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

doi:10.21769/BioProtoc.4854

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

Bio Protoc. 2023 Oct 20;13(20):e4854. doi: 10.21769/BioProtoc.4854.

Authors

Emily Jane Dennis^{1

2

3}, Peter Bibawi^{1

4}, Zahra M Dhanerawala^{1

5}, Laura A Lynch¹, Samuel S-H Wang¹, Carlos D Brody^{1

3}

Affiliations

¹ Princeton Neuroscience Institute, Princeton University, Princeton, New Jersey, USA.
² Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA.
³ Howard Hughes Medical Institute, Princeton University, Princeton, USA.
⁴ Neurology Department, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
⁵ Washington University School of Medicine, St. Louis, Missouri, USA.

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. Key features • This protocol adapts iDISCO (Renier et al., 2014) and uDISCO (Pan et al., 2016) tissue-clearing techniques to consistently clear rat brains. • This protocol also decreases the number of working hours per day to fit in an 8 h workday. Graphical overview.

Keywords: Image registration; Light-sheet imaging; Neuroscience; Rat; Rattus norvegicus; Tissue clearing; iDISCO; uDISCO.

Abstract

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