pipeline

• project
• Project
  • Project.config
  • Project.nuc_seg_name
  • Project.cyto_seg_name
  • Project.sdata_path
  • Project.filehander
  • Project.DEFAULT_IMAGE_DTYPE
  • Project.DEFAULT_SEGMENTATION_DTYPE
  • Project.DEFAULT_SINGLE_CELL_IMAGE_DTYPE
  • Project.sdata
  • Project.update_featurization_f()
  • Project.print_project_status()
  • Project.view_sdata()
  • Project.plot_input_image()
  • Project.plot_he_image()
  • Project.plot_segmentation_masks()
  • Project.plot_single_cell_images()
  • Project.load_input_from_array()
  • Project.load_input_from_tif_files()
  • Project.load_input_from_omezarr()
  • Project.load_input_from_dask()
  • Project.load_input_from_sdata()
  • Project.complete_segmentation()
  • Project.extract()
  • Project.select()
• segmentation
  • Segmentation
  • ShardedSegmentation
• segmentation workflows
  • WGASegmentation
  • ShardedWGASegmentation
  • DAPISegmentation
  • ShardedDAPISegmentation
  • DAPISegmentationCellpose
  • ShardedDAPISegmentationCellpose
  • CytosolSegmentationCellpose
  • ShardedCytosolSegmentationCellpose
  • CytosolOnlySegmentationCellpose
  • ShardedCytosolOnlySegmentationCellpose
  • CytosolSegmentationDownsamplingCellpose
  • ShardedCytosolSegmentationDownsamplingCellpose
  • CytosolOnlySegmentationDownsamplingCellpose
  • ShardedCytosolOnlySegmentationDownsamplingCellpose
• extraction
  • HDF5CellExtraction
• Featurization
  • MLClusterClassifier
  • EnsembleClassifier
  • CellFeaturizer
  • ConvNeXtFeaturizer
• selection
  • LMDSelection