Cell Observatory

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

Copyright notice

All code and data contained within this repository are proprietary.
Unauthorized distribution, reproduction, or use of any part of this code or data is strictly prohibited.
Copyright © 2025, Cell Observatory.
All rights reserved.

Docker images

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

docker pull ghcr.io/cell-observatory/platform:main_torch_cuda_12_8

Clone repository to your host system

git clone --recurse-submodules https://github.com/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/platform -w /app/platform --env PYTHONUNBUFFERED=1 --pull missing -it --rm  --ipc host --gpus all ghcr.io/cell-observatory/platform:main_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 main_torch_cuda_12_8.sif docker://ghcr.io/cell-observatory/platform:main_torch_cuda_12_8