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Automated high-throughput mouse transsynaptic viral tracing using iDISCO+ tissue clearing, light-sheet microscopy, and BrainPipe.

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).

SUBMITTER: Pisano TJ

PROVIDER: S-EPMC9038781 | biostudies-literature | 2022 Jun

REPOSITORIES: biostudies-literature

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Automated high-throughput mouse transsynaptic viral tracing using iDISCO+ tissue clearing, light-sheet microscopy, and BrainPipe.

Pisano Thomas J TJ Hoag Austin T AT Dhanerawala Zahra M ZM Guariglia Sara R SR Jung Caroline C Boele Henk-Jan HJ Seagraves Kelly M KM Verpeut Jessica L JL Wang Samuel S-H SS

STAR protocols 20220414 2

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 cer ...[more]

PMID: 35496792

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