Cell Observatory

• Docker & Apptainer images
• Clone repository to your host system
• Running docker image
• License

Docker images

Our prebuilt image with Python, Torch, and all packages installed for you.

docker pull ghcr.io/cell-observatory/cell_observatory_platform:develop_torch_cuda_12_8

Clone repository to your host system

git clone --recurse-submodules https://github.com/cell-observatory/cell_observatory_platform.git

To later update to the latest, greatest

git pull --recurse-submodules

Note: If you want to run a local version of the image, see the Dockerfile

Running docker image

To run docker image, cd to repo directory or replace $(pwd) with your local path for the repository.

docker run --network host -u 1000 --privileged -v $(pwd):/app/cell_observatory_platform -w /app/cell_observatory_platform --env PYTHONUNBUFFERED=1 --pull missing -it --rm  --ipc host --gpus all ghcr.io/cell-observatory/cell_observatory_platform:develop_torch_cuda_12_8 bash

Running docker image on a cluster via Apptainer

Running an image on a cluster typically requires an Apptainer version of the image, which can be generated by:

apptainer pull --force develop_torch_cuda_12_8.sif docker://ghcr.io/cell-observatory/cell_observatory_platform:develop_torch_cuda_12_8

License

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

Apache License 2.0

Copyright 2025 Cell Observatory.