tools

• parse
• PhenixParser
  • PhenixParser.generate_metadata()
  • PhenixParser.check_for_missing_files()
  • PhenixParser.replace_missing_images()
  • PhenixParser.parse()
  • PhenixParser.sort_wells()
  • PhenixParser.sort_timepoints()
• CombinedPhenixParser
  • CombinedPhenixParser.get_datasets_to_combine()
• stitch
• Stitcher
  • Stitcher.get_stitching_information()
  • Stitcher.save_positions()
  • Stitcher.generate_thumbnail()
  • Stitcher.plot_qc()
  • Stitcher.stitch()
  • Stitcher.write_tif()
  • Stitcher.write_ome_zarr()
  • Stitcher.write_thumbnail()
  • Stitcher.write_spatialdata()
• ParallelStitcher
  • ParallelStitcher.write_tif_parallel()
• ml
  • datasets
  • metrics
  • models
  • plmodels
  • pretrained_models
  • transforms
  • utils
• h5sc
• get_image_with_cellid()
• get_image_index()
• sdata
• write_image()
• write_labels()
• add_element_sdata()
• rename_image_element()
• get_featurization_results_as_df()
• processing (pp)
  • percentile_normalize_image()
  • get_bounding_box_sdata()