Write tutorials for Voronoi segmentation

[kostrykin]

There are multiple workflows concerning Voronoi segmentation, which are from the work on "Building FAIR image analysis pipelines for high-content-screening (HCS) data using Galaxy" by Riccardo Massei:

• Workflow 1: Full workflow for nuclei and cytoplasm segmentation (translated from KNIME)
  https://usegalaxy.eu/u/rmassei88/w/unnamed-workflow-1
• Workflow 2: Nuclei segmentation and feature extraction
  https://usegalaxy.eu/u/rmassei88/w/unnamed-workflow
• Workflow 3: Voronoi segmentation
  https://usegalaxy.eu/u/rmassei88/w/voronoi-segmentation-and-feature-extraction
• Workflow 4: Manual threshold adjustment (not sure what this is)
  https://usegalaxy.eu/u/rmassei88/w/unnamed-workflow-3

The Workflow 3 (Voronoi segmentation) is motivated here: BMCV/galaxy-image-analysis#105 (comment)

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Things to be done:

• It should be easy to write Tools required for conversion of KNIME image analysis workflows to Galaxy BMCV/galaxy-image-analysis#105 (comment) into a tutorial, which reproduces Workflow 3.
• In addition, a follow-up tutorial could cover the usage of Workflow 3 by reproducing Workflow 1. This might be more challenging to write.
• Finally, the follow-up tutorial could also cover the usage of Workflow 1. This is very optional.

[annefou]

I am working on Workflow 3: Voronoi segmentation
https://usegalaxy.eu/u/rmassei88/w/voronoi-segmentation-and-feature-extraction

[kostrykin]

@annefou I understood correctly that you are going to use the BIA retrieval tool for the tutorial?

If so, I would assign #13 to you and mark it as work-in-progress.

[annefou]

The draft PR is available galaxyproject/training-material#5508 (working progress!)