (PartSegCore.segmentation.restartable_segmentation_algorithms.ThresholdBaseAlgorithmParameters attribute) (PartSegCore.segmentation.threshold.MaximumDistanceWatershedParams attribute) model_construct() (PartSegCore.segmentation.watershed.MSOWatershedParams class method) (PartSegCore.segmentation.watershed.WatershedSelection class method) model_copy() (PartSegCore.segmentation.watershed.MSOWatershedParams method) (PartSegCore.segmentation.watershed.WatershedSelection method) model_dump() (PartSegCore.segmentation.watershed.MSOWatershedParams method) (PartSegCore.segmentation.watershed.WatershedSelection method) model_dump_json() (PartSegCore.segmentation.watershed.MSOWatershedParams method) (PartSegCore.segmentation.watershed.WatershedSelection method) model_extra (PartSegCore.segmentation.watershed.MSOWatershedParams property) (PartSegCore.segmentation.watershed.WatershedSelection property) model_fields_set (PartSegCore.segmentation.watershed.MSOWatershedParams property) (PartSegCore.segmentation.watershed.WatershedSelection property) model_json_schema() (PartSegCore.segmentation.watershed.MSOWatershedParams class method) (PartSegCore.segmentation.watershed.WatershedSelection class method) model_parametrized_name() (PartSegCore.segmentation.watershed.MSOWatershedParams class method) (PartSegCore.segmentation.watershed.WatershedSelection class method) model_post_init() (PartSegCore.segmentation.watershed.MSOWatershedParams method) (PartSegCore.segmentation.watershed.WatershedSelection method) model_rebuild() (PartSegCore.segmentation.watershed.MSOWatershedParams class method) (PartSegCore.segmentation.watershed.WatershedSelection class method) model_validate() (PartSegCore.segmentation.watershed.MSOWatershedParams class method) (PartSegCore.segmentation.watershed.WatershedSelection class method)

model_validate_json() (PartSegCore.segmentation.watershed.MSOWatershedParams class method) (PartSegCore.segmentation.watershed.WatershedSelection class method) model_validate_strings() (PartSegCore.segmentation.watershed.MSOWatershedParams class method) (PartSegCore.segmentation.watershed.WatershedSelection class method) module PartSeg.common_backend PartSeg.common_backend.abstract_class PartSeg.common_backend.partially_const_dict PartSeg.common_backend.progress_thread PartSeg.common_backend.segmentation_thread PartSeg.common_gui.error_report PartSeg.common_gui.numpy_qimage PartSeg.state_store PartSegCore.algorithm_describe_base PartSegCore.color_image PartSegCore.image_operations PartSegCore.io_utils PartSegCore.json_hooks PartSegCore.mask.io_functions PartSegCore.mask_create PartSegCore.mask_partition_utils PartSegCore.project_info PartSegCore.roi_info PartSegCore.segmentation PartSegCore.segmentation.restartable_segmentation_algorithms PartSegCore.segmentation.threshold PartSegCore.segmentation.watershed PartSegImage PartSegImage.image_reader MomentsThreshold (class in PartSegCore.segmentation.threshold) mp_eq() (in module PartSegCore.mask_create) MSOWatershed (class in PartSegCore.segmentation.watershed) MSOWatershedParams.Config (class in PartSegCore.segmentation.watershed) mu_mid (PartSegCore.segmentation.restartable_segmentation_algorithms.BaseMultiScaleOpeningParameters attribute) MultipleOtsu (class in PartSegCore.segmentation.threshold) MultipleOtsuThreshold (class in PartSegCore.segmentation.threshold)

N

name (PartSegCore.algorithm_describe_base.AlgorithmSelection attribute) (PartSegCore.algorithm_describe_base.ROIExtractionProfile attribute) (PartSegCore.segmentation.threshold.DoubleThresholdSelection attribute) (PartSegCore.segmentation.threshold.RangeThresholdSelection attribute) (PartSegCore.segmentation.threshold.ThresholdSelection attribute) (PartSegCore.segmentation.watershed.WatershedSelection attribute) name_to_scalar (in module PartSegImage.image_reader) napari_get_settings() (in module PartSeg.common_backend) NeighType (class in PartSegCore.segmentation.watershed) NO (PartSegCore.image_operations.RadiusType attribute)

noise_filter() (PartSegCore.segmentation.NoiseFilteringBase class method) noise_filtering (PartSegCore.segmentation.restartable_segmentation_algorithms.OtsuSegmentParameters attribute) (PartSegCore.segmentation.restartable_segmentation_algorithms.ThresholdBaseAlgorithmParameters attribute) NoiseFilteringBase (class in PartSegCore.segmentation) NoiseFilterType (class in PartSegCore.image_operations) NotSupportedImage num_of_parts (PartSegCore.mask_partition_utils.MaskDistanceSplitParameters attribute) (PartSegCore.segmentation.restartable_segmentation_algorithms.MaskDistanceSplitParameters attribute) number_of_files() (PartSegCore.io_utils.LoadBase class method) (PartSegCore.mask.io_functions.LoadStackImageWithMask class method) NumpyQImage (class in PartSeg.common_gui.numpy_qimage)

O

ObsepImageReader (class in PartSegImage) (class in PartSegImage.image_reader) OifImagReader (class in PartSegImage) (class in PartSegImage.image_reader)

OneThresholdAlgorithm (class in PartSegCore.segmentation.restartable_segmentation_algorithms) open_tar_file() (in module PartSegCore.io_utils) OtsuSegment (class in PartSegCore.segmentation.restartable_segmentation_algorithms) OtsuThreshold (class in PartSegCore.segmentation.threshold)

P

parse_file() (PartSegCore.segmentation.watershed.MSOWatershedParams class method) (PartSegCore.segmentation.watershed.WatershedSelection class method) parse_obj() (PartSegCore.segmentation.watershed.MSOWatershedParams class method) (PartSegCore.segmentation.watershed.WatershedSelection class method) parse_raw() (PartSegCore.segmentation.watershed.MSOWatershedParams class method) (PartSegCore.segmentation.watershed.WatershedSelection class method) partial() (PartSegCore.io_utils.LoadBase class method) (PartSegCore.io_utils.LoadPoints class method) (PartSegCore.mask.io_functions.LoadROI class method) PartiallyConstDict (class in PartSeg.common_backend.partially_const_dict) PartSeg.common_backend module PartSeg.common_backend.abstract_class module PartSeg.common_backend.partially_const_dict module PartSeg.common_backend.progress_thread module PartSeg.common_backend.segmentation_thread module PartSeg.common_gui.error_report module PartSeg.common_gui.numpy_qimage module PartSeg.state_store module PartSegCore.algorithm_describe_base module PartSegCore.color_image module PartSegCore.image_operations module PartSegCore.io_utils module

PartSegCore.json_hooks module PartSegCore.mask.io_functions module PartSegCore.mask_create module PartSegCore.mask_partition_utils module PartSegCore.project_info module PartSegCore.roi_info module PartSegCore.segmentation module PartSegCore.segmentation.restartable_segmentation_algorithms module PartSegCore.segmentation.threshold module PartSegCore.segmentation.watershed module PartSegEncoder (class in PartSegCore.json_hooks) PartSegImage module PartSegImage.image_reader module PathDistanceWatershed (class in PartSegCore.segmentation.watershed) PathWatershed (class in PartSegCore.segmentation.watershed) plane_shape (PartSegImage.Image property) points (PartSegCore.io_utils.PointsInfo attribute) PointsInfo (class in PartSegCore.io_utils) prepare_result() (PartSegCore.segmentation.restartable_segmentation_algorithms.ThresholdBaseAlgorithm method) pretty_print() (PartSegCore.algorithm_describe_base.ROIExtractionProfile method) progress_signal (PartSeg.common_backend.segmentation_thread.SegmentationThread attribute) ProgressTread (class in PartSeg.common_backend.progress_thread) ProjectInfoBase (class in PartSegCore.project_info)

Q

QMessageFromException (class in PartSeg.common_gui.error_report)

QtMeta (class in PartSeg.common_backend.abstract_class) question() (PartSeg.common_gui.error_report.QMessageFromException class method)

R

R2D (PartSegCore.image_operations.RadiusType attribute) R3D (PartSegCore.image_operations.RadiusType attribute) RadiusType (class in PartSegCore.image_operations) range_changed (PartSeg.common_backend.progress_thread.ProgressTread attribute) RangeThreshold (class in PartSegCore.segmentation.threshold) RangeThresholdAlgorithm (class in PartSegCore.segmentation.restartable_segmentation_algorithms) read() (PartSegImage.CziImageReader method) (PartSegImage.GenericImageReader method) (PartSegImage.image_reader.BaseImageReader method) (PartSegImage.image_reader.BaseImageReaderBuffer method) (PartSegImage.image_reader.CziImageReader method) (PartSegImage.image_reader.GenericImageReader method) (PartSegImage.image_reader.ObsepImageReader method) (PartSegImage.image_reader.OifImagReader method) (PartSegImage.image_reader.TiffImageReader method) (PartSegImage.ObsepImageReader method) (PartSegImage.OifImagReader method) (PartSegImage.TiffImageReader method) read_image() (PartSegImage.CziImageReader class method) (PartSegImage.GenericImageReader class method) (PartSegImage.image_reader.BaseImageReader class method) (PartSegImage.image_reader.BaseImageReaderBuffer class method) (PartSegImage.ObsepImageReader class method) (PartSegImage.OifImagReader class method) (PartSegImage.TiffImageReader class method) reflective (PartSegCore.segmentation.watershed.MSOWatershedParams attribute)

Register (class in PartSegCore.algorithm_describe_base) register() (PartSegCore.algorithm_describe_base.AlgorithmSelection class method) (PartSegCore.algorithm_describe_base.Register method) (PartSegCore.segmentation.watershed.WatershedSelection class method) relative_path (PartSegCore.mask.io_functions.SaveROIOptions attribute) remove_hide_element() (PartSeg.common_gui.collapse_checkbox.CollapseCheckbox method) remove_object_touching_border (PartSegCore.segmentation.restartable_segmentation_algorithms.BaseThresholdFlowAlgorithmParameters attribute) RenyiEntropyThreshold (class in PartSegCore.segmentation.threshold) reorder_axes() (PartSegImage.Image class method) report_errors (in module PartSeg.state_store) resolution (in module PartSegCore.color_image) RestartableAlgorithm (class in PartSegCore.segmentation) (class in PartSegCore.segmentation.restartable_segmentation_algorithms) return_order() (PartSegImage.CziImageReader class method) (PartSegImage.GenericImageReader class method) (PartSegImage.image_reader.BaseImageReader class method) (PartSegImage.ObsepImageReader class method) (PartSegImage.OifImagReader class method) (PartSegImage.TiffImageReader class method) reversed_mask (PartSegCore.mask_create.MaskProperty attribute) roi_extraction_parameters (PartSegCore.project_info.HistoryElement attribute) ROIExtractionAlgorithm (class in PartSegCore.segmentation) ROIExtractionProfileMeta (class in PartSegCore.algorithm_describe_base) ROIExtractionResult (class in PartSegCore.segmentation) ROIInfo (class in PartSegCore.roi_info) run() (PartSeg.common_backend.progress_thread.ExecuteFunctionThread method) (PartSeg.common_backend.segmentation_thread.SegmentationThread method)

S

save() (PartSegCore.io_utils.SaveBase class method) (PartSegCore.io_utils.SaveMaskAsTiff class method) (PartSegCore.io_utils.SaveROIAsNumpy class method) (PartSegCore.io_utils.SaveROIAsTIFF class method) (PartSegCore.io_utils.SaveScreenshot class method) (PartSegCore.mask.io_functions.SaveComponents class method) (PartSegCore.mask.io_functions.SaveComponentsImagej class method) (PartSegCore.mask.io_functions.SaveParametersJSON class method) (PartSegCore.mask.io_functions.SaveROI class method) (PartSegImage.IMAGEJImageWriter class method) (PartSegImage.ImageWriter class method) save_components (PartSegCore.mask_create.MaskProperty attribute) save_folder (in module PartSeg.state_store) save_mask() (PartSegImage.IMAGEJImageWriter class method) (PartSegImage.ImageWriter class method) SaveBase (class in PartSegCore.io_utils) SaveComponents (class in PartSegCore.mask.io_functions) SaveComponentsImagej (class in PartSegCore.mask.io_functions) SaveMaskAsTiff (class in PartSegCore.io_utils) SaveParametersJSON (class in PartSegCore.mask.io_functions) SaveROI (class in PartSegCore.mask.io_functions) SaveROIAsNumpy (class in PartSegCore.io_utils) SaveROIAsTIFF (class in PartSegCore.io_utils) SaveScreenshot (class in PartSegCore.io_utils) schema() (PartSegCore.segmentation.watershed.MSOWatershedParams class method) (PartSegCore.segmentation.watershed.WatershedSelection class method) schema_json() (PartSegCore.segmentation.watershed.MSOWatershedParams class method) (PartSegCore.segmentation.watershed.WatershedSelection class method) SegmentationThread (class in PartSeg.common_backend.segmentation_thread) SegmentationType (class in PartSegCore.io_utils) send_report() (PartSeg.common_gui.error_report.ErrorDialog method) set_image() (PartSeg.common_backend.segmentation_thread.SegmentationThread method) set_mask() (PartSeg.common_backend.segmentation_thread.SegmentationThread method) (PartSegCore.segmentation.restartable_segmentation_algorithms.RestartableAlgorithm method) (PartSegCore.segmentation.RestartableAlgorithm method) (PartSegCore.segmentation.ROIExtractionAlgorithm method) (PartSegCore.segmentation.StackAlgorithm method) (PartSegImage.Image method)

set_parameters() (PartSeg.common_backend.segmentation_thread.SegmentationThread method) set_spacing() (PartSegImage.Image method) setup_ui() (PartSeg.common_gui.error_report.ErrorDialog method) ShanbhagThreshold (class in PartSegCore.segmentation.threshold) shape (PartSegImage.Image property) show_error_dialog (in module PartSeg.state_store) side_connection (PartSegCore.segmentation.restartable_segmentation_algorithms.ThresholdBaseAlgorithmParameters attribute) simple_mask() (PartSegCore.mask_create.MaskProperty class method) SitkThreshold (class in PartSegCore.segmentation.threshold) spacing (PartSegCore.mask.io_functions.SaveROIOptions attribute) (PartSegImage.Image property) split() (PartSegCore.mask_partition_utils.MaskDistanceSplit static method) sprawl() (PartSegCore.segmentation.BaseWatershed class method) (PartSegCore.segmentation.watershed.BaseWatershed class method) (PartSegCore.segmentation.watershed.DistanceWatershed class method) (PartSegCore.segmentation.watershed.FDTWatershed class method) (PartSegCore.segmentation.watershed.MSOWatershed class method) (PartSegCore.segmentation.watershed.PathDistanceWatershed class method) (PartSegCore.segmentation.watershed.PathWatershed class method) stack_pos (PartSegImage.Image property) StackAlgorithm (class in PartSegCore.segmentation) start() (PartSeg.common_backend.segmentation_thread.SegmentationThread method) staticMetaObject (PartSeg.common_backend.progress_thread.ExecuteFunctionThread attribute) (PartSeg.common_backend.progress_thread.ProgressTread attribute) (PartSeg.common_gui.error_report.DataImportErrorDialog attribute) (PartSeg.common_gui.error_report.ErrorDialog attribute) (PartSeg.common_gui.error_report.ExceptionList attribute) (PartSeg.common_gui.error_report.QMessageFromException attribute) step_changed (PartSeg.common_backend.progress_thread.ProgressTread attribute) step_limits (PartSegCore.segmentation.restartable_segmentation_algorithms.BaseMultiScaleOpeningParameters attribute) (PartSegCore.segmentation.watershed.MSOWatershedParams attribute) substitute() (PartSegImage.Image method) swap_time_and_stack() (PartSegImage.Image method)

T

threshold (PartSegCore.segmentation.restartable_segmentation_algorithms.BaseMultiScaleOpeningParameters attribute) (PartSegCore.segmentation.restartable_segmentation_algorithms.BaseThresholdFlowAlgorithmParameters attribute) (PartSegCore.segmentation.restartable_segmentation_algorithms.OneThresholdAlgorithmParameters attribute) (PartSegCore.segmentation.restartable_segmentation_algorithms.RangeThresholdAlgorithmParameters attribute) (PartSegCore.segmentation.restartable_segmentation_algorithms.ThresholdBaseAlgorithmParametersAnnot attribute) (PartSegCore.segmentation.threshold.MaximumDistanceWatershedParams attribute) (PartSegCore.segmentation.threshold.SingleThresholdParams attribute) threshold_operator() (PartSegCore.segmentation.restartable_segmentation_algorithms.LowerThresholdAlgorithm static method) (PartSegCore.segmentation.restartable_segmentation_algorithms.LowerThresholdFlowAlgorithm static method) (PartSegCore.segmentation.restartable_segmentation_algorithms.LowerThresholdMultiScaleOpening static method) (PartSegCore.segmentation.restartable_segmentation_algorithms.UpperThresholdAlgorithm static method) (PartSegCore.segmentation.restartable_segmentation_algorithms.UpperThresholdFlowAlgorithm static method) (PartSegCore.segmentation.restartable_segmentation_algorithms.UpperThresholdMultiScaleOpening static method)

ThresholdBaseAlgorithm (class in PartSegCore.segmentation.restartable_segmentation_algorithms) TiffFileException, [1] TiffImageReader (class in PartSegImage) (class in PartSegImage.image_reader) time_pos (PartSegImage.Image property) times (PartSegImage.Image property) to_binary_image() (in module PartSegCore.image_operations) TriangleThreshold (class in PartSegCore.segmentation.threshold) TwoLevelThresholdBaseAlgorithm (class in PartSegCore.segmentation.restartable_segmentation_algorithms)

U

units (PartSegCore.mask_partition_utils.BorderRimParameters attribute) (PartSegCore.segmentation.restartable_segmentation_algorithms.BorderRimParameters attribute) update_array_shape() (PartSegImage.CziImageReader class method) (PartSegImage.GenericImageReader class method) (PartSegImage.image_reader.BaseImageReader class method) (PartSegImage.image_reader.CziImageReader class method) (PartSegImage.ObsepImageReader class method) (PartSegImage.OifImagReader class method) (PartSegImage.TiffImageReader class method) update_class_path() (PartSegCore.algorithm_describe_base.AlgorithmSelection class method) (PartSegCore.segmentation.watershed.WatershedSelection class method)

update_forward_refs() (PartSegCore.segmentation.watershed.MSOWatershedParams class method) (PartSegCore.segmentation.watershed.WatershedSelection class method) update_values() (PartSegCore.algorithm_describe_base.AlgorithmSelection class method) (PartSegCore.segmentation.watershed.WatershedSelection class method) upper (PartSegCore.roi_info.BoundInfo attribute) upper_component (PartSegCore.segmentation.threshold.MultipleOtsuDoubleThresholdParams attribute) upper_threshold (PartSegCore.segmentation.restartable_segmentation_algorithms.TwoThreshold attribute) UpperThresholdAlgorithm (class in PartSegCore.segmentation.restartable_segmentation_algorithms) UpperThresholdFlowAlgorithm (class in PartSegCore.segmentation.restartable_segmentation_algorithms) UpperThresholdMultiScaleOpening (class in PartSegCore.segmentation.restartable_segmentation_algorithms)

V

val_serializer() (PartSegCore.algorithm_describe_base.AlgorithmSelection method) (PartSegCore.segmentation.watershed.WatershedSelection method) validate() (PartSegCore.segmentation.watershed.MSOWatershedParams class method) (PartSegCore.segmentation.watershed.WatershedSelection class method) validate_values() (PartSegCore.algorithm_describe_base.ROIExtractionProfile class method) valley (PartSegCore.segmentation.restartable_segmentation_algorithms.OtsuSegmentParameters attribute) (PartSegCore.segmentation.threshold.DoubleOtsuParams attribute) (PartSegCore.segmentation.threshold.MultipleOtsuDoubleThresholdParams attribute) (PartSegCore.segmentation.threshold.MultipleOtsuThresholdParams attribute) value (PartSegImage.Channel property)

values (PartSegCore.algorithm_describe_base.AlgorithmSelection attribute) (PartSegCore.algorithm_describe_base.ROIExtractionProfile attribute) (PartSegCore.segmentation.threshold.DoubleThresholdSelection attribute) (PartSegCore.segmentation.threshold.RangeThresholdSelection attribute) (PartSegCore.segmentation.threshold.ThresholdSelection attribute) (PartSegCore.segmentation.watershed.WatershedSelection attribute) values() (PartSegCore.algorithm_describe_base.Register method) verify_mask() (PartSegImage.image_reader.TiffImageReader static method) (PartSegImage.TiffImageReader static method) voxel_size (PartSegImage.Image property)

W

warning() (PartSeg.common_gui.error_report.QMessageFromException class method) WatershedSelection.Config (class in PartSegCore.segmentation.watershed)

with_traceback() (PartSegImage.TiffFileException method) WrongFileTypeException

Y

YenThreshold (class in PartSegCore.segmentation.threshold)