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brainglobe-heatmap

Rendering anatomical heatmaps with brainrender and matplotlib

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

Science Score: 57.0%

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Keywords

atlas brainglobe neuroanatomy visualization
Last synced: 6 months ago · JSON representation ·

Repository

Rendering anatomical heatmaps with brainrender and matplotlib

Basic Info
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  • Stars: 44
  • Watchers: 4
  • Forks: 15
  • Open Issues: 8
  • Releases: 9
Topics
atlas brainglobe neuroanatomy visualization
Created about 4 years ago · Last pushed 6 months ago
Metadata Files
Readme License Citation

README.md

Python Version PyPI Downloads Wheel Development Status Tests codecov Code style: black Imports: isort pre-commit Contributions Twitter

brainglobe-heatmap

brainglobe-heatmap allows you to create heatmaps, mapping scalar values for each brain region (e.g., number of labelled cells in each region) to a color and creating visualizations in 2D (using matplotlib or 3D (using brainrender).

Hansen_2025_Fig1

2D heatmap generated using matplotlib - adapted from Fig 1. from Hansen et al (2025)

heatmap_3d

3D heatmap generated using brainrender

Usage

For full documentation, please see the BrainGlobe documentation. Examples can be found in the examples directory of this repository.

Quickstart

Installation

pip install brainglobe-heatmap

2D heatmap

```python

import brainglobe_heatmap as bgh

values = dict( # scalar values for each region TH=1, RSP=0.2, AI=0.4, SS=-3, MO=2.6, PVZ=-4, LZ=-3, VIS=2, AUD=0.3, RHP=-0.2, STR=0.5, CB=0.5, FRP=-1.7, HIP=3, PA=-4, )

f = bgh.Heatmap( values, position=5000, orientation="frontal", vmin=-5, vmax=3, format="2D", ).show() ```

3D heatmap

```python

import brainglobe_heatmap as bgh

values = dict( # scalar values for each region TH=1, RSP=0.2, AI=0.4, SS=-3, MO=2.6, PVZ=-4, LZ=-3, VIS=2, AUD=0.3, RHP=-0.2, STR=0.5, CB=0.5, FRP=-1.7, HIP=3, PA=-4, )

scene = bgh.Heatmap( values, position=(8000, 5000, 5000), orientation="frontal", thickness=1000, vmin=-5, vmax=3, format="3D", ).show()

```

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-heatmap

If you use brainglobe-heatmap in your work, please cite it as:

Federico Claudi, Adam Tyson, Luigi Petrucco, Mathieu Bourdenx, carlocastoldi, Rami Hamati, & Alessandro Felder. (2024). brainglobe/brainglobe-heatmap. Zenodo. https://doi.org/10.5281/zenodo.10375287

If you use brainrender via brainglobe-heatmap (i.e. for 3D visualisation), please also cite it: Claudi, F., Tyson, A. L., Petrucco, L., Margrie, T.W., Portugues, R., Branco, T. (2021) "Visualizing anatomically registered data with Brainrender&quot; <i>eLife</i> 2021;10:e65751 [doi.org/10.7554/eLife.65751](https://doi.org/10.7554/eLife.65751)

BibTeX:

bibtex @article{Claudi2021, author = {Claudi, Federico and Tyson, Adam L. and Petrucco, Luigi and Margrie, Troy W. and Portugues, Ruben and Branco, Tiago}, doi = {10.7554/eLife.65751}, issn = {2050084X}, journal = {eLife}, pages = {1--16}, pmid = {33739286}, title = {{Visualizing anatomically registered data with brainrender}}, volume = {10}, year = {2021} }

Owner

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

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-heatmap
message: >-
  If you use this software, please cite it using the
  metadata from this file.
type: software
authors:
  - given-names: Federico
    family-names: Claudi
  - given-names: Luigi
    family-names: Petrucco
  - given-names: BrainGlobe
    family-names: Developers
    email: hello@brainglobe.info
repository-code: 'https://github.com/brainglobe/brainglobe-heatmap'
url: 'https://brainglobe.info'
abstract: >-
  brainglobe-heatmap allows you to create heatmaps, mapping
  scalar values for each brain region (e.g., number of
  labelled cells in each region) to a color and creating
  beautiful visualizations in 2D or 3D.
license: MIT
date-released: '2023-12-23'
doi: 10.5281/zenodo.10375274
year: 2023

GitHub Events

Total
  • Create event: 14
  • Release event: 2
  • Issues event: 11
  • Watch event: 8
  • Delete event: 11
  • Issue comment event: 50
  • Push event: 29
  • Pull request review comment event: 15
  • Pull request review event: 41
  • Pull request event: 46
  • Fork event: 5
Last Year
  • Create event: 14
  • Release event: 2
  • Issues event: 11
  • Watch event: 8
  • Delete event: 11
  • Issue comment event: 50
  • Push event: 29
  • Pull request review comment event: 15
  • Pull request review event: 41
  • Pull request event: 46
  • Fork event: 5

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 7
  • Total pull requests: 50
  • Average time to close issues: about 15 hours
  • Average time to close pull requests: 7 days
  • Total issue authors: 5
  • Total pull request authors: 11
  • Average comments per issue: 0.57
  • Average comments per pull request: 1.24
  • Merged pull requests: 39
  • Bot issues: 0
  • Bot pull requests: 18
Past Year
  • Issues: 5
  • Pull requests: 23
  • Average time to close issues: about 15 hours
  • Average time to close pull requests: 10 days
  • Issue authors: 4
  • Pull request authors: 6
  • Average comments per issue: 0.8
  • Average comments per pull request: 1.83
  • Merged pull requests: 18
  • Bot issues: 0
  • Bot pull requests: 11
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Top Authors
Issue Authors
  • adamltyson (3)
  • zenWai (2)
  • leesuyee (2)
  • alessandrofelder (1)
  • joseale2310 (1)
  • IgorTatarnikov (1)
Pull Request Authors
  • pre-commit-ci[bot] (20)
  • adamltyson (13)
  • IgorTatarnikov (8)
  • carlocastoldi (4)
  • zenWai (3)
  • willGraham01 (2)
  • lochhh (1)
  • K-Meech (1)
  • alessandrofelder (1)
  • samclothier (1)
  • RobertoDF (1)
Top Labels
Issue Labels
bug (5) enhancement (4) good first issue (1)
Pull Request Labels
enhancement (1) bug (1)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 554 last-month
  • Total dependent packages: 2
  • Total dependent repositories: 0
  • Total versions: 7
  • Total maintainers: 1
pypi.org: brainglobe-heatmap

Rendering anatomical heatmaps with brainrender and matplotlib

  • Versions: 7
  • Dependent Packages: 2
  • Dependent Repositories: 0
  • Downloads: 554 Last month
Rankings
Dependent packages count: 10.2%
Average: 38.6%
Dependent repos count: 67.0%
Maintainers (1)
alessandrofelder
Last synced: 6 months ago

Dependencies

pyproject.toml pypi
.github/workflows/test_and_deploy.yml actions
  • actions/download-artifact v3 composite
  • neuroinformatics-unit/actions/build_sdist_wheels v2 composite
  • neuroinformatics-unit/actions/check_manifest v2 composite
  • neuroinformatics-unit/actions/lint v2 composite
  • neuroinformatics-unit/actions/test v2 composite
  • pypa/gh-action-pypi-publish v1.5.0 composite