skan v0.13.1

This is a minor convenience and bug fix release, and recommended for all users.

Bug fixes

• #256: Fix ‘buffer source array is read-only’ error. This error was caused by a still-outstanding bug in scikit-image: scikit-image/scikit-image#6378.

Documentation

• #255: Update docs to use zarr v3.

Maintenance

• #253, by @k-dominik: Move magicgui to optional dependencies. This makes skan more lightweight for those who don’t want/need the napari plugin.

• #254: Use windows-2022 VMs to test on Windows, use pyvista graphics.

skan v0.13.0

This is a minor step forward from v0.12.x which adds a new API: skan.csr.PathGraph is a more abstract version of a Skeleton, which only needs a pixel adjacency matrix to work, rather than a full skeleton image. The motivations for PathGraph are numerous:

• a simpler dataclass object that doesn’t require complex instantiation logic. See e.g. Glyph’s Stop Writing __init__ Methods

• making it easier to compute the pixel adjacency matrix separately, for example using dask when the images don’t fit in memory, and having an API for which you can provide this matrix (rather than having to modify a Skeleton instance in-place).

• allowing more flexible use cases, for example to use skan to measure tracks, as in live-image-tracking-tools/traccuracy#251.

Due to some urgent need to use this code in the wild, this release doesn’t provide any documentation examples. Indeed, the new class may see some changes in upcoming releases based on user feedback. See the discussion in jni/skan#246 for details. Look for further refinement of this idea in the 0.13.x releases!

New features

• #246: New API: PathGraph dataclass