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

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 journal › Article › peer-review

2 Scopus citations

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 language	English (US)
Article number	101289
Journal	STAR Protocols
Volume	3
Issue number	2
DOIs	https://doi.org/10.1016/j.xpro.2022.101289
State	Published - Jun 17 2022

All Science Journal Classification (ASJC) codes

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

Keywords

Bioinformatics
Computer sciences
Microscopy
Neuroscience

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10.1016/j.xpro.2022.101289

Cite this

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title = "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).",

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doi = "10.1016/j.xpro.2022.101289",

language = "English (US)",

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AU - Hoag, Austin T.

AU - Dhanerawala, Zahra M.

AU - Guariglia, Sara R.

AU - Jung, Caroline

AU - Boele, Henk Jan

AU - Seagraves, Kelly M.

AU - Verpeut, Jessica L.

AU - Wang, Samuel S.H.

PY - 2022/6/17

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KW - Microscopy

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

Abstract

All Science Journal Classification (ASJC) codes

Keywords

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