Implementation of a web server for CellPose.
Install dependencies:
pip install -r requirements.txt
Run the server:
uvicorn main:app --host 0.0.0.0 --port 8000
The server will be running on http://localhost:8000.
A documentation of the endpoints is automatically generated at http://localhost:8000/docs.
GET endpoints
- http://localhost:8000/ : Running algorithm message.
- http://localhost:8000/version: Version of the
imaging-server-kitpackage. - http://localhost:8000/cellpose/info: Web page displaying project metadata.
- http://localhost:8000/cellpose/demo: Plotly Dash web demo app.
- http://localhost:8000/cellpose/parameters: Json Schema representation of algorithm parameters.
- http://localhost:8000/cellpose/sample_images: Byte string representation of the sample images.
POST endpoints
- http://localhost:8000/cellpose/process: Processing endpoint to run the algorithm.
To build the docker image and run a container for the algorithm server in a single command, use:
docker compose up
The server will be running on http://localhost:8000.
Build the docker image:
docker build -t serverkit-cellpose .
Run the server in a container:
docker run -it --rm -p 8000:8000 serverkit-cellpose:latest
The server will be running on http://localhost:8000.
If you have implemented unit tests in the tests/ folder, you can run them using pytest:
pytest
if you are developing your server locally, or
docker run --rm serverkit-cellpose:latest pytest
to run the tests in a docker container.
[EPFL only] Publishing a docker image to registry.rcp.epfl.ch
docker tag serverkit-cellpose registry.rcp.epfl.ch/imaging-server-kit/serverkit-cellpose
docker push registry.rcp.epfl.ch/imaging-server-kit/serverkit-cellpose
nuclei_2d.tif: Fluorescence microscopy image and mask from the 2018 kaggle DSB challenge (Caicedo et al. "Nucleus segmentation across imaging experiments: the 2018 Data Science Bowl." Nature methods 16.12).