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
      • HDF5SingleCellDataset.dir_list
      • HDF5SingleCellDataset.dir_labels
      • HDF5SingleCellDataset.index_list
      • HDF5SingleCellDataset.select_channel
      • HDF5SingleCellDataset.transform
      • HDF5SingleCellDataset.return_id
      • HDF5SingleCellDataset.return_fake_id
      • HDF5SingleCellDataset.max_level
      • HDF5SingleCellDataset.stats()
      • HDF5SingleCellDataset.len()
      • HDF5SingleCellDataset.getitem()
    • LabelledHDF5SingleCellDataset
      • LabelledHDF5SingleCellDataset.dir_list
      • LabelledHDF5SingleCellDataset.label_colum
      • LabelledHDF5SingleCellDataset.label_dtype
      • LabelledHDF5SingleCellDataset.label_column_transform
      • LabelledHDF5SingleCellDataset.index_list
      • LabelledHDF5SingleCellDataset.select_channel
      • LabelledHDF5SingleCellDataset.transform
      • LabelledHDF5SingleCellDataset.return_id
      • LabelledHDF5SingleCellDataset.return_fake_id
      • LabelledHDF5SingleCellDataset.max_level
      • LabelledHDF5SingleCellDataset.stats()
      • LabelledHDF5SingleCellDataset.len()
      • LabelledHDF5SingleCellDataset.getitem()
  • metrics
    • precision()
    • recall()
  • models
    • VGGBase
      • VGGBase.make_layers()
      • VGGBase.make_layers_MLP()
      • VGGBase.forward()
    • VGG1
    • VGG2
  • plmodels
    • MultilabelSupervisedModel
      • MultilabelSupervisedModel.network
      • MultilabelSupervisedModel.train_metrics
      • MultilabelSupervisedModel.val_metrics
      • MultilabelSupervisedModel.test_metrics
      • MultilabelSupervisedModel.forward()
      • MultilabelSupervisedModel.configure_optimizers()
      • MultilabelSupervisedModel.on_train_epoch_end()
      • MultilabelSupervisedModel.on_validation_epoch_end()
      • MultilabelSupervisedModel.confusion_plot()
      • MultilabelSupervisedModel.training_step()
      • MultilabelSupervisedModel.validation_step()
      • MultilabelSupervisedModel.test_step()
      • MultilabelSupervisedModel.test_epoch_end()
      • MultilabelSupervisedModel.forward()
      • MultilabelSupervisedModel.configure_optimizers()
      • MultilabelSupervisedModel.training_step()
      • MultilabelSupervisedModel.validation_step()
      • MultilabelSupervisedModel.test_step()
  • pretrained_models
    • autophagy_classifier()
  • transforms
    • RandomRotation
    • GaussianNoise
    • GaussianBlur
    • ChannelReducer
    • ChannelSelector
  • utils
    • combine_datasets_balanced()
    • split_dataset_fractions()