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

TitleAutomated high-throughput mouse transsynaptic viral tracing using iDISCO+ tissue clearing, light-sheet microscopy, and BrainPipe.
Publication TypeJournal Article
Year of Publication2022
AuthorsPisano, TJ, Hoag, AT, Dhanerawala, ZM, Guariglia, SR, Jung, C, Boele, H-J, Seagraves, KM, Verpeut, JL, Wang, SS-H
JournalSTAR Protoc
Volume3
Issue2
Pagination101289
Date Published2022/06/17
ISSN2666-1667
KeywordsAnimals, Brain, Cerebellum, Mice, Microscopy, Fluorescence, Software
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).

DOI10.1016/j.xpro.2022.101289
Alternate JournalSTAR Protoc
PubMed ID35496792
PubMed Central IDPMC9038781