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@github-actions github-actions released this 17 Feb 07:49
· 15 commits to main since this release
v0.11.0
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jni Juan Nunez-Iglesias
SSH Key Fingerprint: PHWfvTNW7c5dSIW7c7G1YqH6dbYJv41iwVSRXx/rThE Learn about vigilant mode.

skan v0.11.0

This release of skan incorporates several bug fixes, new API features, and
documentation improvements. It also finalizes an API change started in 0.10.0:
now junction points are always resolved using a minimum spanning tree, and the
uniquify_junctions and junction_mode arguments to Skeleton are
deprecated (see our FAQ). Finally, this is the first release
containing a napari plugin!
Currently all it does is skeletonize a Labels layer, but this is just the
beginning for GUI-based skeleton analysis.

Thanks to everyone who has helped make this release possible, including
Kushaan Gupta, Lucy
Liu, Ryan Ly,
James Ryan, and
Simon Savary! Not to speak of all the
contributors who make our upstream libraries possible! 🙏

API changes

  • #143: the unique_junctions and
    junction_mode keyword arguments are removed. Junctions are always resolved
    by finding the minimum spanning tree of the junction pixels. This PR also
    speeds up building of the pixel graph.

New features

  • #150,
    #164: add Sholl analysis. (Thanks to
    Kushaan Gupta for the collaboration that
    led to this feature!)
  • #184: add napari plugin.

Bug fixes

  • #152: Some pixel graphs had missing
    paths in their skeletons because of a mistake in how the graphs were
    traversed. Thanks Simon Savary for the detailed
    report that led to the fix! (#147)
  • #193,
    #183: fix the calculation of the
    buffer size needed for the pixel path graph in the presence of 0-degree
    nodes (isolated pixels).
  • #135: the unique_junctions keyword
    argument to the Skeleton class is deprecated. Use instead junction_mode.
    Note however that this option will be removed in 0.11, so you should pin your
    skan dependency if you need this behavior.
  • #139: the skan GUI and corresponding
    skan.gui module and skan command have all been removed. A new, much more
    sophisticated napari plugin is in development at
    https://github.com/kevinyamauchi/napari-skeleton-curator and will be folded
    into a future version of skan (probably v0.11).

Documentation

  • #155,
    #156,
    #159: Add documentation on 3D display
    of skeletons in napari.
  • #173,
    #175,
    #177: support multiple versions of
    documentation. (!) (This series of PRs in particular is close to my heart
    because deprecations and API changes like those listed above are much more
    painful if the old versions are just erased! Thanks to Lucy
    Liu     for her efforts and expertise here!)
  • #194,
    #195: overhaul of documentation and
    build infrastructure.

Misc

Assets 2