jni/skan

View on GitHub

Python module to analyse skeleton (thin object) images

Stars: 149
Forks: 45
Open beginner issues: 0
Indexed issues: 63

Dominant language: Python
License: BSD-3-Clause
Last GitHub push: Jun 26, 2026
Latest indexed: Sep 18, 2026
Contributing guide: No contributing guide
Code of conduct: No code of conduct
Beginner labels: good first issue
PR merge metrics: No merged PRs in 30d

Open All

63 open issues indexed

Figure out ahead of time when the skeletonisation is bad Open

jni/skan#9 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
Improve performance when processing many files Open

jni/skan#10 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
Add interactive skeleton overlay viewer Open

jni/skan#11 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
Additional subplots for pipeline plot Open

jni/skan#12 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 18, 2026
Additional summary statistics to output at the end of the run Open

jni/skan#13 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 18, 2026
Use Hessian filter or shape index to find skeleton Open

jni/skan#17 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
Scaling of Brightness & Contrast Open

jni/skan#27 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
Allow different smoothing methods Open

jni/skan#35 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 18, 2026
Handle cycles Open

jni/skan#36 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
I think a simple network is better Open

jni/skan#43 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 18, 2026
Add connectivity as an option Open

jni/skan#44 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
Skeletons traced where no branches exist Open

jni/skan#53 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 18, 2026
Compute standard deviation of shape index Open

jni/skan#54 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
Add interactive overlay show/hide Open

jni/skan#57 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
Rename Skeleton.path_* to Skeleton.branch_* Open

jni/skan#60 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
Suggestion for API: Return pixel_indices in different format Open

jni/skan#68 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
Suggestion for API: Return degrees as flat array Open

jni/skan#69 · 4 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
Retrieve skeleton tree structure Open

jni/skan#70 · 6 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
mesh size under-measured for discontinuous networks Open

jni/skan#75 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
How to make the path smooth? Open

jni/skan#77 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 18, 2026
how to remove branch according to the length? Open

jni/skan#78 · 1 comment · 1 reaction · 0 assignees · Indexed Sep 18, 2026
Bug report Open

jni/skan#79 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
Network to raster array Open

jni/skan#80 · 3 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
Reading a an SWC file into a Skeleton object Open

jni/skan#81 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 18, 2026
ValueError: cannot infer dimensions from zero sized index arrays Open

bug

jni/skan#90 · 10 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
Possible incorrect classification of branch types Open

jni/skan#92 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
Point (0,0) appears falsely in pixel coordinates when using skeleton_to_csgraph Open

jni/skan#93 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 18, 2026
Median and maximum width Open

jni/skan#96 · 5 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
Feature request: Add function to prune skeleton Open

jni/skan#97 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 18, 2026
Save skeleton to OBJ Open

good first issue

jni/skan#99 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
Update documentation to use new Skeleton class, and deprecate old functions Open

documentation good first issue

jni/skan#100 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 18, 2026
Numba deprecation warning on import of skan Open

jni/skan#103 · 0 comments · 2 reactions · 0 assignees · Indexed Sep 18, 2026
Skan returns pixel 0,0 under all conditions Open

jni/skan#108 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 18, 2026
Branch thickness Open

jni/skan#109 · 5 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
Should path indices start from 1? Open

jni/skan#114 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
Notes on interacting with skeletons in napari Open

jni/skan#115 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
Feature request: add napari plugin Open

jni/skan#116 · 5 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
Add feature to remove cycles from skeleton graph Open

jni/skan#118 · 13 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
Feature request: allow passing in pre-existing csr pixel graph to Skeleton obj Open

jni/skan#119 · 3 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
Consider removing degree image from Skeleton class Open

jni/skan#120 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 18, 2026
Better documentation for how skan handles skeleton junctions Open

documentation good first issue

jni/skan#121 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
Move documentation to use jupyter-book instead of nb2plots Open

documentation

jni/skan#122 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
Implement various measures of tortuosity Open

jni/skan#126 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
Fix remaining issues with GitHub Actions Open

jni/skan#130 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 18, 2026
Empty stripes after skeleton analysis with skan Open

jni/skan#144 · 4 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
Example datasets Open

jni/skan#149 · 0 comments · 2 reactions · 0 assignees · Indexed Sep 18, 2026
Example datasets for documentation pages Open

jni/skan#154 · 7 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
Potential new feature: advanced skeletonisation algorithms Open

jni/skan#160 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
Potential problem in branch-type classification of cycle Open

jni/skan#166 · 6 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026
Make function to match napari's labels colormap in shapes Open

jni/skan#168 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 18, 2026

jni/skan

Get new issues in your inbox