Mouse 3D Atlas

Explore mouse brain areas and individual neurons with this interactive tool.

Nikhil Bhattasali

Published

10 Nov 2020

Reading Time

4 min

Tags

neurosciencemouse brain

Updated

9 Jan 2021

Importance

Highlights

This interactive tool allows you to explore the mouse brain in 3D.

This interactive tool allows you to explore the mouse brain in 3D. It combines compartment data from the Allen Mouse Brain Atlas

[1]

with individual neuron reconstructions from the Janelia MouseLight Project

[2]

Check it out: https://mouse-brain.nikhilxb.vercel.app/atlas

Features:

Show meshes (grey matter, white matter, ventricles) at different levels of detail.
Orbit, pan, and zoom around meshes of interest.
Explode model like an engineering diagram.
Change mesh materials: hidden, transparent, visible.
Change mesh hemisphere visibility: left, medial, right.
Search for specific neurons to display using the query builder.
Quickly control selection/camera/visibility using Vim-style keyboard shortcuts.
Save camera/object/query state using snapshots.

Acknowledgements

Special thanks to Tom Dean, Fiene Kuijper, and Quintin Frerichs for their helpful feedback on this tool and their always interesting conversations about how to push neuroscience forward. I also greatly appreciate the researchers at the Allen Institute and Janelia Research Campus for curating the public datasets that this tool builds on which are so valuable to the community.

References

Genome-Wide Atlas of Gene Expression in the Adult Mouse Brain [link]
E.S. Lein, M.J. Hawrylycz, N. Ao, M. Ayres, A. Bensinger, A. Bernard, A.F. Boe, M.S. Boguski, K.S. Brockway, E.J. Byrnes, et al. Nature, vol. 445(7124), p. 168–176 (2007).
Reconstruction of 1,000 Projection Neurons Reveals New Cell Types and Organization of Long-Range Connectivity in the Mouse Brain [link]
J. Winnubst, E. Bas, T. Ferreira, Z. Wu, M. Economo, P. Edson, B. Arthur, C. Bruns, K. Rokicki, D. Schauder, et al. Cell, vol. 179, p. (2019).

Citation

@article{mouseatlas2020,
  title   = {Mouse 3D Atlas},
  author  = {Nikhil Bhattasali},
  year    = {2020},
  journal = {Signals, Symbols, and Systems},
  url     = {https://sigsymsys.blog/mouse-atlas/}
}