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

Area of Science:

• Neuroscience
• Biotechnology
• Imaging Science

Background:

• Whole-brain clearing and imaging are established in mice but not rats.
• Existing protocols inadequately clear rat brains for advanced imaging.
• This limits whole-brain neuroscience research in rat models.

Purpose of the Study:

• Adapt and optimize existing tissue-clearing methods for rat brains.
• Develop an open-source, high-resolution 3D rat brain atlas.
• Facilitate advanced whole-brain neuroscience studies in rats.

Main Methods:

• Adapted iDISCO and uDISCO tissue-clearing techniques for rat brains.
• Developed an 8-hour workday protocol for increased efficiency.
• Created a 25 μm resolution 3D rat brain atlas using cleared tissue.

Main Results:

• Successfully adapted and optimized tissue-clearing protocols for consistent rat brain clearing.
• Generated an open-source 3D rat brain atlas with 25 μm resolution.
• Registered and imported existing labeled volumes into the atlas.
• Made all code and data publicly available.

Conclusions:

• The developed protocol enables consistent whole-brain clearing in rats.
• The open-source 3D rat atlas and associated data significantly advance rat neuroscience.
• This work lowers barriers for modern whole-brain imaging and analysis in rats.