├── .github └── workflows │ └── run_tests.yml ├── .gitignore ├── README.rst ├── cellstar ├── __init__.py ├── core │ ├── __init__.py │ ├── config.py │ ├── image_repo.py │ ├── parallel │ │ ├── __init__.py │ │ └── snake_grow.py │ ├── point.py │ ├── polar_transform.py │ ├── seed.py │ ├── seeder.py │ ├── snake.py │ └── snake_filter.py ├── parameter_fitting │ ├── __init__.py │ ├── pf_auto_params.py │ ├── pf_mutator.py │ ├── pf_process.py │ ├── pf_rank_process.py │ ├── pf_rank_snake.py │ ├── pf_runner.py │ └── pf_snake.py ├── segmentation.py └── utils │ ├── __init__.py │ ├── calc_util.py │ ├── debug_util.py │ ├── image_util.py │ ├── index.py │ └── params_util.py ├── examples ├── input_images │ └── sample_brightfield.tif ├── output_segmentation │ └── sample_brightfield_segmented.tif └── use_cellstar.py ├── requirements_cp424.txt ├── requirements_py27.txt ├── requirements_py38.txt ├── requirements_py39.txt ├── setup.py ├── tests ├── __init__.py ├── data │ └── sample_brightfield.tif ├── debug_utils.py ├── expected │ ├── rank_fitting │ │ ├── background.tif │ │ ├── brighter.tif │ │ ├── brighter_original.tif │ │ ├── cell_border_mask.tif │ │ ├── cell_content_mask.tif │ │ ├── darker.tif │ │ ├── darker_original.tif │ │ ├── foreground_mask.tif │ │ ├── image_back_difference.tif │ │ ├── image_mask.tif │ │ ├── seeds_0.png │ │ ├── seeds_1.png │ │ ├── seeds_2.png │ │ ├── seeds_3.png │ │ ├── seeds_4.png │ │ ├── seeds_5.png │ │ ├── snakes_rainbow_0.png │ │ ├── snakes_rainbow_1.png │ │ ├── snakes_rainbow_2.png │ │ ├── snakes_rainbow_3.png │ │ ├── snakes_rainbow_4.png │ │ └── snakes_rainbow_5.png │ ├── sample_brightfield │ │ ├── background.tif │ │ ├── brighter.tif │ │ ├── brighter_original.tif │ │ ├── cell_border_mask.tif │ │ ├── cell_content_mask.tif │ │ ├── darker.tif │ │ ├── darker_original.tif │ │ ├── foreground_mask.tif │ │ ├── image_back_difference.tif │ │ ├── image_mask.tif │ │ ├── seeds_0.png │ │ ├── seeds_1.png │ │ ├── seeds_2.png │ │ ├── seeds_3.png │ │ ├── segmented.tif │ │ ├── snakes_rainbow_0.png │ │ ├── snakes_rainbow_1.png │ │ ├── snakes_rainbow_2.png │ │ └── snakes_rainbow_3.png │ ├── synthetic │ │ ├── background.tif │ │ ├── brighter.tif │ │ ├── brighter_original.tif │ │ ├── cell_border_mask.tif │ │ ├── cell_content_mask.tif │ │ ├── darker.tif │ │ ├── darker_original.tif │ │ ├── foreground_mask.tif │ │ ├── image_back_difference.tif │ │ └── image_mask.tif │ └── synthetic_3 │ │ ├── background.tif │ │ ├── brighter.tif │ │ ├── brighter_original.tif │ │ ├── cell_border_mask.tif │ │ ├── cell_content_mask.tif │ │ ├── darker.tif │ │ ├── darker_original.tif │ │ ├── foreground_mask.tif │ │ ├── image_back_difference.tif │ │ └── image_mask.tif ├── input_utils.py ├── test_cell_star.py ├── test_fitting.py ├── test_image_repo.py ├── test_input_utils.py └── test_segmentation.py └── utils ├── __init__.py ├── experiments.py ├── explorer.py ├── test_contour_pf.py ├── test_param_fitting.py └── test_rank_pf.py /.github/workflows/run_tests.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/.github/workflows/run_tests.yml -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/.gitignore -------------------------------------------------------------------------------- /README.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/README.rst -------------------------------------------------------------------------------- /cellstar/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/cellstar/__init__.py -------------------------------------------------------------------------------- /cellstar/core/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/cellstar/core/__init__.py -------------------------------------------------------------------------------- /cellstar/core/config.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/cellstar/core/config.py -------------------------------------------------------------------------------- /cellstar/core/image_repo.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/cellstar/core/image_repo.py -------------------------------------------------------------------------------- /cellstar/core/parallel/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/cellstar/core/parallel/__init__.py -------------------------------------------------------------------------------- /cellstar/core/parallel/snake_grow.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/cellstar/core/parallel/snake_grow.py -------------------------------------------------------------------------------- /cellstar/core/point.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/cellstar/core/point.py -------------------------------------------------------------------------------- /cellstar/core/polar_transform.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/cellstar/core/polar_transform.py -------------------------------------------------------------------------------- /cellstar/core/seed.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/cellstar/core/seed.py -------------------------------------------------------------------------------- /cellstar/core/seeder.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/cellstar/core/seeder.py -------------------------------------------------------------------------------- /cellstar/core/snake.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/cellstar/core/snake.py -------------------------------------------------------------------------------- /cellstar/core/snake_filter.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/cellstar/core/snake_filter.py -------------------------------------------------------------------------------- /cellstar/parameter_fitting/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/cellstar/parameter_fitting/__init__.py -------------------------------------------------------------------------------- /cellstar/parameter_fitting/pf_auto_params.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/cellstar/parameter_fitting/pf_auto_params.py -------------------------------------------------------------------------------- /cellstar/parameter_fitting/pf_mutator.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/cellstar/parameter_fitting/pf_mutator.py -------------------------------------------------------------------------------- /cellstar/parameter_fitting/pf_process.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/cellstar/parameter_fitting/pf_process.py -------------------------------------------------------------------------------- /cellstar/parameter_fitting/pf_rank_process.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/cellstar/parameter_fitting/pf_rank_process.py -------------------------------------------------------------------------------- /cellstar/parameter_fitting/pf_rank_snake.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/cellstar/parameter_fitting/pf_rank_snake.py -------------------------------------------------------------------------------- /cellstar/parameter_fitting/pf_runner.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/cellstar/parameter_fitting/pf_runner.py -------------------------------------------------------------------------------- /cellstar/parameter_fitting/pf_snake.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/cellstar/parameter_fitting/pf_snake.py -------------------------------------------------------------------------------- /cellstar/segmentation.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/cellstar/segmentation.py -------------------------------------------------------------------------------- /cellstar/utils/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/cellstar/utils/__init__.py -------------------------------------------------------------------------------- /cellstar/utils/calc_util.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/cellstar/utils/calc_util.py -------------------------------------------------------------------------------- /cellstar/utils/debug_util.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/cellstar/utils/debug_util.py -------------------------------------------------------------------------------- /cellstar/utils/image_util.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/cellstar/utils/image_util.py -------------------------------------------------------------------------------- /cellstar/utils/index.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/cellstar/utils/index.py -------------------------------------------------------------------------------- /cellstar/utils/params_util.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/cellstar/utils/params_util.py -------------------------------------------------------------------------------- /examples/input_images/sample_brightfield.tif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/examples/input_images/sample_brightfield.tif -------------------------------------------------------------------------------- /examples/output_segmentation/sample_brightfield_segmented.tif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/examples/output_segmentation/sample_brightfield_segmented.tif -------------------------------------------------------------------------------- /examples/use_cellstar.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/examples/use_cellstar.py -------------------------------------------------------------------------------- /requirements_cp424.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/requirements_cp424.txt -------------------------------------------------------------------------------- /requirements_py27.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/requirements_py27.txt -------------------------------------------------------------------------------- /requirements_py38.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/requirements_py38.txt -------------------------------------------------------------------------------- /requirements_py39.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/requirements_py39.txt -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/setup.py -------------------------------------------------------------------------------- /tests/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/tests/__init__.py -------------------------------------------------------------------------------- /tests/data/sample_brightfield.tif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/tests/data/sample_brightfield.tif -------------------------------------------------------------------------------- /tests/debug_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/tests/debug_utils.py -------------------------------------------------------------------------------- /tests/expected/rank_fitting/background.tif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/tests/expected/rank_fitting/background.tif -------------------------------------------------------------------------------- /tests/expected/rank_fitting/brighter.tif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/tests/expected/rank_fitting/brighter.tif -------------------------------------------------------------------------------- /tests/expected/rank_fitting/brighter_original.tif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/tests/expected/rank_fitting/brighter_original.tif -------------------------------------------------------------------------------- /tests/expected/rank_fitting/cell_border_mask.tif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/tests/expected/rank_fitting/cell_border_mask.tif -------------------------------------------------------------------------------- /tests/expected/rank_fitting/cell_content_mask.tif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/tests/expected/rank_fitting/cell_content_mask.tif -------------------------------------------------------------------------------- /tests/expected/rank_fitting/darker.tif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/tests/expected/rank_fitting/darker.tif -------------------------------------------------------------------------------- /tests/expected/rank_fitting/darker_original.tif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/tests/expected/rank_fitting/darker_original.tif -------------------------------------------------------------------------------- /tests/expected/rank_fitting/foreground_mask.tif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/tests/expected/rank_fitting/foreground_mask.tif -------------------------------------------------------------------------------- /tests/expected/rank_fitting/image_back_difference.tif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/tests/expected/rank_fitting/image_back_difference.tif -------------------------------------------------------------------------------- /tests/expected/rank_fitting/image_mask.tif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/tests/expected/rank_fitting/image_mask.tif -------------------------------------------------------------------------------- /tests/expected/rank_fitting/seeds_0.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/tests/expected/rank_fitting/seeds_0.png -------------------------------------------------------------------------------- /tests/expected/rank_fitting/seeds_1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/tests/expected/rank_fitting/seeds_1.png -------------------------------------------------------------------------------- /tests/expected/rank_fitting/seeds_2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/tests/expected/rank_fitting/seeds_2.png -------------------------------------------------------------------------------- /tests/expected/rank_fitting/seeds_3.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/tests/expected/rank_fitting/seeds_3.png -------------------------------------------------------------------------------- /tests/expected/rank_fitting/seeds_4.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/tests/expected/rank_fitting/seeds_4.png -------------------------------------------------------------------------------- /tests/expected/rank_fitting/seeds_5.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/tests/expected/rank_fitting/seeds_5.png -------------------------------------------------------------------------------- /tests/expected/rank_fitting/snakes_rainbow_0.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/tests/expected/rank_fitting/snakes_rainbow_0.png -------------------------------------------------------------------------------- /tests/expected/rank_fitting/snakes_rainbow_1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/tests/expected/rank_fitting/snakes_rainbow_1.png -------------------------------------------------------------------------------- /tests/expected/rank_fitting/snakes_rainbow_2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/tests/expected/rank_fitting/snakes_rainbow_2.png -------------------------------------------------------------------------------- /tests/expected/rank_fitting/snakes_rainbow_3.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/tests/expected/rank_fitting/snakes_rainbow_3.png -------------------------------------------------------------------------------- /tests/expected/rank_fitting/snakes_rainbow_4.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/tests/expected/rank_fitting/snakes_rainbow_4.png -------------------------------------------------------------------------------- /tests/expected/rank_fitting/snakes_rainbow_5.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/tests/expected/rank_fitting/snakes_rainbow_5.png -------------------------------------------------------------------------------- /tests/expected/sample_brightfield/background.tif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/tests/expected/sample_brightfield/background.tif -------------------------------------------------------------------------------- /tests/expected/sample_brightfield/brighter.tif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/tests/expected/sample_brightfield/brighter.tif -------------------------------------------------------------------------------- /tests/expected/sample_brightfield/brighter_original.tif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/tests/expected/sample_brightfield/brighter_original.tif -------------------------------------------------------------------------------- /tests/expected/sample_brightfield/cell_border_mask.tif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/tests/expected/sample_brightfield/cell_border_mask.tif -------------------------------------------------------------------------------- /tests/expected/sample_brightfield/cell_content_mask.tif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/tests/expected/sample_brightfield/cell_content_mask.tif -------------------------------------------------------------------------------- /tests/expected/sample_brightfield/darker.tif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/tests/expected/sample_brightfield/darker.tif -------------------------------------------------------------------------------- /tests/expected/sample_brightfield/darker_original.tif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/tests/expected/sample_brightfield/darker_original.tif -------------------------------------------------------------------------------- /tests/expected/sample_brightfield/foreground_mask.tif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/tests/expected/sample_brightfield/foreground_mask.tif -------------------------------------------------------------------------------- /tests/expected/sample_brightfield/image_back_difference.tif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/tests/expected/sample_brightfield/image_back_difference.tif -------------------------------------------------------------------------------- /tests/expected/sample_brightfield/image_mask.tif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/tests/expected/sample_brightfield/image_mask.tif -------------------------------------------------------------------------------- /tests/expected/sample_brightfield/seeds_0.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/tests/expected/sample_brightfield/seeds_0.png -------------------------------------------------------------------------------- /tests/expected/sample_brightfield/seeds_1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/tests/expected/sample_brightfield/seeds_1.png -------------------------------------------------------------------------------- /tests/expected/sample_brightfield/seeds_2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/tests/expected/sample_brightfield/seeds_2.png -------------------------------------------------------------------------------- /tests/expected/sample_brightfield/seeds_3.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/tests/expected/sample_brightfield/seeds_3.png -------------------------------------------------------------------------------- /tests/expected/sample_brightfield/segmented.tif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/tests/expected/sample_brightfield/segmented.tif -------------------------------------------------------------------------------- /tests/expected/sample_brightfield/snakes_rainbow_0.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/tests/expected/sample_brightfield/snakes_rainbow_0.png -------------------------------------------------------------------------------- /tests/expected/sample_brightfield/snakes_rainbow_1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/tests/expected/sample_brightfield/snakes_rainbow_1.png -------------------------------------------------------------------------------- /tests/expected/sample_brightfield/snakes_rainbow_2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/tests/expected/sample_brightfield/snakes_rainbow_2.png -------------------------------------------------------------------------------- /tests/expected/sample_brightfield/snakes_rainbow_3.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/tests/expected/sample_brightfield/snakes_rainbow_3.png -------------------------------------------------------------------------------- /tests/expected/synthetic/background.tif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/tests/expected/synthetic/background.tif -------------------------------------------------------------------------------- /tests/expected/synthetic/brighter.tif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/tests/expected/synthetic/brighter.tif -------------------------------------------------------------------------------- /tests/expected/synthetic/brighter_original.tif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/tests/expected/synthetic/brighter_original.tif -------------------------------------------------------------------------------- /tests/expected/synthetic/cell_border_mask.tif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/tests/expected/synthetic/cell_border_mask.tif -------------------------------------------------------------------------------- /tests/expected/synthetic/cell_content_mask.tif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/tests/expected/synthetic/cell_content_mask.tif -------------------------------------------------------------------------------- /tests/expected/synthetic/darker.tif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/tests/expected/synthetic/darker.tif -------------------------------------------------------------------------------- /tests/expected/synthetic/darker_original.tif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/tests/expected/synthetic/darker_original.tif -------------------------------------------------------------------------------- /tests/expected/synthetic/foreground_mask.tif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/tests/expected/synthetic/foreground_mask.tif -------------------------------------------------------------------------------- /tests/expected/synthetic/image_back_difference.tif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/tests/expected/synthetic/image_back_difference.tif -------------------------------------------------------------------------------- /tests/expected/synthetic/image_mask.tif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/tests/expected/synthetic/image_mask.tif -------------------------------------------------------------------------------- /tests/expected/synthetic_3/background.tif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/tests/expected/synthetic_3/background.tif -------------------------------------------------------------------------------- /tests/expected/synthetic_3/brighter.tif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/tests/expected/synthetic_3/brighter.tif -------------------------------------------------------------------------------- /tests/expected/synthetic_3/brighter_original.tif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/tests/expected/synthetic_3/brighter_original.tif -------------------------------------------------------------------------------- /tests/expected/synthetic_3/cell_border_mask.tif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/tests/expected/synthetic_3/cell_border_mask.tif -------------------------------------------------------------------------------- /tests/expected/synthetic_3/cell_content_mask.tif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/tests/expected/synthetic_3/cell_content_mask.tif -------------------------------------------------------------------------------- /tests/expected/synthetic_3/darker.tif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/tests/expected/synthetic_3/darker.tif -------------------------------------------------------------------------------- /tests/expected/synthetic_3/darker_original.tif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/tests/expected/synthetic_3/darker_original.tif -------------------------------------------------------------------------------- /tests/expected/synthetic_3/foreground_mask.tif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/tests/expected/synthetic_3/foreground_mask.tif -------------------------------------------------------------------------------- /tests/expected/synthetic_3/image_back_difference.tif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/tests/expected/synthetic_3/image_back_difference.tif -------------------------------------------------------------------------------- /tests/expected/synthetic_3/image_mask.tif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/tests/expected/synthetic_3/image_mask.tif -------------------------------------------------------------------------------- /tests/input_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/tests/input_utils.py -------------------------------------------------------------------------------- /tests/test_cell_star.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/tests/test_cell_star.py -------------------------------------------------------------------------------- /tests/test_fitting.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/tests/test_fitting.py -------------------------------------------------------------------------------- /tests/test_image_repo.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/tests/test_image_repo.py -------------------------------------------------------------------------------- /tests/test_input_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/tests/test_input_utils.py -------------------------------------------------------------------------------- /tests/test_segmentation.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/tests/test_segmentation.py -------------------------------------------------------------------------------- /utils/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/utils/__init__.py -------------------------------------------------------------------------------- /utils/experiments.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/utils/experiments.py -------------------------------------------------------------------------------- /utils/explorer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/utils/explorer.py -------------------------------------------------------------------------------- /utils/test_contour_pf.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/utils/test_contour_pf.py -------------------------------------------------------------------------------- /utils/test_param_fitting.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/utils/test_param_fitting.py -------------------------------------------------------------------------------- /utils/test_rank_pf.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Fafa87/cellstar/HEAD/utils/test_rank_pf.py --------------------------------------------------------------------------------