Module Documentation

• pipeline
  • project
    • Project
      • Project
  • segmentation
    • Segmentation
      • Segmentation
    • ShardedSegmentation
      • ShardedSegmentation
  • segmentation workflows
    • WGASegmentation
      • WGASegmentation.process()
    • ShardedWGASegmentation
      • ShardedWGASegmentation.method
    • DAPISegmentation
      • DAPISegmentation.process()
    • ShardedDAPISegmentation
      • ShardedDAPISegmentation.method
    • DAPISegmentationCellpose
      • DAPISegmentationCellpose.process()
    • ShardedDAPISegmentationCellpose
      • ShardedDAPISegmentationCellpose.method
    • CytosolSegmentationCellpose
      • CytosolSegmentationCellpose.process()
    • ShardedCytosolSegmentationCellpose
      • ShardedCytosolSegmentationCellpose.method
    • CytosolSegmentationDownsamplingCellpose
      • CytosolSegmentationDownsamplingCellpose.process()
    • ShardedCytosolSegmentationDownsamplingCellpose
      • ShardedCytosolSegmentationDownsamplingCellpose.method
    • CytosolOnlySegmentationCellpose
    • Sharded_CytosolOnly_Cellpose_Segmentation
      • Sharded_CytosolOnly_Cellpose_Segmentation.method
    • CytosolOnly_Segmentation_Downsampling_Cellpose
      • CytosolOnly_Segmentation_Downsampling_Cellpose.process()
    • Sharded_CytosolOnly_Segmentation_Downsampling_Cellpose
      • Sharded_CytosolOnly_Segmentation_Downsampling_Cellpose.method
  • extraction
    • HDF5CellExtraction
      • HDF5CellExtraction
  • classification
    • MLClusterClassifier
      • MLClusterClassifier
    • CellFeaturizer
      • CellFeaturizer
  • selection
    • LMDSelection
      • LMDSelection
• processing
  • images
  • masks
• io
  • memory mapped file handling
    • dask_array_from_path()
    • calculate_chunk_sizes()
    • calculate_chunk_sizes_chunks()
    • mmap_dask_array_contigious()
    • mmap_dask_array_chunked()
    • load_hdf5_contigious()
    • load_hdf5_chunk()
  • file readers
    • read_ome_zarr()
• tools
  • parse
  • PhenixParser
    • PhenixParser.copy_files()
    • PhenixParser.parse()
    • PhenixParser.sort_wells()
    • PhenixParser.sort_timepoints()
  • CombinedPhenixParser
  • stitch
  • Stitcher
    • Stitcher.create_cache()
    • Stitcher.clear_cache()
    • Stitcher.initialize_outdir()
    • Stitcher.get_channel_info()
    • Stitcher.setup_rescaling()
    • Stitcher.reorder_channels()
    • Stitcher.initialize_reader()
    • Stitcher.save_positions()
    • Stitcher.generate_thumbnail()
    • Stitcher.initialize_aligner()
    • Stitcher.plot_qc()
    • Stitcher.perform_alignment()
    • Stitcher.initialize_mosaic()
    • Stitcher.assemble_mosaic()
    • Stitcher.stitch()
    • Stitcher.write_tif()
    • Stitcher.write_ome_zarr()
    • Stitcher.write_thumbnail()
    • Stitcher.write_spatialdata()
  • ParallelStitcher
    • ParallelStitcher.initialize_aligner()
    • ParallelStitcher.initialize_mosaic()
    • ParallelStitcher.assemble_mosaic()
    • ParallelStitcher.write_tif_parallel()
  • ml
    • datasets
      • HDF5SingleCellDataset
      • LabelledHDF5SingleCellDataset
    • metrics
      • precision()
      • recall()
    • models
      • VGGBase
      • VGG1
      • VGG2
    • plmodels
      • MultilabelSupervisedModel
    • pretrained_models
      • autophagy_classifier()
    • transforms
      • RandomRotation
      • GaussianNoise
      • GaussianBlur
      • ChannelReducer
      • ChannelSelector
    • utils
      • combine_datasets_balanced()
      • split_dataset_fractions()