Index

A

actk (module) actk.bin (module) actk.bin.all (module) actk.bin.cli (module) actk.constants (module) actk.exceptions (module) actk.steps (module) actk.steps.diagnostic_sheets (module) actk.steps.diagnostic_sheets.diagnostic_sheets (module) actk.steps.raw (module) actk.steps.raw.raw (module)

actk.steps.single_cell_features (module) actk.steps.single_cell_features.single_cell_features (module) actk.steps.single_cell_images (module) actk.steps.single_cell_images.single_cell_images (module) actk.steps.standardize_fov_array (module) actk.steps.standardize_fov_array.standardize_fov_array (module) actk.utils (module) actk.utils.dataset_utils (module) actk.utils.image_utils (module) All (class in actk.bin.all) AllExpectedInputs (actk.constants.DatasetFields attribute)

B

Brightfield (actk.constants.Channels attribute)

C

cell_id (actk.steps.diagnostic_sheets.diagnostic_sheets.DiagnosticSheetError attribute) (actk.steps.diagnostic_sheets.diagnostic_sheets.DiagnosticSheetResult attribute) (actk.steps.single_cell_features.single_cell_features.SingleCellFeaturesError attribute) (actk.steps.single_cell_features.single_cell_features.SingleCellFeaturesResult attribute) (actk.steps.single_cell_images.single_cell_images.CellImagesError attribute) (actk.steps.single_cell_images.single_cell_images.CellImagesResult attribute) CellFeaturesPath (actk.constants.DatasetFields attribute) CellId (actk.constants.DatasetFields attribute) CellImage2DAllProjectionsPath (actk.constants.DatasetFields attribute) CellImage2DYXProjectionPath (actk.constants.DatasetFields attribute) CellImage3DPath (actk.constants.DatasetFields attribute) CellImagesError (class in actk.steps.single_cell_images.single_cell_images) CellImagesResult (class in actk.steps.single_cell_images.single_cell_images)

CellIndex (actk.constants.DatasetFields attribute) ChannelIndexBrightfield (actk.constants.DatasetFields attribute) ChannelIndexDNA (actk.constants.DatasetFields attribute) ChannelIndexMembrane (actk.constants.DatasetFields attribute) ChannelIndexMembraneSegmentation (actk.constants.DatasetFields attribute) ChannelIndexNucleusSegmentation (actk.constants.DatasetFields attribute) ChannelIndexStructure (actk.constants.DatasetFields attribute) Channels (class in actk.constants) check_required_fields() (in module actk.utils.dataset_utils) checkout() (actk.bin.all.All method) clean() (actk.bin.all.All method) cli() (in module actk.bin.cli) crop_raw_channels_with_segmentation() (in module actk.utils.image_utils)

D

DatasetFields (class in actk.constants) DefaultOrderList (actk.constants.Channels attribute) DiagnosticSheetError (class in actk.steps.diagnostic_sheets.diagnostic_sheets) DiagnosticSheetPath (actk.constants.DatasetFields attribute)

DiagnosticSheetResult (class in actk.steps.diagnostic_sheets.diagnostic_sheets) DiagnosticSheets (class in actk.steps) (class in actk.steps.diagnostic_sheets) (class in actk.steps.diagnostic_sheets.diagnostic_sheets) DNA (actk.constants.Channels attribute)

E

error (actk.steps.diagnostic_sheets.diagnostic_sheets.DiagnosticSheetError attribute) (actk.steps.single_cell_features.single_cell_features.SingleCellFeaturesError attribute) (actk.steps.single_cell_images.single_cell_images.CellImagesError attribute) (actk.steps.standardize_fov_array.standardize_fov_array.StandardizeFOVArrayError attribute)

F

fov_id (actk.steps.standardize_fov_array.standardize_fov_array.StandardizeFOVArrayError attribute) (actk.steps.standardize_fov_array.standardize_fov_array.StandardizeFOVArrayResult attribute)

FOVId (actk.constants.DatasetFields attribute)

G

get_features_from_image() (in module actk.utils.image_utils)

get_module_version() (in module actk) get_normed_image_array() (in module actk.utils.image_utils)

M

Membrane (actk.constants.Channels attribute) MembraneSegmentation (actk.constants.Channels attribute)

MembraneSegmentationReadPath (actk.constants.DatasetFields attribute) MissingDataError

N

NucleusSegmentation (actk.constants.Channels attribute)

NucleusSegmentationReadPath (actk.constants.DatasetFields attribute)

P

path (actk.steps.single_cell_features.single_cell_features.SingleCellFeaturesResult attribute) (actk.steps.standardize_fov_array.standardize_fov_array.StandardizeFOVArrayResult attribute) path_2d_all_proj (actk.steps.single_cell_images.single_cell_images.CellImagesResult attribute) path_2d_yx_proj (actk.steps.single_cell_images.single_cell_images.CellImagesResult attribute)

path_3d (actk.steps.single_cell_images.single_cell_images.CellImagesResult attribute) prepare_image_for_feature_extraction() (in module actk.utils.image_utils) pull() (actk.bin.all.All method) push() (actk.bin.all.All method)

R

Raw (class in actk.steps) (class in actk.steps.raw) (class in actk.steps.raw.raw) run() (actk.bin.all.All method) (actk.steps.diagnostic_sheets.diagnostic_sheets.DiagnosticSheets method) (actk.steps.diagnostic_sheets.DiagnosticSheets method) (actk.steps.DiagnosticSheets method) (actk.steps.Raw method) (actk.steps.raw.Raw method) (actk.steps.raw.raw.Raw method) (actk.steps.single_cell_features.single_cell_features.SingleCellFeatures method) (actk.steps.single_cell_features.SingleCellFeatures method) (actk.steps.single_cell_images.single_cell_images.SingleCellImages method) (actk.steps.single_cell_images.SingleCellImages method) (actk.steps.SingleCellFeatures method) (actk.steps.SingleCellImages method) (actk.steps.standardize_fov_array.standardize_fov_array.StandardizeFOVArray method) (actk.steps.standardize_fov_array.StandardizeFOVArray method) (actk.steps.StandardizeFOVArray method)

S

save_path (actk.steps.diagnostic_sheets.diagnostic_sheets.DiagnosticSheetResult attribute) select_and_adjust_segmentation_ceiling() (in module actk.utils.image_utils) SingleCellFeatures (class in actk.steps) (class in actk.steps.single_cell_features) (class in actk.steps.single_cell_features.single_cell_features) SingleCellFeaturesError (class in actk.steps.single_cell_features.single_cell_features) SingleCellFeaturesResult (class in actk.steps.single_cell_features.single_cell_features) SingleCellImages (class in actk.steps) (class in actk.steps.single_cell_images) (class in actk.steps.single_cell_images.single_cell_images)

SourceReadPath (actk.constants.DatasetFields attribute) StandardizedFOVPath (actk.constants.DatasetFields attribute) StandardizeFOVArray (class in actk.steps) (class in actk.steps.standardize_fov_array) (class in actk.steps.standardize_fov_array.standardize_fov_array) StandardizeFOVArrayError (class in actk.steps.standardize_fov_array.standardize_fov_array) StandardizeFOVArrayResult (class in actk.steps.standardize_fov_array.standardize_fov_array) Structure (actk.constants.Channels attribute)