geobrain 0.1.1

An interactive framework for atlas-based visualization of quantitative histological traits.

GeoBrain is an interactive Python framework for atlas-based visualization of quantitative histological data. It maps region-wise metrics derived from atlas-registered workflows, such as QUINT [1], onto the Allen Mouse Brain Common Coordinate Framework (CCFv3) [2]. Built on Plotly, geobrain provides interactive 2D atlas navigation, group comparisons, customizable color mapping, web-based dashboard for exploratory analysis and publication-quality exports.

Installation

Requires Python 3.12+. Install from PyPI:

uv venv
source .venv/bin/activate      # Linux / macOS
.venv\Scripts\activate         # Windows
uv pip install geobrain

Or from source:

git clone https://github.com/anna-teruel/geobrain
cd geobrain
uv venv
.venv\Scripts\activate
uv pip install .

Then launch the dashboard with:

geobrain

Documentation

• Using the dashboard — launching the app and the full workflow: load atlas, build slices, compute scores, view and export.
• Filtering & coloring rendered slices — how to color regions by score, filter and select which regions stay highlighted, and apply a flat color.
• Understanding Scores — score definitions, normalization methods and interpretation.
• Tutorial — end-to-end example using the API.

License

This project is licensed under the MIT License © 2026 Anna Teruel-Sanchis and Konrad Danielewski.

See the LICENSE file for details.

References

[1] Yates, S. C., et al. (2019). QUINT: Workflow for Quantification and Spatial Analysis of Features in Histological Images From Rodent Brain. Frontiers in Neuroinformatics, 13, 75.

[2] Wang, Q., et al. (2020). The Allen Mouse Brain Common Coordinate Framework: A 3D Reference Atlas. Cell, 181(4), 936–953.e20.