Stardist Nuclei Segmentation

This repository relies on the library https://github.com/stardist/stardist and packages the StarDist algorithm into a Cytomine Task compatible with the Cytomine App engine (ie. a docker container image reading image where to detect objects from an input directory and generating detected objects as geometries into an output directory).

How to run it manually ?

Get the docker image

From the task bundle

Either from an existing task bundle

$> unzip com.cytomine.nuclei.segmentation.stardist-0.3.0.zip
Archive:  ./com.cytomine.nuclei-segmentation.stardist-0.3.0.zip
  inflating: com.cytomine.nuclei.segmentation.stardist-0.3.0.tar
  inflating: descriptor.yml
$> docker image load --input com.cytomine.nuclei.segmentation.stardist-0.3.0.tar
0949773899cf: Loading layer [==================================================>]   84.2MB/84.2MB
95c8f57bd29d: Loading layer [==================================================>]  3.405MB/3.405MB
95ce64f868d0: Loading layer [==================================================>]  30.56MB/30.56MB
eca2faa8f0ea: Loading layer [==================================================>]   5.12kB/5.12kB
d6bd5066234c: Loading layer [==================================================>]  12.91MB/12.91MB
631efc3b95e1: Loading layer [==================================================>]  1.536kB/1.536kB
c70e485b159b: Loading layer [==================================================>]   2.56kB/2.56kB
84cc4f8d1ed4: Loading layer [==================================================>]  2.087GB/2.087GB
e05ca7daf251: Loading layer [==================================================>]   5.78MB/5.78MB
987f4b5a221e: Loading layer [==================================================>]  6.656kB/6.656kB
Loaded image: com/cytomine/nuclei-segmentation/stardist:0.3.0

Build the docker image yourself

docker build -t com/cytomine/nuclei-segmentation/stardist:0.3.0 .

Run on data

From this repository, run :

docker run -v ./examples/inputs:/inputs -v ./local-outputs:/outputs --rm -it com/cytomine/nuclei-segmentation/stardist:0.3.0

You can then explore the results in the ./local-outputs directory.

Build bundle to upload on Cytomine

1. Build the docker image as described above
2. save it as tar archive

docker save -o com.cytomine.nuclei.segmentation.stardist-0.3.0.tar com/cytomine/nuclei-segmentation/stardist:0.3.0

3. Build the bundle

zip com.cytomine.nuclei.segmentation.stardist-0.3.0.zip descriptor.yml com.cytomine.nuclei.segmentation.stardist-0.3.0.tar

4. Upload the bundle on Cytomine