actk package

Subpackages

• actk.bin package
  • Submodules
  • actk.bin.all module
  • actk.bin.cli module
  • Module contents
• actk.steps package
  • Subpackages
    • actk.steps.diagnostic_sheets package
      • Submodules
      • actk.steps.diagnostic_sheets.diagnostic_sheets module
      • Module contents
    • actk.steps.raw package
      • Submodules
      • actk.steps.raw.raw module
      • Module contents
    • actk.steps.single_cell_features package
      • Submodules
      • actk.steps.single_cell_features.single_cell_features module
      • Module contents
    • actk.steps.single_cell_images package
      • Submodules
      • actk.steps.single_cell_images.single_cell_images module
      • Module contents
    • actk.steps.standardize_fov_array package
      • Submodules
      • actk.steps.standardize_fov_array.standardize_fov_array module
      • Module contents
  • Module contents
• actk.utils package
  • Submodules
  • actk.utils.dataset_utils module
  • actk.utils.image_utils module
  • Module contents

Submodules

actk.constants module

class actk.constants.Channels

Bases: object

Brightfield = 'brightfield'

DNA = 'dna'

DefaultOrderList = ['nucleus_segmentation', 'membrane_segmentation', 'dna', 'membrane', 'structure', 'brightfield']

Membrane = 'membrane'

MembraneSegmentation = 'membrane_segmentation'

NucleusSegmentation = 'nucleus_segmentation'

Structure = 'structure'

class actk.constants.DatasetFields

Bases: object

AllExpectedInputs = ['CellId', 'CellIndex', 'FOVId', 'SourceReadPath', 'NucleusSegmentationReadPath', 'MembraneSegmentationReadPath', 'ChannelIndexDNA', 'ChannelIndexMembrane', 'ChannelIndexStructure', 'ChannelIndexBrightfield', 'ChannelIndexNucleusSegmentation', 'ChannelIndexMembraneSegmentation']

CellFeaturesPath = 'CellFeaturesPath'

CellId = 'CellId'

CellImage2DAllProjectionsPath = 'CellImage2DAllProjectionsPath'

CellImage2DYXProjectionPath = 'CellImage2DYXProjectionPath'

CellImage3DPath = 'CellImage3DPath'

CellIndex = 'CellIndex'

ChannelIndexBrightfield = 'ChannelIndexBrightfield'

ChannelIndexDNA = 'ChannelIndexDNA'

ChannelIndexMembrane = 'ChannelIndexMembrane'

ChannelIndexMembraneSegmentation = 'ChannelIndexMembraneSegmentation'

ChannelIndexNucleusSegmentation = 'ChannelIndexNucleusSegmentation'

ChannelIndexStructure = 'ChannelIndexStructure'

DiagnosticSheetPath = 'DiagnosticSheetPath'

FOVId = 'FOVId'

MembraneSegmentationReadPath = 'MembraneSegmentationReadPath'

NucleusSegmentationReadPath = 'NucleusSegmentationReadPath'

SourceReadPath = 'SourceReadPath'

StandardizedFOVPath = 'StandardizedFOVPath'

actk.exceptions module

exception actk.exceptions.MissingDataError(dataset: Union[pandas.core.frame.DataFrame, dask.dataframe.core.DataFrame], missing_fields: List[str])

Bases: Exception

Module contents

Top-level package for actk.

actk.get_module_version()