Add workflow for segmentation and counting of cell nuclei in fluorescence microscopy images

[kostrykin]

As part of the Imaging Hackathon in Freiburg.

Add workflow for segmentation and counting of cell nuclei in fluorescence microscopy images.

This workflow performs segmentation and counting of cell nuclei using fluorescence microscopy images. The segmentation step is performed using Otsu thresholding (Otsu, 1979).

Created by following the tutorial: https://github.com/galaxyproject/iwc/blob/main/workflows/README.md#adding-workflows

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Strangely, planemo workflow_lint reports a couple of issues:

Applying linter best_practices... WARNING
.. WARNING: Input input_image of workflow step The fluorescence microscopy images to be segmented. Must be the single image channel, which contains the cell nuclei. is disconnected.

…but this workflow step is the input of the workflow, so it cannot be connected to anything.

There also are a few more warnings, which I suspect to be consequential errors, since the Best Practices check in galaxy reports that everything is fine with the workflow:

Let me know if anything needs to be done about those warnings!

[mvdbeek]

Looks great, thanks so much @kostrykin! Yes, planemo lint isn't as smart as the best practice panel, I've got some work in galaxyproject/planemo#1417 to improve that.