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

doi:10.1016/j.xpro.2022.101289

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

STAR Protoc. 2022 Apr 14;3(2):101289. doi: 10.1016/j.xpro.2022.101289. eCollection 2022 Jun 17.

Authors

Thomas J Pisano¹, Austin T Hoag¹, Zahra M Dhanerawala¹, Sara R Guariglia¹, Caroline Jung¹, Henk-Jan Boele^{1

2}, Kelly M Seagraves¹, Jessica L Verpeut¹, Samuel S-H Wang¹

Affiliations

¹ Neuroscience Institute, Princeton University, Washington Road, Princeton, NJ 08544, USA.
² Department of Neuroscience, Erasmus University Medical Center, Rotterdam, the Netherlands.

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).

Keywords: Bioinformatics; Computer sciences; Microscopy; Neuroscience.

Publication types

Research Support, Non-U.S. Gov't
Research Support, N.I.H., Extramural

MeSH terms

Animals
Brain* / diagnostic imaging
Cerebellum*
Mice
Microscopy, Fluorescence / methods
Software

Abstract

Publication types

MeSH terms

Grants and funding