├── .gitignore ├── .pre-commit-config.yaml ├── .travis.yml ├── LICENSE ├── README.md ├── bin ├── background_subtraction │ └── run_background_subtraction.py ├── best_focus │ ├── best_z_identification.py │ ├── best_z_paths.py │ ├── file_manipulation.py │ └── run_best_focus_selection.py ├── codex_stitching │ ├── bigstitcher_dataset_meta.py │ ├── directory_management.py │ ├── generate_bigstitcher_macro.py │ ├── image_stitching.py │ ├── run_stitching.py │ └── secondary_stitcher │ │ ├── mask_stitching.py │ │ ├── match_masks.py │ │ ├── secondary_stitcher.py │ │ └── secondary_stitcher_runner.py ├── convert_to_ometiff.py ├── create_cytokit_config.py ├── dataset_info │ ├── collect_dataset_info.py │ ├── collect_dataset_info_old.py │ └── run_collection.py ├── illumination_correction │ ├── generate_basic_macro.py │ └── run_illumination_correction.py ├── pipeline_utils │ ├── dataset_listing.py │ └── pipeline_config_reader.py ├── slicing │ ├── modify_pipeline_config.py │ ├── run_slicing.py │ └── slicer.py └── utils.py ├── docker ├── codex_scripts │ ├── Dockerfile │ └── environment.yml ├── cytokit │ ├── Dockerfile │ ├── cytokit_wrapper.py │ └── setup_data_directory.py └── fiji_bigstitcher │ └── Dockerfile_fiji ├── docker_images.txt ├── metadata_examples ├── channelnames.txt ├── channelnames_report.csv ├── experiment.json ├── exposure_times.txt └── segmentation.json ├── pipeline-manifest.json ├── pipeline.cwl ├── pipeline_release_mgmt.yaml ├── pyproject.toml ├── requirements-test.txt ├── steps ├── illumination_first_stitching.cwl ├── illumination_first_stitching │ ├── best_focus.cwl │ ├── collect_dataset_info.cwl │ ├── create_yaml_config.cwl │ ├── first_stitching.cwl │ ├── illumination_correction.cwl │ └── slicing.cwl ├── ometiff_second_stitching-manifest.json ├── ometiff_second_stitching.cwl ├── ometiff_second_stitching │ ├── background_subtraction.cwl │ ├── ome_tiff_creation.cwl │ └── second_stitching.cwl ├── run_cytokit-manifest.json └── run_cytokit.cwl ├── subm.yaml └── 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