skan v0.11.1#

This is a bugfix release. It adds napari.yaml to the manifest so that it is correctly shipped with skan, and it fixes compatibility issues with more recent versions of openpyxl. With thanks to James Ryan!

Bug fixes#

  • #202: 🐞 Bug Fix: Include napari.yaml in build

  • #203: Remove deprecated code from

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 and will be folded into a future version of skan (probably v0.11).


  • #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.