Princeton RAtlas: A Common Coordinate Framework for Fully cleared, Whole Rattus norvegicus Brains

Emily Jane Dennis, Peter Bibawi, Zahra M. Dhanerawala, Laura A. Lynch, Samuel S.H. Wang, Carlos D. Brody

Research output: Contribution to journalArticlepeer-review

Abstract

Whole-brain clearing and imaging methods are becoming more common in mice but have yet to become standard in rats, at least partially due to inadequate clearing from most available protocols. Here, we build on recent mouse-tissue clearing and light-sheet imaging methods and develop and adapt them to rats. We first used cleared rat brains to create an open-source, 3D rat atlas at 25 μm resolution. We then registered and imported other existing labeled volumes and made all of the code and data available for the community (https://github.com/emilyjanedennis/PRA) to further enable modern, whole-brain neuroscience in the rat.

Original languageEnglish (US)
Article numbere4854
JournalBio-protocol
Volume13
Issue number20
DOIs
StatePublished - Oct 20 2023

All Science Journal Classification (ASJC) codes

  • Neuroscience(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Immunology and Microbiology(all)
  • Plant Science

Keywords

  • Image registration
  • Light-sheet imaging
  • Neuroscience
  • Rat
  • Rattus norvegicus
  • Tissue clearing
  • iDISCO
  • uDISCO

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