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https://github.com/berenslab/skeliner

A lightweight neuromorphological mesh skeletonizer.

https://github.com/berenslab/skeliner

Science Score: 26.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (3.7%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

A lightweight neuromorphological mesh skeletonizer.

Basic Info
  • Host: GitHub
  • Owner: berenslab
  • License: gpl-3.0
  • Language: Python
  • Default Branch: main
  • Size: 49 MB
Statistics
  • Stars: 0
  • Watchers: 2
  • Forks: 0
  • Open Issues: 0
  • Releases: 13
Created about 1 year ago · Last pushed 10 months ago
Metadata Files
Readme License

README.md

skeliner

A lightweight skeletonizer that converts neuron meshes into biophysical‑modelling‑ready SWC morphologies. It heuristically detects the soma, extracts an acyclic center‑line skeleton, estimates per‑node radii, and bridges small gaps.

Installation

bash pip install skeliner

or

bash git clone https://github.com/berenslab/skeliner.git pip install -e "skeliner[dev]"

Usage

See example notebooks for usage.

Owner

  • Name: Berens Lab @ University of Tübingen
  • Login: berenslab
  • Kind: organization
  • Email: philipp.berens@uni-tuebingen.de
  • Location: Tübingen, Germany

Department of Data Science at the Hertie Institute for AI in Brain Health, University of Tübingen

GitHub Events

Total
  • Create event: 23
  • Release event: 9
  • Issues event: 3
  • Delete event: 7
  • Push event: 72
  • Pull request event: 22
Last Year
  • Create event: 23
  • Release event: 9
  • Issues event: 3
  • Delete event: 7
  • Push event: 72
  • Pull request event: 22

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 2
  • Total pull requests: 13
  • Average time to close issues: about 14 hours
  • Average time to close pull requests: 2 days
  • Total issue authors: 1
  • Total pull request authors: 1
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 10
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 2
  • Pull requests: 13
  • Average time to close issues: about 14 hours
  • Average time to close pull requests: 2 days
  • Issue authors: 1
  • Pull request authors: 1
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 10
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • huangziwei (2)
Pull Request Authors
  • huangziwei (13)
Top Labels
Issue Labels
bug (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 222 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 14
  • Total maintainers: 1
pypi.org: skeliner

A lightweight neuromorphological mesh skeletonizer.

  • Versions: 14
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 222 Last month
Rankings
Dependent packages count: 9.1%
Average: 30.0%
Dependent repos count: 51.0%
Maintainers (1)
berenslab
Last synced: 10 months ago

Dependencies

pyproject.toml pypi
  • ipykernel >=6.29.5
  • matplotlib >=3.9.4
  • networkx >=3.2.1
  • numpy >=2.0.2
  • pandas >=2.2.3
  • pykdtree >=1.4.1
  • scipy >=1.13.1
  • trimesh >=4.6.9
  • watermark >=2.5.0
uv.lock pypi
  • appnope 0.1.4
  • asttokens 3.0.0
  • backports-tarfile 1.2.0
  • certifi 2025.4.26
  • cffi 1.17.1
  • charset-normalizer 3.4.2
  • colorama 0.4.6
  • comm 0.2.2
  • contourpy 1.3.0
  • contourpy 1.3.2
  • cryptography 44.0.3
  • cycler 0.12.1
  • debugpy 1.8.14
  • decorator 5.2.1
  • docutils 0.21.2
  • exceptiongroup 1.3.0
  • executing 2.2.0
  • fonttools 4.58.0
  • id 1.5.0
  • idna 3.10
  • importlib-metadata 8.7.0
  • importlib-resources 6.5.2
  • iniconfig 2.1.0
  • ipykernel 6.29.5
  • ipython 8.18.1
  • ipython 8.36.0
  • ipython 9.2.0
  • ipython-pygments-lexers 1.1.1
  • jaraco-classes 3.4.0
  • jaraco-context 6.0.1
  • jaraco-functools 4.1.0
  • jedi 0.19.2
  • jeepney 0.9.0
  • jupyter-client 8.6.3
  • jupyter-core 5.7.2
  • keyring 25.6.0
  • kiwisolver 1.4.7
  • kiwisolver 1.4.8
  • markdown-it-py 3.0.0
  • matplotlib 3.9.4
  • matplotlib 3.10.3
  • matplotlib-inline 0.1.7
  • maturin 1.8.6
  • mdurl 0.1.2
  • more-itertools 10.7.0
  • nest-asyncio 1.6.0
  • networkx 3.2.1
  • networkx 3.4.2
  • nh3 0.2.21
  • numpy 2.0.2
  • numpy 2.2.5
  • packaging 25.0
  • pandas 2.2.3
  • parso 0.8.4
  • pexpect 4.9.0
  • pillow 11.2.1
  • platformdirs 4.3.8
  • pluggy 1.5.0
  • prompt-toolkit 3.0.51
  • psutil 7.0.0
  • ptyprocess 0.7.0
  • pure-eval 0.2.3
  • pycparser 2.22
  • pygments 2.19.1
  • pykdtree 1.4.1
  • pyparsing 3.2.3
  • pytest 8.3.5
  • python-dateutil 2.9.0.post0
  • pytz 2025.2
  • pywin32 310
  • pywin32-ctypes 0.2.3
  • pyzmq 26.4.0
  • readme-renderer 44.0
  • requests 2.32.3
  • requests-toolbelt 1.0.0
  • rfc3986 2.0.0
  • rich 14.0.0
  • ruff 0.11.9
  • scipy 1.13.1
  • scipy 1.15.3
  • secretstorage 3.3.3
  • setuptools 80.7.1
  • six 1.17.0
  • skeliner 0.1.0
  • stack-data 0.6.3
  • tomli 2.2.1
  • tornado 6.4.2
  • traitlets 5.14.3
  • trimesh 4.6.9
  • twine 6.1.0
  • typing-extensions 4.13.2
  • tzdata 2025.2
  • urllib3 2.4.0
  • watermark 2.5.0
  • wcwidth 0.2.13
  • zipp 3.21.0