What ultramicroscope settings can be used to achieve imaging of the entire depth of a rat brain?

Evan DeFrancesco
Evan DeFrancesco
Dec 2, 2024
protocol Protocol: Princeton RAtlas: A Common Coordinate Framework for Fully cleared, Whole Rattus norvegicus Brains

Hello again, one more question I have for you is how did you achieve imaging of the entire depth of a rat brain on an ultramicroscope? What was the working distance of the dipping cap you used?


Thank you again!

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Emily Jane Dennis Answered Dec 4, 2024

Janelia Research Campus

Hi again,


I'd recommend calling the company, as the answer will depend on your exact microscope and parts available. We used a 1.1x objective with a 16mm working distance and the provided STL file for a brain holder/chamber. The dipping cap should be chosen based on the refractive index solution used and doesn't have an affect on the working distance. Note that udisco and idisco have different amounts of shrinkage of the brain which will also affect working distances required

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