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Use minimum spanning tree to simplify junctions #135

Merged
merged 2 commits into from
Sep 7, 2021
Merged

Use minimum spanning tree to simplify junctions #135

merged 2 commits into from
Sep 7, 2021

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jni
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@jni jni commented Sep 7, 2021

Closes #133

Joint work with @kevinyamauchi

  • Add function to use MST on junctions
  • Add minimum spanning tree junction mode

This has the added benefit of doing true pruning on the graph.

jni added 2 commits September 7, 2021 19:16
- new default mode
- pruning now works without caveats (probably!)
- deprecate unique_junctions
@jni
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jni commented Sep 7, 2021

btw @kevinyamauchi is your skan plugin published? Now that we have this it would be super awesome to test interactively on real skeletons!

@kevinyamauchi
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@marlene09 and I haven't published the plugin we are making on pypi yet. However, it's available here: https://github.com/kevinyamauchi/napari-skeleton-curator. We are currently working on a widget for interactive pruning (2D and 3D) on the add-pruning-widget branch (sorry, no real docs yet).

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jni commented Sep 7, 2021

CI failures are unrelated to the PR, I'm gonna merge! I'll do a bit of API cleanup in a follow-up PR and then release 0.10! 🎉

@jni jni merged commit 623c9ad into master Sep 7, 2021
@jni jni deleted the mst branch September 7, 2021 23:35
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jni commented Sep 7, 2021

@kevinyamauchi None of my plugins are documented at all. It's bad 😂 but kind of inevitable... napari plugins is such a blue ocean right now! 🎉

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Idea: don't collapse junction pixels
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