Data

Tools

Indexes

Applications

Experiments

Open Source Science

netplotbrain

A package to create simple 3D network visualizations on a brain.

https://github.com/wiheto/netplotbrain

Science Score: 59.0%

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
    Found 4 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ✓
    Committers with academic emails
    1 of 7 committers (14.3%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (14.1%) to scientific vocabulary
Last synced: 6 months ago · JSON representation

Repository

A package to create simple 3D network visualizations on a brain.

Basic Info
  • Host: GitHub
  • Owner: wiheto
  • License: apache-2.0
  • Language: Python
  • Default Branch: main
  • Size: 73.6 MB
Statistics
  • Stars: 77
  • Watchers: 2
  • Forks: 9
  • Open Issues: 15
  • Releases: 3
Created over 5 years ago · Last pushed 7 months ago
Metadata Files
Readme Changelog License Zenodo

README.md

netplotbrain: visualizing networks in 3D on a brain

CircleCI Codacy Badge DOI Coverage Status Binder

Painlessly plot networks on a brain in python. The package is still in early development and better documentation/tutorials/examples are in the works.

See homepage for more details, examples, documentation

See Network Neuroscience paper for a general turorial

Note

From V0.2.1 keyword arguments now include underscores after the figure component to enhance readability. This means 'nodealpha' becomes 'nodealpha', 'templatevoxelsize' becomes 'templatevoxelsize'.

Features

  1. Easy to specify properties: integration with pandas entails node and edge size/colour can easily be specified.
  2. Flexibility: multiple node and template styles. Easily create multiple angles to view the figure.
  3. TemplateFlow integration to download any template or atlas.

Installation

pip install netplotbrain

Add the -U flag to upgrade from an earlier version.

Works best in python 3.9 and up.

Get involved

We hope to develop this package. Please feel free to get in touch about what feature you want/would like to implement/would like to contribute to.

Citation

If using netplotbrain in an academic article, please cite the package and the libraries it relies on.

Suggestion of text in methods section:

Methods

Network plots were generated using netplotbrain (Fanton & Thompson 2023), which utilizes templateflow (Ciric et al 2021), matplotlib (Hunter 2007), pandas (McKinney 2011), numpy (Harris et al 2020), scipy (Virtanen et al 2020), nibabel (Brett et al 2020), and scikit-image (van der Walt et al 2014).

References

Brett, Matthew, Markiewicz, Christopher J., Hanke, Michael, Côté, Marc-Alexandre, Cipollini, Ben, McCarthy, Paul, et al (2020, November 28). nipy/nibabel: 3.2.1 (Version 3.2.1). Zenodo. http://doi.org/10.5281/zenodo.4295521

Ciric, R., Lorenz, R., Thompson, W. H., Goncalves, M., MacNicol, E., Markiewicz, C., ... & Esteban, O. (2021). TemplateFlow: a community archive of imaging templates and atlases for improved consistency in neuroimaging. bioRxiv.

Fanton, S., & Thompson, W. H. NetPlotBrain: A Python package for visualising networks and brains. Network Neuroscience, 1-21.

Harris, C. R., Millman, K. J., van der Walt, S. J., Gommers, R., Virtanen, P., Cournapeau, D., ... & Oliphant, T. E. (2020). Array programming with NumPy. Nature, 585(7825), 357-362.

Hunter, J. D. (2007). Matplotlib: A 2D graphics environment. IEEE Annals of the History of Computing, 9(03), 90-95.

McKinney, W. (2011). pandas: a foundational Python library for data analysis and statistics. Python for High Performance and Scientific Computing, 14(9), 1-9.

Van der Walt, S., Schönberger, J. L., Nunez-Iglesias, J., Boulogne, F., Warner, J. D., Yager, N., ... & Yu, T. (2014). scikit-image: image processing in Python. PeerJ, 2, e453.

Virtanen, P., Gommers, R., Oliphant, T. E., Haberland, M., Reddy, T., Cournapeau, D., ... & van Mulbregt, P. (2020). SciPy 1.0: fundamental algorithms for scientific computing in Python. Nature methods, 17(3), 261-272.

Owner

  • Name: William Hedley Thompson
  • Login: wiheto
  • Kind: user
  • Location: Gothenburg, Sweden

Post doc at Karolinska Institutet

GitHub Events

Total
  • Issues event: 5
  • Watch event: 12
  • Issue comment event: 13
  • Push event: 23
  • Pull request review comment event: 1
  • Pull request review event: 1
  • Pull request event: 3
  • Fork event: 1
Last Year
  • Issues event: 5
  • Watch event: 12
  • Issue comment event: 13
  • Push event: 23
  • Pull request review comment event: 1
  • Pull request review event: 1
  • Pull request event: 3
  • Fork event: 1

Committers

Last synced: almost 3 years ago

All Time
  • Total Commits: 393
  • Total Committers: 7
  • Avg Commits per committer: 56.143
  • Development Distribution Score (DDS): 0.557
Top Committers
Name Email Commits
wiheto w****n@k****e 174
wiheto w****n@g****e 117
Silvia Fanton 6****n@u****m 50
William Hedley Thompson w****o@u****m 39
wiheto w****n@a****e 10
Syam Gadde s****e@d****u 2
xthowi x****i@p****n 1
Committer Domains (Top 20 + Academic)
pop-os.localdomain: 1 duke.edu: 1 ait.gu.se: 1 gu.se: 1 ki.se: 1

Issues and Pull Requests

Last synced: 7 months ago

All Time
  • Total issues: 50
  • Total pull requests: 25
  • Average time to close issues: 4 months
  • Average time to close pull requests: about 1 month
  • Total issue authors: 12
  • Total pull request authors: 4
  • Average comments per issue: 1.58
  • Average comments per pull request: 1.44
  • Merged pull requests: 23
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 6
  • Pull requests: 1
  • Average time to close issues: 4 days
  • Average time to close pull requests: 2 months
  • Issue authors: 3
  • Pull request authors: 1
  • Average comments per issue: 2.5
  • Average comments per pull request: 3.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • wiheto (34)
  • hasibagen (4)
  • mkkubins (2)
  • silviafan (2)
  • kirass1 (1)
  • neudorf (1)
  • YuanYuan527 (1)
  • oesteban (1)
  • npdrbong (1)
  • LeiGuo0812 (1)
  • edhutch1 (1)
  • anichinthakindimgh (1)
Pull Request Authors
  • wiheto (13)
  • silviafan (11)
  • seblome (2)
  • SyamGadde (1)
Top Labels
Issue Labels
bug (8) enhancement (6) documentation (3) good first issue (3)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 98 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 4
  • Total maintainers: 1
pypi.org: netplotbrain

Package to plot networks on brains

  • Versions: 4
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 98 Last month
Rankings
Dependent packages count: 10.1%
Stargazers count: 10.2%
Forks count: 15.3%
Average: 15.7%
Downloads: 21.4%
Dependent repos count: 21.6%
Maintainers (1)
wiheto
Last synced: 7 months ago

Dependencies

.rtdrequirements.txt pypi
  • mkdocstrings >=0.15.0
  • scikit-image >=0.17.2
requirements.txt pypi
  • matplotlib >=3.4.2
  • networkx >=2.8.4
  • nibabel >=3.1.0
  • numpy >=1.18.1
  • pandas >=1.2.4
  • pillow >=8.4.0
  • scikit-image >=0.19.1
  • scipy >=1.4.1
  • templateflow >=0.6.3
setup.py pypi
  • matplotlib >=3.3.3
  • nibabel >=3.1.0
  • numpy >=1.18.1
  • scipy >=1.4.1
  • templateflow >=0.6.3