├── .github └── workflows │ └── test.yml ├── .gitignore ├── .readthedocs.yaml ├── Makefile ├── Manifest.in ├── README.md ├── docs ├── Makefile ├── make.bat └── source │ ├── api.md │ ├── changelog.md │ ├── concepts.md │ ├── conf.py │ ├── examples.md │ ├── index.md │ ├── install.md │ ├── log_config.md │ ├── testing.md │ └── usage.md ├── imc ├── __init__.py ├── cli.py ├── data_models │ ├── __init__.py │ ├── project.py │ ├── roi.py │ └── sample.py ├── defaults.py ├── demo │ ├── __init__.py │ ├── generate_data.py │ └── get_demo_data.py ├── exceptions.py ├── graphics.py ├── interactive_volume_viewer.py ├── logo.png ├── ops │ ├── __init__.py │ ├── adjacency.py │ ├── clustering.py │ ├── community.py │ ├── compensation.py │ ├── domain.py │ ├── mixture.py │ ├── quant.py │ └── signal.py ├── py.typed ├── scripts │ ├── __init__.py │ ├── illustrate.py │ ├── inspect_ilastik_model.py │ ├── inspect_mcds.py │ ├── phenotype.py │ ├── predict.py │ ├── prepare.py │ ├── process.py │ ├── quantify.py │ ├── segment_stacks.py │ └── view.py ├── segmentation.py ├── tests │ ├── __init__.py │ ├── _test_layers.py │ ├── conftest.py │ ├── test_full_analysis.py │ ├── test_graphics.py │ ├── test_obj_creation.py │ └── test_serialization.py ├── types.py └── utils.py ├── noxfile.py ├── pyproject.toml └── requirements ├── requirements.cellpose.txt ├── requirements.deepcell.txt ├── requirements.dev.txt ├── requirements.doc.txt ├── requirements.stardist.txt └── requirements.txt /.github/workflows/test.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ElementoLab/imc/HEAD/.github/workflows/test.yml -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ElementoLab/imc/HEAD/.gitignore -------------------------------------------------------------------------------- /.readthedocs.yaml: 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