├── .gitignore ├── README.md ├── examples ├── bbbc039_seg_config.py ├── combined_set_config.py └── vanvalen_data_config.py └── unet4nuclei ├── 00-download-dataset.ipynb ├── 01-preprocessing.ipynb ├── 02-training.ipynb ├── 03-prediction.ipynb ├── 04-evaluation.ipynb ├── batch_prediction.py ├── config.py ├── elastic-deformation.ipynb ├── full-experiment.ipynb └── utils ├── __init__.py ├── augmentation.py ├── contours_to_labels.ipynb ├── data_provider.py ├── dirtools.py ├── evaluation.py ├── experiment.py ├── metrics.py ├── model_builder.py ├── objectives.py ├── preprocessing.py └── visualize.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/carpenterlab/unet4nuclei/HEAD/.gitignore -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 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