An interactive 3D atlas of gene expression in the mouse brain

  1. Harry Carey
  2. Sébastien Piluso
  3. Ingvild Bjerke
  4. Xiaoyun Gui
  5. Sharon Yates
  6. Sophia Pieschnik
  7. Signý Benediktsdóttir
  8. Archana Golla
  9. Maja Puchades
  10. Timo Dickscheid
  11. Trygve Leergaard
  12. Simon McMullan
  13. Henry Markram
  14. Daniel Keller
  15. Jan Bjaalie
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Abstract

The Allen Mouse Brain Atlas provides gene expression data for over 20,000 genes and has been extensively used in neuroscience. However, it’s constrained by a resolution of 200 µm³. We improved this to 25 µm³ for 4,083 genes by re-registering 401,660 sections to atlas space. From this, we produced an atlas with regions defined by shared molecular signatures and built an interactive online platform allowing exploration of gene expression patterns.

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