diff --git a/README.md b/README.md index 84043c1..bfd0308 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,6 @@ # Cell Detection -[![Downloads](https://pepy.tech/badge/celldetection?l)](https://pepy.tech/project/celldetection) +[![Downloads](https://static.pepy.tech/badge/celldetection?l)](https://pepy.tech/project/celldetection) [![Test](https://github.com/FZJ-INM1-BDA/celldetection/workflows/Test/badge.svg)](https://github.com/FZJ-INM1-BDA/celldetection/actions?query=workflow%3ATest) [![PyPI](https://img.shields.io/pypi/v/celldetection?l)](https://pypi.org/project/celldetection/) [![Documentation Status](https://readthedocs.org/projects/celldetection/badge/?version=latest)](https://celldetection.readthedocs.io/en/latest/?badge=latest) @@ -283,6 +283,52 @@ model = cd.models.ResNet50(in_channels=3, nd=3) +## 🐳 Docker + +Find us on Docker Hub: https://hub.docker.com/r/ericup/celldetection + +You can pull the latest version of `celldetection` via: +``` +docker pull ericup/celldetection:latest +``` + +
+ CPN inference via Docker with GPU + +``` +docker run --rm \ + -v $PWD/docker/outputs:/outputs/ \ + -v $PWD/docker/inputs/:/inputs/ \ + -v $PWD/docker/models/:/models/ \ + --gpus="device=0" \ + celldetection:latest /bin/bash -c \ + "python cpn_inference.py --tile_size=1024 --stride=768 --precision=32-true" +``` +
+
+ CPN inference via Docker with CPU + +``` +docker run --rm \ + -v $PWD/docker/outputs:/outputs/ \ + -v $PWD/docker/inputs/:/inputs/ \ + -v $PWD/docker/models/:/models/ \ + celldetection:latest /bin/bash -c \ + "python cpn_inference.py --tile_size=1024 --stride=768 --precision=32-true --accelerator=cpu" +``` +
+ + + +### Apptainer + +You can also pull our Docker images for the use with [Apptainer](https://apptainer.org/) (formerly [Singularity](https://github.com/apptainer/singularity)) with this command: + +``` +apptainer pull --dir . --disable-cache docker://ericup/celldetection:latest +``` + + ## 🤗 Hugging Face Spaces Find us on Hugging Face and upload your own images for segmentation: https://huggingface.co/spaces/ericup/celldetection