Signals, Symbols, and Systems

Mouse 3D Atlas

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

By

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.

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This interactive tool allows you to explore the mouse brain in 3D. It combines compartment data from the Allen Mouse Brain Atlas lein2007allen with individual neuron reconstructions from the Janelia MouseLight Project winnubst2019mouselight.

Mouse 3D Atlas

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

@article{lein2007allen, title = {Genome-Wide Atlas of Gene Expression in the Adult Mouse Brain}, author = {Lein, Ed S. and Hawrylycz, Michael J. and Ao, Nancy and Ayres, Mikael and Bensinger, Amy and Bernard, Amy and Boe, Andrew F. and Boguski, Mark S. and Brockway, Kevin S. and Byrnes, Emi J. and Chen, Lin and Chen, Li and Chen, Tsuey-Ming and Chi Chin, Mei and Chong, Jimmy and Crook, Brian E. and Czaplinska, Aneta and Dang, Chinh N. and Datta, Suvro and Dee, Nick R. and Desaki, Aimee L. and Desta, Tsega and Diep, Ellen and Dolbeare, Tim A. and Donelan, Matthew J. and Dong, Hong-Wei and Dougherty, Jennifer G. and Duncan, Ben J. and Ebbert, Amanda J. and Eichele, Gregor and Estin, Lili K. and Faber, Casey and Facer, Benjamin A. and Fields, Rick and Fischer, Shanna R. and Fliss, Tim P. and Frensley, Cliff and Gates, Sabrina N. and Glattfelder, Katie J. and Halverson, Kevin R. and Hart, Matthew R. and Hohmann, John G. and Howell, Maureen P. and Jeung, Darren P. and Johnson, Rebecca A. and Karr, Patrick T. and Kawal, Reena and Kidney, Jolene M. and Knapik, Rachel H. and Kuan, Chihchau L. and Lake, James H. and Laramee, Annabel R. and Larsen, Kirk D. and Lau, Christopher and Lemon, Tracy A. and Liang, Agnes J. and Liu, Ying and Luong, Lon T. and Michaels, Jesse and Morgan, Judith J. and Morgan, Rebecca J. and Mortrud, Marty T. and Mosqueda, Nerick F. and Ng, Lydia L. and Ng, Randy and Orta, Geralyn J. and Overly, Caroline C. and Pak, Tu H. and Parry, Sheana E. and Pathak, Sayan D. and Pearson, Owen C. and Puchalski, Ralph B. and Riley, Zackery L. and Rockett, Hannah R. and Rowland, Stephen A. and Royall, Joshua J. and Ruiz, Marcos J. and Sarno, Nadia R. and Schaffnit, Katherine and Shapovalova, Nadiya V. and Sivisay, Taz and Slaughterbeck, Clifford R. and Smith, Simon C. and Smith, Kimberly A. and Smith, Bryan I. and Sodt, Andy J. and Stewart, Nick N. and Stumpf, Kenda-Ruth and Sunkin, Susan M. and Sutram, Madhavi and Tam, Angelene and Teemer, Carey D. and Thaller, Christina and Thompson, Carol L. and Varnam, Lee R. and Visel, Axel and Whitlock, Ray M. and Wohnoutka, Paul E. and Wolkey, Crissa K. and Wong, Victoria Y. and Wood, Matthew and Yaylaoglu, Murat B. and Young, Rob C. and Youngstrom, Brian L. and Feng Yuan, Xu and Zhang, Bin and Zwingman, Theresa A. and Jones, Allan R.}, year = 2007, month = jan, day = {01}, journal = {Nature}, volume = 445, number = 7124, pages = {168–176}, doi = {10.1038/nature05453}, issn = {1476–4687}, url = {https:\/\/doi.org/10.1038/nature05453}, } @article{winnubst2019mouselight, author = {Winnubst, Johan and Bas, Erhan and Ferreira, Tiago and Wu, Zhuhao and Economo, Michael and Edson, Patrick and Arthur, Ben and Bruns, Christopher and Rokicki, Konrad and Schauder, David and Olbris, Donald and Murphy, Sean and Ackerman, David and Arshadi, Cameron and Baldwin, Perry and Blake, Regina and Hasan, Mashtura and Ramirez, Daniel and Chandrashekar, Jayaram}, year = {2019}, month = {09}, pages = {}, title = {Reconstruction of 1,000 Projection Neurons Reveals New Cell Types and Organization of Long-Range Connectivity in the Mouse Brain}, volume = {179}, journal = {Cell}, doi = {10.1016/j.cell.2019.07.042}, url = {http:\/\/doi.org/10.1016/j.cell.2019.07.042} }

Citation

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

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