| Title | Automated high-throughput mouse transsynaptic viral tracing using iDISCO+ tissue clearing, light-sheet microscopy, and BrainPipe. |
| Publication Type | Journal Article |
| Year of Publication | 2022 |
| Authors | Pisano, TJ, Hoag, AT, Dhanerawala, ZM, Guariglia, SR, Jung, C, Boele, H-J, Seagraves, KM, Verpeut, JL, Wang, SS-H |
| Journal | STAR Protoc |
| Volume | 3 |
| Issue | 2 |
| Pagination | 101289 |
| Date Published | 2022 Jun 17 |
| ISSN | 2666-1667 |
| Keywords | Animals, Brain, Cerebellum, Mice, Microscopy, Fluorescence, Software |
| Abstract | <p>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).</p> |
| DOI | 10.1016/j.xpro.2022.101289 |
| Alternate Journal | STAR Protoc |
| PubMed ID | 35496792 |
| PubMed Central ID | PMC9038781 |
| Grant List | R01 NS045193 / NS / NINDS NIH HHS / United States R01 MH115750 / MH / NIMH NIH HHS / United States U19 NS104648 / NS / NINDS NIH HHS / United States F31 NS089303 / NS / NINDS NIH HHS / United States |
