BrainPainter v2: Mouse Brain Visualization Software

TL;DR

BrainPainter v2 extends the original brain visualization software to generate detailed 3D images of mouse brains, incorporating new views, hemisphere-specific visualizations, and a user-friendly interface, aiding neuroscience research.

Contribution

The paper introduces Mouse Brain visualization capabilities to BrainPainter, along with a Blender-based rendering pipeline and a Docker API interface for improved usability.

Findings

Enables visualization of mouse brain regions based on the Allen Mouse Brain Atlas.

Provides new rendering angles and hemisphere-specific visualization options.

Facilitates modeling of disease progression and complex animations in neuroscience studies.

Abstract

BrainPainter is a software for the 3D visualization of human brain structures; it generates colored brain images using user-defined biomarker data for each brain region. However, BrainPainter is only able to generate human brain images. In this paper, we present updates to the existing BrainPainter software which enables the generation of mouse brain images. We load meshes for each mouse brain region, based on the Allen Mouse Brain Atlas, into Blender, a powerful 3D computer graphics engine. We then use Blender to color each region and generate images of subcortical, outer-cortical, inner-cortical, top and bottom view renders. In addition to those views, we add new render angles and separate visualization settings for the left and right hemispheres. While BrainPainter traditionally ran from the browser ( https://brainpainter.csail.mit.edu ), we also created a graphical user interface that launches image-generation requests in a user-friendly way, by connecting to the Blender backend via a Docker API. We illustrate a use case of BrainPainter for modeling the progression of tau protein accumulation in a mouse study. Our contributions can help neuroscientists visualize brains in mouse studies and show disease progression. In addition, integration into Blender can subsequently enable the generation of complex animations using a moving camera, generation of complex mesh deformations that simulate tumors and other pathologies, as well as visualization of toxic proteins using Blender's particle system.