Closed camisowers closed 11 months ago
I think the best option for now is to pin scikit-image for now. I was able to get the filtering using the new version to look somewhat better by changing a few parameters, but this will need a bit more testing to make sure it's consistent across different images.
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Describe the bug The current fiber segmentation notebook gives worse outputs than previously, although nothing has been changed in our code. Turns out by bumping scikit-image >=0.20 in ark, the frangi filtering step is now pretty different because of the changes made in this PR (scikit-image/scikit-image/pull/6446).
previous vs current ouput
Expected behavior It should look better.
We'll probably need to explore a bit to see what's the best decision moving forward, but here's a few options to consider first:
frangi()
by tweaking some parametersTo Reproduce Run the fiber segmentation on the example data.