ImageJ Service

Installation:

conda create -n imagej-service python=3.8
conda install -y -c conda-forge pyimagej=1.3.2 openjdk=8
pip install -r requirements.txt

Usage

Download and install ImageJ or Fiji from here: https://imagej.net/software/fiji/downloads, then start the service in the terminal:

python run_imagej_service.py --imagej-dir=/home/Fiji.app --server-url=https://ai.imjoy.io

Keep the terminal open, now you can access the service in a jupyter notebook (in the browser) via this link.

In the above example, we used the public hypha server hosted at https://ai.imjoy.io, if you want to start your local server, follow the instructions here: https://ha.amun.ai/#/?id=getting-started

Development

To test pyimagej, run:

Xvfb $DISPLAY -screen 0 1024x768x16 &
python3 -c 'import imagej; ij = imagej.init("/home/Fiji.app", headless=False); print(ij.getVersion()); ij.dispose()'

To run the docker container:

docker run --net=host --rm -it -v $PWD/imagej:/app hypha-app-engine_imagej:latest sh -c "python /app/run_imagej_service.py --server-url=https://ai.imjoy.io"