Brainrender: a python-based software for visualizing anatomically registered data

Abstract

Here we present brainrender, an open source python package for rendering three-dimensional neuroanatomical data aligned to the Allen Mouse Atlas. Brainrender can be used to explore, visualise and compare data from publicly available datasets (e.g. from the Mouse Light project from Janelia) as well as data generated within individual laboratories. Brainrender facilitates the exploration of neuroanatomical data with three-dimensional renderings, aiding the design and interpretation of experiments and the dissemination of anatomical findings. Additionally, brainrender can also be used to generate high-quality, publication-ready, figures for scientific publications. -wide atlas of gene expression in the adult mouse brain. Nature, 445(7124):168-176, January 2007.

BrainGlobe Atlas API: a common interface for neuroanatomical atlases

“…The same code can be used for easily developing new atlases in BG-AtlasAPI's format and we encourage users to contribute new atlases to the project by submitting new scripts to bg-atlasgen. BG-atlasAPI's flexible infrastructure already proved crucial in the development and extension of two software tools for use in neuroscience: brainreg (Tyson, Rousseau, & Margrie, 2020) for 3D registration of image data between sample and atlas coordinate space and brainrender (Claudi, Tyson, & Branco, 2020) for 3D visualisation of both user-generated data and atlas data. We hope that other developers will use the API, and develop tools that can be used across neuroscience and other research fields, increasing their reach, and preventing duplication of effort.…”

The mouse brain after foot-shock in 4D: temporal dynamics at a single-cell resolution

“…Abbreviations are explained in Suppl. Table 2. c) Cartoon of the brain areas identified in b; created with brainrender 8 d). Functional order of brain areas’ c-fos activity following foot-shock.…”

“…The dashed box indicates the mean and SD per group along the posterior-anterior axis. c) Cartoon visualization of the right BLA in the same orientation of a1 and b, created with brainrender (Claudi et al, 2020). Brain areas use different strategies of activation, which can change after stress…”

A deep learning algorithm for 3D cell detection in whole mouse brain image datasets

“…This deformation field was applied to the coordinates of the detected cells for each sample, transforming them into atlas coordinate space. Plots were generated using Matplotlib (62), and image visualisation was performed using napari (54) and brainrender (63).…”