🪐 Reference Deployment

Follow the steps below to set up and run a server providing access to several Imaging Server Kit algorithms using Docker.

Algorithms

• StarDist
• CellPose
• Spotiflow
• Rembg
• Scikit-image LoG detector
• Orientationpy

Setup

This repository uses Git submodules to refer to each algorithm server. Clone the repository with all submodules:

git clone --recurse-submodules https://github.com/Imaging-Server-Kit/serverkit-deploy-docker

Make sure to have Docker and Docker Compose installed. From inside the repository, run the command:

docker compose up

This will

• Pull the base imaging-server-kit image from Docker Hub.
• Build the algorithm server docker images specified in docker-compose.yml
• Run a server on http://localhost:8000 with all algorithms available

You can then connect to the server and run the algorithms from Python, Napari, or QuPath.

Contributing

Contributions are very welcome.

License

This project is distributed under the terms of the BSD-3 license.

Issues

If you encounter any problems, please file an issue along with a detailed description.