This is a SegServe executor for the Cellpose and Omnipose cell segmentation method implementation.
Make sure you have anaconda installed and an active environment with mlflow. Then execute
pip install mlflow
mlflow run ./ -e omnipose -P input_images=<path to your local image or image folder (*.png)>The resulting segmentation should be written to output.json and logged as an artifact in the mlflow run.
The wrapper is used to deploy the Cellpose/Omnipose methods in the SegServe runtime environment. SegServe can be used to host 3rd party segmentation algorithms and execute them on a central computer while providing a REST interface for clients. Therefore, end-users do not need any powerful hardware/GPU.