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

Thomas J. Pisano, Austin T. Hoag, Zahra M. Dhanerawala, Sara R. Guariglia, Caroline Jung, Henk Jan Boele, Kelly M. Seagraves, Jessica L. Verpeut, Samuel S.H. Wang

Research output: Contribution to journalArticlepeer-review

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).

Original languageEnglish (US)
Article number101289
JournalSTAR Protocols
Volume3
Issue number2
DOIs
StatePublished - Jun 17 2022

Keywords

  • Bioinformatics
  • Computer sciences
  • Microscopy
  • Neuroscience

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Neuroscience(all)
  • Immunology and Microbiology(all)

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