jni/skan issues and pull requests

#229 - Add numpy 2 compatibility

Pull Request - State: closed - Opened by jni 3 months ago

#228 - SKAN Skeleton not compatible with numpy 2.0

Issue - State: closed - Opened by erberj 3 months ago - 6 comments

#227 - SKAN C

Issue - State: closed - Opened by erberj 3 months ago

#226 - conda install error

Issue - State: closed - Opened by smith6jt-cop 4 months ago - 1 comment

#225 - Incorrect edge discovery when having two small loops

Issue - State: open - Opened by jni 5 months ago - 1 comment
Labels: bug

#224 - Add function to make nx Graph from Skeleton

Pull Request - State: closed - Opened by ns-rse 9 months ago - 9 comments

#223 - How to cite Skan

Issue - State: open - Opened by ns-rse 10 months ago - 2 comments

#222 - Docs build should be checked by CI

Issue - State: open - Opened by jni 10 months ago

#221 - Fix documentation builds

Pull Request - State: closed - Opened by jni 11 months ago

#220 - Allow mean pixel value inference from int arrays, not just float

Pull Request - State: closed - Opened by TimMonko 11 months ago - 3 comments

#219 - Data is always 1 despite input image

Issue - State: closed - Opened by TimMonko 12 months ago - 6 comments
Labels: bug, good first issue

#218 - Update formatting on pyproject.toml to match skimage

Pull Request - State: closed - Opened by jni 12 months ago

#217 - Use pyproject.toml for package metadata

Pull Request - State: closed - Opened by jni 12 months ago

#216 - Pyproject.toml

Pull Request - State: closed - Opened by ns-rse 12 months ago - 2 comments

#215 - Convert '-' to '_' in summary dataframe

Pull Request - State: closed - Opened by ns-rse 12 months ago - 11 comments
Labels: deprecation, api-change

#214 - Add support for iterative pruning based on user-specified discard conditions

Pull Request - State: open - Opened by ns-rse 12 months ago - 16 comments

#213 - Standardise package configuration on pyproject.toml

Issue - State: closed - Opened by ns-rse 12 months ago - 2 comments

#212 - Improved error reporting and tests for prune_paths() methods

Pull Request - State: closed - Opened by ns-rse about 1 year ago - 3 comments

#211 - Napari plugin documentation

Issue - State: open - Opened by haesleinhuepf about 1 year ago - 1 comment

#210 - cache skeleton_image shape for path_label_image

Pull Request - State: closed - Opened by jarodhanko-crafco about 1 year ago - 3 comments

#209 - path_lengths seems uncessarily slow for 2d Euclidean distance

Issue - State: closed - Opened by jarodhanko-crafco about 1 year ago - 2 comments

#208 - Skeleton.path_label_image requires keep_images=True

Issue - State: closed - Opened by jarodhanko-crafco about 1 year ago - 3 comments

#207 - Pending Deprecation in Numba 0.57.0.

Issue - State: closed - Opened by erberj about 1 year ago - 3 comments

#206 - ValueError: not enough values to unpack (expected 2, got 0)

Issue - State: closed - Opened by ns-rse about 1 year ago - 12 comments

#205 - Use sphinx-multiversion to build documentation

Issue - State: closed - Opened by ns-rse over 1 year ago - 1 comment

#204 - Prepare for v0.11.1

Pull Request - State: closed - Opened by jni over 1 year ago

#203 - Remove deprecated code from `io.py`

Pull Request - State: closed - Opened by jamesyan-git over 1 year ago - 2 comments

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

Pull Request - State: closed - Opened by jamesyan-git over 1 year ago - 2 comments

#201 - Add widget to generate shape layer and colour by features

Pull Request - State: closed - Opened by jamesyan-git over 1 year ago - 1 comment

#200 - Changed skeletonize plugin result to match labels colour

Pull Request - State: closed - Opened by jamesyan-git over 1 year ago

#199 - Update dependencies' minimum version according to NEP-29

Pull Request - State: closed - Opened by jni over 1 year ago

#198 - Update version to v0.12.0.dev0

Pull Request - State: closed - Opened by jni over 1 year ago

#197 - Improve docs on what the skan measurements actually mean

Issue - State: open - Opened by GenevieveBuckley over 1 year ago - 1 comment

#196 - Add release notes for v0.11

Pull Request - State: closed - Opened by jni over 1 year ago

#195 - Minor cleanup of documentation

Pull Request - State: closed - Opened by jni over 1 year ago

#194 - Fix numerous docs and build issues

Pull Request - State: closed - Opened by jni over 1 year ago

#193 - fix n_points calculation (handling of 0-deg nodes), with tests

Pull Request - State: closed - Opened by jni over 1 year ago

#192 - skeletonize widget could work with integer labels

Issue - State: closed - Opened by jni over 1 year ago

#191 - 0.11.0 release?

Issue - State: closed - Opened by rly over 1 year ago - 3 comments

#190 - Remove numpydoc [docs] requirement

Pull Request - State: closed - Opened by rly over 1 year ago

#189 - Use networkx 2.7 and replace deprecated fcn

Pull Request - State: closed - Opened by rly over 1 year ago - 1 comment

#188 - Move numpydoc req from install reqs to doc reqs

Pull Request - State: closed - Opened by rly over 1 year ago - 1 comment

#187 - Tests failing due to networkx 3 incompatibility

Issue - State: closed - Opened by rly over 1 year ago - 1 comment

#186 - Does numpydoc need to be an install_requires dependency?

Issue - State: closed - Opened by rly over 1 year ago - 3 comments

#185 - Consider using sybil to check docs are building correctly

Issue - State: open - Opened by jni over 1 year ago

#184 - Add napari plugin with skeletonize widget

Pull Request - State: closed - Opened by jamesyan-git almost 2 years ago - 7 comments

#183 - fix n_points calculation (handling of 0-deg nodes)

Pull Request - State: closed - Opened by ssavary almost 2 years ago - 3 comments

#182 - _build_skeleton_path_graph() incorrectly handles degree-0 nodes in calculation of n_points

Issue - State: closed - Opened by ssavary almost 2 years ago - 2 comments

#181 - Found a path not build

Issue - State: open - Opened by fgbxx almost 2 years ago - 3 comments

#180 - How to find endpoints and junction points?

Issue - State: open - Opened by siddagra over 2 years ago

#179 - 3D Labels view is broken in docs

Issue - State: closed - Opened by jni over 2 years ago

#178 - DOC Prepend version with 'v' in switcher

Pull Request - State: closed - Opened by lucyleeow over 2 years ago - 1 comment

#177 - DOC Fix version switcher

Pull Request - State: closed - Opened by lucyleeow over 2 years ago

#176 - ValueError: not enough values to unpack (expected 3, got 2)

Issue - State: closed - Opened by assia855 over 2 years ago - 4 comments

#175 - DOC Update deploy docs workflow for multiversion

Pull Request - State: closed - Opened by lucyleeow over 2 years ago - 2 comments

#174 - Degrees array size not matching Coordinates

Issue - State: open - Opened by dzeego over 2 years ago - 1 comment

#173 - DOC Add versions and use pydata theme

Pull Request - State: closed - Opened by lucyleeow over 2 years ago - 3 comments

#172 - DOC Add versions to documentation

Pull Request - State: closed - Opened by lucyleeow over 2 years ago - 5 comments

#171 - Remove read the docs yml file as it is not used

Pull Request - State: closed - Opened by lucyleeow over 2 years ago - 1 comment

#170 - "too many values to unpack (expect 2)" when ran skeleton_to_csgraph

Issue - State: closed - Opened by XDengN over 2 years ago - 4 comments

#169 - Port prune branches function from napari-skeleton-curator

Issue - State: closed - Opened by jni over 2 years ago - 1 comment

#168 - Make function to match napari's labels colormap in shapes

Issue - State: open - Opened by jni over 2 years ago

#167 - Drop Python 3.7 support

Pull Request - State: closed - Opened by kushaangupta over 2 years ago - 4 comments

#166 - Potential problem in branch-type classification of cycle

Issue - State: open - Opened by kushaangupta over 2 years ago - 6 comments

#165 - Drop Py 3.7 support

Issue - State: closed - Opened by jni over 2 years ago

#164 - Add graph center speedup

Pull Request - State: closed - Opened by kushaangupta over 2 years ago - 2 comments

#163 - Add versioned docs with pydata or napari sphinx themes

Issue - State: closed - Opened by jni over 2 years ago - 1 comment

#162 - Speedup idea for finding the graph center for Sholl analysis

Issue - State: closed - Opened by jni over 2 years ago - 2 comments

#161 - Bug report: draw.overlay_skeleton_networkx

Issue - State: closed - Opened by dani-lbnl over 2 years ago - 5 comments

#160 - Potential new feature: advanced skeletonisation algorithms

Issue - State: open - Opened by jni over 2 years ago

#159 - Turn off automatic gui=qt event loop when building docs

Pull Request - State: closed - Opened by jni over 2 years ago

#158 - Add versioning to skan docs

Issue - State: closed - Opened by jni over 2 years ago - 1 comment

#157 - Use material sphinx theme

Pull Request - State: closed - Opened by jni over 2 years ago

#156 - Use xvfb action instead of manually creating display

Pull Request - State: closed - Opened by jni over 2 years ago

#155 - Add docs page on visualizing 3D skeletons

Pull Request - State: closed - Opened by jni over 2 years ago - 1 comment

#154 - Example datasets for documentation pages

Issue - State: open - Opened by jni over 2 years ago - 7 comments

#153 - Get Junctions or Bifurcation from 3D skeletons

Issue - State: closed - Opened by dzeego over 2 years ago - 3 comments

#152 - Change visited from nodes to edges

Pull Request - State: closed - Opened by jni over 2 years ago

#151 - Fix doc builds and migrate to myst-nb

Pull Request - State: closed - Opened by jni over 2 years ago

#150 - Add Sholl analysis for Skeleton object

Pull Request - State: closed - Opened by jni over 2 years ago - 4 comments

#149 - Example datasets

Issue - State: open - Opened by GenevieveBuckley over 2 years ago

#148 - Add Sholl analysis for Skeleton object

Pull Request - State: closed - Opened by kushaangupta over 2 years ago - 15 comments

#147 - Missing single-edge paths between two junctions

Issue - State: closed - Opened by ssavary over 2 years ago - 3 comments

#146 - Figures are not currently being rendered in the docs

Issue - State: closed - Opened by jni over 2 years ago - 12 comments

#145 - Move master branch references to main

Pull Request - State: closed - Opened by jni almost 3 years ago

#144 - Empty stripes after skeleton analysis with skan

Issue - State: open - Opened by EdwinHernandezG almost 3 years ago - 4 comments

#143 - New pixel graph implementation

Pull Request - State: closed - Opened by jni almost 3 years ago - 4 comments

#142 - Add release notes to documentation and GH releases

Pull Request - State: closed - Opened by jni almost 3 years ago

#141 - Add release-on-tag-push action

Pull Request - State: closed - Opened by jni almost 3 years ago

#140 - Part 1 of docs overhaul

Pull Request - State: closed - Opened by jni almost 3 years ago

#139 - Fix CI

Pull Request - State: closed - Opened by jni almost 3 years ago - 3 comments

#138 - Opt-in to find main branches

Pull Request - State: closed - Opened by jni almost 3 years ago - 3 comments

GitHub / jni/skan issues and pull requests