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() spdata write_image() add_element_sdata() processing (pp) percentile_normalize_image()