├── .github └── workflows │ ├── docker-publish.yml │ ├── python-package.yml │ ├── python-publish.yml │ └── stale.yml ├── .gitignore ├── .readthedocs.yaml ├── LICENSE ├── MANIFEST.in ├── README.md ├── assets ├── bbbc039-cpn-u22-demo-arrow.png ├── bbbc039-cpn-u22-demo.png ├── bbbc041-cpn-u22-demo.png └── neurips-cellseg-demo.png ├── celldetection ├── __init__.py ├── __meta__.py ├── callbacks │ ├── __init__.py │ ├── dropout.py │ └── keepalive.py ├── data │ ├── __init__.py │ ├── cpn.py │ ├── datasets │ │ ├── __init__.py │ │ ├── bbbc038.py │ │ ├── bbbc039.py │ │ ├── bbbc041.py │ │ ├── generic.py │ │ └── synth.py │ ├── instance_eval.py │ ├── misc.py │ ├── segmentation.py │ ├── toydata.py │ └── transforms.py ├── models │ ├── __init__.py │ ├── commons.py │ ├── convnext.py │ ├── convnextv2.py │ ├── cpn.py │ ├── densenet.py │ ├── features.py │ ├── filters.py │ ├── fpn.py │ ├── hosted.py │ ├── inference.py │ ├── lightning_base.py │ ├── lightning_cpn.py │ ├── loss.py │ ├── mamba.py │ ├── manet.py │ ├── mobilenetv3.py │ ├── normalization.py │ ├── ppm.py │ ├── resnet.py │ ├── smp.py │ ├── timmodels.py │ └── unet.py ├── mpi │ ├── __init__.py │ └── mpi.py ├── ops │ ├── __init__.py │ ├── boxes.py │ ├── commons.py │ ├── cpn.py │ ├── draw.py │ ├── features.py │ ├── loss.py │ └── normalization.py ├── optim │ ├── __init__.py │ └── lr_scheduler.py ├── util │ ├── __init__.py │ ├── logging.py │ ├── schedule.py │ ├── shm_cache.py │ ├── timer.py │ └── util.py └── visualization │ ├── __init__.py │ ├── cmaps.py │ └── images.py ├── celldetection_scripts ├── __init__.py └── cpn_inference.py ├── demos ├── Cell Detection with Contour Proposal Networks.ipynb ├── demo-binary.ipynb └── demo-multiclass.ipynb ├── docker ├── Dockerfile ├── DockerfileNvidia └── README.md ├── docs ├── Makefile ├── make.bat ├── mk.sh ├── requirements.txt └── source │ ├── _static │ ├── css │ │ └── theme.css │ └── img │ │ └── magnify.svg │ ├── _templates │ └── layout.html │ ├── celldetection.callbacks.rst │ ├── 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