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).

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

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

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

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:

@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}
}