Fix crash in puncta detection on large images#28
Merged
clarenceyapp merged 4 commits intoHMS-IDAC:masterfrom Oct 26, 2025
Merged
Fix crash in puncta detection on large images#28clarenceyapp merged 4 commits intoHMS-IDAC:masterfrom
clarenceyapp merged 4 commits intoHMS-IDAC:masterfrom
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skimage 0.16.2 has a bug where images above a certain size cause an out-of-bounds array read in the cython code, leading to a segfault and hard crash. This upgrades us to skimage 0.20.0 which has a fix. Workarounds are required for other API changes and new bugs.
clarenceyapp
approved these changes
Oct 25, 2025
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Found a severe performance regression. Testing the fix now. |
It turns out the code is almost completely compatible with the latest version of all the dependencies. It ended up being a lot simpler to upgrade everything than chase all the issues with the older versions one by one.
Not necessary for the puncta detection fix, but this does make the script more ergonomic.
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I slipped in a commit with some improvements to the multi-processing and log output, hope that's OK. |
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skimage 0.16.2 has a bug where images above a certain size cause an out-of-bounds array read in the cython code, leading to a segfault and hard crash. This upgrades us to skimage 0.20.0 which has a fix. Workarounds are required for other API changes and new bugs.