Create outline overlay using mesmer segmentation mask

[janinemelsen]

Could you maybe show how to create an outline overlay plot using the segmentation mask (and membrane and nucleus channel) as generated by mesmer in the mcmicro pipeline? The original python implementation expects a certain input (and output) format, which is automatically adjusted by the mcmicro pipeline, so I prefer to stick to your nice pipeline;)

As suggested in the post below, I tried to use the 'make_outline_overlay' function, however this error is thrown: 'ValueError: Predictions must be 4D, got (1000, 1500)'

Thank you!

Janine

deepcell.utils.plot_utils provides make_outline_overlay that draws outline from prediction mask from mesmer. I've used it sucessfully (though it's a bit limiting). Perhaps that's useful?

Originally posted by @aandytu in #479 (comment)