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Updated: Sep 25, 2025
Viral Tracing of Genetically Defined Neural Circuitry
Published on: October 17, 2012
Automated high-throughput mouse transsynaptic viral tracing using iDISCO+ tissue clearing, light-sheet microscopy,
Thomas J Pisano1, Austin T Hoag1, Zahra M Dhanerawala1
1Neuroscience Institute, Princeton University, Washington Road, Princeton, NJ 08544, USA.
Abstract:
Transsynaptic viral tracing requires tissue sectioning, manual cell counting, and anatomical assignment, all of which are time intensive. We describe a protocol for BrainPipe, a scalable software for automated anatomical alignment and object counting in light-sheet microscopy volumes. BrainPipe can be generalized to new counting tasks by using a new atlas and training a neural network for object detection. Combining viral tracing, iDISCO+ tissue clearing, and BrainPipe facilitates mapping of cerebellar connectivity to the rest of the murine brain. For complete details on the use and execution of this protocol, please refer to Pisano et al. (2021).
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