brainglobe-segmentation

Segmentation of anatomical structures in a common coordinate space

https://github.com/brainglobe/brainglobe-segmentation

Science Score: 67.0%

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

✓
CITATION.cff file
Found CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
✓
DOI references
Found 4 DOI reference(s) in README
○
Academic publication links
✓
Committers with academic emails
2 of 9 committers (22.2%) from academic institutions
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Institutional organization owner
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (12.4%) to scientific vocabulary

Keywords

brainreg cellfinder napari neuroanatomy neuroscience segmentation

Keywords from Contributors

microscopy cell-detection image-analysis imaging atlases brain registration visualisation anatomy napari-plugin

Last synced: 6 months ago · JSON representation ·

Repository

Segmentation of anatomical structures in a common coordinate space

Basic Info

Host: GitHub
Owner: brainglobe
License: bsd-3-clause
Language: Python
Default Branch: main
Homepage: https://brainglobe.info/documentation/brainglobe-segmentation/index.html
Size: 11.1 MB

Statistics

Stars: 33
Watchers: 6
Forks: 12
Open Issues: 12
Releases: 0

Topics

brainreg cellfinder napari neuroanatomy neuroscience segmentation

Created over 5 years ago · Last pushed 7 months ago

Metadata Files

Readme License Citation

README.md

brainglobe-segmentation

Segmentation of anatomical structures in a common coordinate space

Installation

PyPI pip install brainglobe-segmentation

conda conda install -c conda-forge brainglobe-segmentation

N.B. Your data will need to be registered to an anatomical atlas first.

Usage

See user guide.

Seeking help or contributing

We are always happy to help users of our tools, and welcome any contributions. If you would like to get in contact with us for any reason, please see the contact page of our website.

Citing brainglobe-segmentation

If you find brainglobe-segmentation useful, and use it in your research, please let us know and also cite the paper:

Tyson, A. L., Vélez-Fort, M., Rousseau, C. V., Cossell, L., Tsitoura, C., Lenzi, S. C., Obenhaus, H. A., Claudi, F., Branco, T., Margrie, T. W. (2022). Accurate determination of marker location within whole-brain microscopy images. Scientific Reports, 12, 867 doi.org/10.1038/s41598-021-04676-9

Owner

Name: BrainGlobe
Login: brainglobe
Kind: organization
Location: London/Munich

Website: https://brainglobe.info/
Twitter: brain_globe
Repositories: 28
Profile: https://github.com/brainglobe

Open python tools for morphological analyses in systems neuroscience

Citation (CITATION.cff)

# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!

cff-version: 1.2.0
title: brainglobe-segmentation
message: >-
  If you use this software, please cite it using the
  metadata from this file.
type: software
authors:
  - given-names: Adam
    family-names: Tyson
    email: hello@brainglobe.info
    affiliation: 'Sainsbury Wellcome Centre, University College London'
  - given-names: Horst
    family-names: Obenhaus
  - given-names: BrainGlobe
    family-names: Developers
    email: hello@brainglobe.info
repository-code: 'https://github.com/brainglobe/brainglobe-segmentation'
url: 'https://brainglobe.info'
abstract: >-
  Segmentation of anatomical structures in a common
  coordinate space.
license: BSD-3-Clause
date-released: '2024-01-16'
year: 2024
preferred-citation:
  type: article
  authors:
  - given-names: Adam
    family-names: Tyson
    affiliation: 'Sainsbury Wellcome Centre, University College London'
  - given-names: Mateo
    family-names: Velez-Fort
  - given-names: Charly V.
    family-names: Rousseau
  - given-names: Lee
    family-names: Cossell
  - given-names: Chryssanthi
    family-names: Tsitoura
  - given-names: Stephen C.
    family-names: Lenzi
  - given-names: Horst A.
    family-names: Obenhaus
  - given-names: Federico
    family-names: Claudi
  - given-names: Tiago
    family-names: Branco
  - given-names: Troy W.
    family-names: Margrie
  doi: "10.1038/s41598-021-04676-9"
  url: "https://doi.org/10.1038/s41598-021-04676-9"
  journal: "Scientific Reports"
  month: 1
  year: 2022
  title: "Accurate determination of marker location within whole-brain microscopy images"
  issue: 1
  volume: 12
citation-sentence: "This project makes use of the brainglobe-segmentation plugin for segmentation of objects and regions of the brain."

GitHub Events

Total

Create event: 18
Release event: 4
Issues event: 4
Watch event: 4
Delete event: 16
Issue comment event: 4
Push event: 21
Pull request review comment event: 1
Pull request review event: 21
Pull request event: 28
Fork event: 2

Last Year

Create event: 18
Release event: 4
Issues event: 4
Watch event: 4
Delete event: 16
Issue comment event: 4
Push event: 21
Pull request review comment event: 1
Pull request review event: 21
Pull request event: 28
Fork event: 2

Committers

Last synced: about 2 years ago

All Time

Total Commits: 182
Total Committers: 9
Avg Commits per committer: 20.222
Development Distribution Score (DDS): 0.505

Past Year

Commits: 83
Committers: 4
Avg Commits per committer: 20.75
Development Distribution Score (DDS): 0.422

Top Committers

Name	Email	Commits
Adam Tyson	c**e@a**m	90
Adam Tyson	a**n@u**k	53
pre-commit-ci[bot]	6****]	16
David Stansby	d**y@g**m	15
Will Graham	3****1	4
Hotte	h**s@g**m	1
Hotte	h**s@n**o	1
juanma9613	j**m@f**i	1
Draga Doncila Pop	1****a	1

Committer Domains (Top 20 + Academic)

factored.ai: 1 ntnu.no: 1 ucl.ac.uk: 1 adamltyson.com: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 2
Total pull requests: 14
Average time to close issues: 8 months
Average time to close pull requests: about 8 hours
Total issue authors: 2
Total pull request authors: 4
Average comments per issue: 3.5
Average comments per pull request: 0.0
Merged pull requests: 12
Bot issues: 0
Bot pull requests: 8

Past Year

Issues: 1
Pull requests: 14
Average time to close issues: 4 days
Average time to close pull requests: about 8 hours
Issue authors: 1
Pull request authors: 4
Average comments per issue: 3.0
Average comments per pull request: 0.0
Merged pull requests: 12
Bot issues: 0
Bot pull requests: 8

View more stats

Top Authors

Issue Authors

Yanting-Yao (1)
alessandrofelder (1)
karolinasocha (1)
adamltyson (1)
Isabella06242 (1)

Pull Request Authors

pre-commit-ci[bot] (19)
adamltyson (9)
IgorTatarnikov (7)
alessandrofelder (5)
willGraham01 (4)
K-Meech (2)
lochhh (1)

Top Labels

Issue Labels

bug (3) enhancement (2)

Pull Request Labels

bug (2)

Packages

Total packages: 1
Total downloads:
- pypi 633 last-month

Total dependent packages: 2
Total dependent repositories: 0
Total versions: 14
Total maintainers: 2

pypi.org: brainglobe-segmentation

Segmentation of anatomical structures in a common coordinate space

Homepage: https://brainglobe.info/
Documentation: https://brainglobe.info/documentation/brainglobe-segmentation/index.html
License: BSD-3-Clause
Latest release: 1.3.3
published 9 months ago

Versions: 14
Dependent Packages: 2
Dependent Repositories: 0
Downloads: 633 Last month

Rankings

Dependent packages count: 9.8%

Forks count: 11.4%

Stargazers count: 12.6%

Average: 25.4%

Dependent repos count: 67.9%

Maintainers (2)

willGraham01 alessandrofelder

Last synced: 7 months ago

Dependencies

.github/workflows/plugin_preview.yml actions

actions/checkout v2 composite
chanzuckerberg/napari-hub-preview-action v0.1 composite

.github/workflows/test_and_deploy.yml actions

actions/checkout v2 composite
actions/setup-python v2 composite
brainglobe/actions/lint v1 composite
brainglobe/actions/test v1 composite
tlambert03/setup-qt-libs v1 composite