├── .gitignore ├── .pre-commit-config.yaml ├── LICENSE ├── Makefile ├── README.md ├── cellulus ├── __init__.py ├── cli.py ├── configs │ ├── __init__.py │ ├── dataset_config.py │ ├── experiment_config.py │ ├── inference_config.py │ ├── model_config.py │ ├── train_config.py │ └── utils.py ├── criterions │ ├── __init__.py │ └── oce_loss.py ├── datasets │ ├── __init__.py │ ├── meta_data.py │ └── zarr_dataset.py ├── detect.py ├── evaluate.py ├── infer.py ├── models │ ├── __init__.py │ └── unet.py ├── predict.py ├── segment.py ├── train.py └── utils │ ├── __init__.py │ ├── greedy_cluster.py │ ├── logger.py │ ├── mean_shift.py │ └── misc.py ├── docs ├── api │ ├── dataset_config.md │ ├── experiment_config.md │ ├── inference_config.md │ ├── meta_data.md │ ├── model_config.md │ ├── oce_loss.md │ ├── train_config.md │ └── zarr_dataset.md ├── examples │ ├── 2d │ │ ├── 01-data.py │ │ ├── 02-train.py │ │ └── 03-infer.py │ └── 3d │ │ ├── 01-data.py │ │ ├── 02-train.py │ │ └── 03-infer.py ├── getting-started.md ├── index.md └── overrides │ ├── css │ ├── style.css │ └── zerogrid.css │ ├── home.html │ ├── main.html │ └── resources │ ├── .DS_Store │ ├── bibtex.txt │ ├── images │ ├── loss.png │ ├── results.png │ └── teaser.png │ ├── paper │ ├── paper_01.png │ ├── paper_02.png │ ├── paper_03.png │ ├── paper_04.png │ ├── paper_05.png │ ├── paper_06.png │ ├── paper_07.png │ ├── paper_08.png │ ├── paper_09.png │ ├── paper_10.png │ ├── paper_11.png │ ├── paper_12.png │ ├── paper_13.png │ └── paper_14.png │ └── pdf │ ├── .DS_Store │ └── cellulus.pdf ├── mkdocs.yml ├── pyproject.toml └── tests ├── conftest.py ├── test_api.py └── train.toml /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/funkelab/cellulus/HEAD/.gitignore -------------------------------------------------------------------------------- /.pre-commit-config.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/funkelab/cellulus/HEAD/.pre-commit-config.yaml -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/funkelab/cellulus/HEAD/LICENSE -------------------------------------------------------------------------------- /Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/funkelab/cellulus/HEAD/Makefile -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/funkelab/cellulus/HEAD/README.md -------------------------------------------------------------------------------- /cellulus/__init__.py: -------------------------------------------------------------------------------- 1 | __version__ = "0.1.0" 2 | -------------------------------------------------------------------------------- /cellulus/cli.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/funkelab/cellulus/HEAD/cellulus/cli.py -------------------------------------------------------------------------------- /cellulus/configs/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/funkelab/cellulus/HEAD/cellulus/configs/__init__.py -------------------------------------------------------------------------------- /cellulus/configs/dataset_config.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/funkelab/cellulus/HEAD/cellulus/configs/dataset_config.py -------------------------------------------------------------------------------- /cellulus/configs/experiment_config.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/funkelab/cellulus/HEAD/cellulus/configs/experiment_config.py -------------------------------------------------------------------------------- /cellulus/configs/inference_config.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/funkelab/cellulus/HEAD/cellulus/configs/inference_config.py -------------------------------------------------------------------------------- /cellulus/configs/model_config.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/funkelab/cellulus/HEAD/cellulus/configs/model_config.py -------------------------------------------------------------------------------- /cellulus/configs/train_config.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/funkelab/cellulus/HEAD/cellulus/configs/train_config.py -------------------------------------------------------------------------------- /cellulus/configs/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/funkelab/cellulus/HEAD/cellulus/configs/utils.py -------------------------------------------------------------------------------- /cellulus/criterions/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/funkelab/cellulus/HEAD/cellulus/criterions/__init__.py -------------------------------------------------------------------------------- /cellulus/criterions/oce_loss.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/funkelab/cellulus/HEAD/cellulus/criterions/oce_loss.py -------------------------------------------------------------------------------- /cellulus/datasets/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/funkelab/cellulus/HEAD/cellulus/datasets/__init__.py -------------------------------------------------------------------------------- /cellulus/datasets/meta_data.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/funkelab/cellulus/HEAD/cellulus/datasets/meta_data.py -------------------------------------------------------------------------------- /cellulus/datasets/zarr_dataset.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/funkelab/cellulus/HEAD/cellulus/datasets/zarr_dataset.py -------------------------------------------------------------------------------- /cellulus/detect.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/funkelab/cellulus/HEAD/cellulus/detect.py -------------------------------------------------------------------------------- /cellulus/evaluate.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/funkelab/cellulus/HEAD/cellulus/evaluate.py -------------------------------------------------------------------------------- /cellulus/infer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/funkelab/cellulus/HEAD/cellulus/infer.py -------------------------------------------------------------------------------- /cellulus/models/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/funkelab/cellulus/HEAD/cellulus/models/__init__.py -------------------------------------------------------------------------------- /cellulus/models/unet.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/funkelab/cellulus/HEAD/cellulus/models/unet.py -------------------------------------------------------------------------------- /cellulus/predict.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/funkelab/cellulus/HEAD/cellulus/predict.py -------------------------------------------------------------------------------- /cellulus/segment.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/funkelab/cellulus/HEAD/cellulus/segment.py -------------------------------------------------------------------------------- /cellulus/train.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/funkelab/cellulus/HEAD/cellulus/train.py -------------------------------------------------------------------------------- /cellulus/utils/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/funkelab/cellulus/HEAD/cellulus/utils/__init__.py -------------------------------------------------------------------------------- /cellulus/utils/greedy_cluster.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/funkelab/cellulus/HEAD/cellulus/utils/greedy_cluster.py -------------------------------------------------------------------------------- /cellulus/utils/logger.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/funkelab/cellulus/HEAD/cellulus/utils/logger.py -------------------------------------------------------------------------------- /cellulus/utils/mean_shift.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/funkelab/cellulus/HEAD/cellulus/utils/mean_shift.py -------------------------------------------------------------------------------- /cellulus/utils/misc.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/funkelab/cellulus/HEAD/cellulus/utils/misc.py -------------------------------------------------------------------------------- /docs/api/dataset_config.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/funkelab/cellulus/HEAD/docs/api/dataset_config.md -------------------------------------------------------------------------------- /docs/api/experiment_config.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/funkelab/cellulus/HEAD/docs/api/experiment_config.md -------------------------------------------------------------------------------- /docs/api/inference_config.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/funkelab/cellulus/HEAD/docs/api/inference_config.md -------------------------------------------------------------------------------- /docs/api/meta_data.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/funkelab/cellulus/HEAD/docs/api/meta_data.md -------------------------------------------------------------------------------- /docs/api/model_config.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/funkelab/cellulus/HEAD/docs/api/model_config.md -------------------------------------------------------------------------------- /docs/api/oce_loss.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/funkelab/cellulus/HEAD/docs/api/oce_loss.md -------------------------------------------------------------------------------- /docs/api/train_config.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/funkelab/cellulus/HEAD/docs/api/train_config.md -------------------------------------------------------------------------------- /docs/api/zarr_dataset.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/funkelab/cellulus/HEAD/docs/api/zarr_dataset.md -------------------------------------------------------------------------------- /docs/examples/2d/01-data.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/funkelab/cellulus/HEAD/docs/examples/2d/01-data.py -------------------------------------------------------------------------------- /docs/examples/2d/02-train.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/funkelab/cellulus/HEAD/docs/examples/2d/02-train.py -------------------------------------------------------------------------------- /docs/examples/2d/03-infer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/funkelab/cellulus/HEAD/docs/examples/2d/03-infer.py -------------------------------------------------------------------------------- /docs/examples/3d/01-data.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/funkelab/cellulus/HEAD/docs/examples/3d/01-data.py -------------------------------------------------------------------------------- /docs/examples/3d/02-train.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/funkelab/cellulus/HEAD/docs/examples/3d/02-train.py -------------------------------------------------------------------------------- /docs/examples/3d/03-infer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/funkelab/cellulus/HEAD/docs/examples/3d/03-infer.py -------------------------------------------------------------------------------- /docs/getting-started.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/funkelab/cellulus/HEAD/docs/getting-started.md -------------------------------------------------------------------------------- /docs/index.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/funkelab/cellulus/HEAD/docs/index.md -------------------------------------------------------------------------------- /docs/overrides/css/style.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/funkelab/cellulus/HEAD/docs/overrides/css/style.css -------------------------------------------------------------------------------- /docs/overrides/css/zerogrid.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/funkelab/cellulus/HEAD/docs/overrides/css/zerogrid.css -------------------------------------------------------------------------------- /docs/overrides/home.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/funkelab/cellulus/HEAD/docs/overrides/home.html -------------------------------------------------------------------------------- /docs/overrides/main.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/funkelab/cellulus/HEAD/docs/overrides/main.html -------------------------------------------------------------------------------- /docs/overrides/resources/.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/funkelab/cellulus/HEAD/docs/overrides/resources/.DS_Store -------------------------------------------------------------------------------- /docs/overrides/resources/bibtex.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/funkelab/cellulus/HEAD/docs/overrides/resources/bibtex.txt -------------------------------------------------------------------------------- /docs/overrides/resources/images/loss.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/funkelab/cellulus/HEAD/docs/overrides/resources/images/loss.png -------------------------------------------------------------------------------- /docs/overrides/resources/images/results.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/funkelab/cellulus/HEAD/docs/overrides/resources/images/results.png -------------------------------------------------------------------------------- /docs/overrides/resources/images/teaser.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/funkelab/cellulus/HEAD/docs/overrides/resources/images/teaser.png -------------------------------------------------------------------------------- /docs/overrides/resources/paper/paper_01.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/funkelab/cellulus/HEAD/docs/overrides/resources/paper/paper_01.png -------------------------------------------------------------------------------- /docs/overrides/resources/paper/paper_02.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/funkelab/cellulus/HEAD/docs/overrides/resources/paper/paper_02.png -------------------------------------------------------------------------------- /docs/overrides/resources/paper/paper_03.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/funkelab/cellulus/HEAD/docs/overrides/resources/paper/paper_03.png -------------------------------------------------------------------------------- /docs/overrides/resources/paper/paper_04.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/funkelab/cellulus/HEAD/docs/overrides/resources/paper/paper_04.png -------------------------------------------------------------------------------- /docs/overrides/resources/paper/paper_05.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/funkelab/cellulus/HEAD/docs/overrides/resources/paper/paper_05.png -------------------------------------------------------------------------------- /docs/overrides/resources/paper/paper_06.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/funkelab/cellulus/HEAD/docs/overrides/resources/paper/paper_06.png -------------------------------------------------------------------------------- /docs/overrides/resources/paper/paper_07.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/funkelab/cellulus/HEAD/docs/overrides/resources/paper/paper_07.png -------------------------------------------------------------------------------- /docs/overrides/resources/paper/paper_08.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/funkelab/cellulus/HEAD/docs/overrides/resources/paper/paper_08.png -------------------------------------------------------------------------------- /docs/overrides/resources/paper/paper_09.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/funkelab/cellulus/HEAD/docs/overrides/resources/paper/paper_09.png -------------------------------------------------------------------------------- /docs/overrides/resources/paper/paper_10.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/funkelab/cellulus/HEAD/docs/overrides/resources/paper/paper_10.png -------------------------------------------------------------------------------- /docs/overrides/resources/paper/paper_11.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/funkelab/cellulus/HEAD/docs/overrides/resources/paper/paper_11.png -------------------------------------------------------------------------------- /docs/overrides/resources/paper/paper_12.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/funkelab/cellulus/HEAD/docs/overrides/resources/paper/paper_12.png -------------------------------------------------------------------------------- /docs/overrides/resources/paper/paper_13.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/funkelab/cellulus/HEAD/docs/overrides/resources/paper/paper_13.png -------------------------------------------------------------------------------- /docs/overrides/resources/paper/paper_14.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/funkelab/cellulus/HEAD/docs/overrides/resources/paper/paper_14.png -------------------------------------------------------------------------------- /docs/overrides/resources/pdf/.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/funkelab/cellulus/HEAD/docs/overrides/resources/pdf/.DS_Store -------------------------------------------------------------------------------- /docs/overrides/resources/pdf/cellulus.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/funkelab/cellulus/HEAD/docs/overrides/resources/pdf/cellulus.pdf -------------------------------------------------------------------------------- /mkdocs.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/funkelab/cellulus/HEAD/mkdocs.yml -------------------------------------------------------------------------------- /pyproject.toml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/funkelab/cellulus/HEAD/pyproject.toml -------------------------------------------------------------------------------- /tests/conftest.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/funkelab/cellulus/HEAD/tests/conftest.py -------------------------------------------------------------------------------- /tests/test_api.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/funkelab/cellulus/HEAD/tests/test_api.py -------------------------------------------------------------------------------- /tests/train.toml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/funkelab/cellulus/HEAD/tests/train.toml --------------------------------------------------------------------------------