Protocol for using serial two-photon tomography to map cell types and cerebrovasculature at single-cell resolution in the whole adult mouse brain
Summary: Here, we present a protocol using serial two-photon tomography (STPT) to quantitatively map genetically defined cell types and cerebrovasculature at single-cell resolution across the entire adult mouse brain. We describe the preparation of brain tissue and sample embedding for cell type and...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2023-03-01
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| Series: | STAR Protocols |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2666166723000060 |
| _version_ | 1797946317203308544 |
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| author | Josephine K. Liwang Hannah C. Bennett Hyun-Jae Pi Yongsoo Kim |
| author_facet | Josephine K. Liwang Hannah C. Bennett Hyun-Jae Pi Yongsoo Kim |
| author_sort | Josephine K. Liwang |
| collection | DOAJ |
| description | Summary: Here, we present a protocol using serial two-photon tomography (STPT) to quantitatively map genetically defined cell types and cerebrovasculature at single-cell resolution across the entire adult mouse brain. We describe the preparation of brain tissue and sample embedding for cell type and vascular STPT imaging and image processing using MATLAB codes. We detail the computational analyses for cell signal detection, vascular tracing, and three-dimensional image registration to anatomical atlases, which can be implemented for brain-wide mapping of different cell types.For complete details on the use and execution of this protocol, please refer to Wu et al. (2022),1 Son et al. (2022),2 Newmaster et al. (2020),3 Kim et al. (2017),4 and Ragan et al. (2012).5 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. |
| first_indexed | 2024-04-10T21:09:06Z |
| format | Article |
| id | doaj.art-be48413c0537486095ac64e9e645afcf |
| institution | Directory Open Access Journal |
| issn | 2666-1667 |
| language | English |
| last_indexed | 2024-04-10T21:09:06Z |
| publishDate | 2023-03-01 |
| publisher | Elsevier |
| record_format | Article |
| series | STAR Protocols |
| spelling | doaj.art-be48413c0537486095ac64e9e645afcf2023-01-21T04:21:39ZengElsevierSTAR Protocols2666-16672023-03-0141102048Protocol for using serial two-photon tomography to map cell types and cerebrovasculature at single-cell resolution in the whole adult mouse brainJosephine K. Liwang0Hannah C. Bennett1Hyun-Jae Pi2Yongsoo Kim3Department of Neural and Behavioral Sciences, College of Medicine, The Pennsylvania State University, Hershey, PA 17033, USADepartment of Neural and Behavioral Sciences, College of Medicine, The Pennsylvania State University, Hershey, PA 17033, USADepartment of Neural and Behavioral Sciences, College of Medicine, The Pennsylvania State University, Hershey, PA 17033, USADepartment of Neural and Behavioral Sciences, College of Medicine, The Pennsylvania State University, Hershey, PA 17033, USA; Corresponding authorSummary: Here, we present a protocol using serial two-photon tomography (STPT) to quantitatively map genetically defined cell types and cerebrovasculature at single-cell resolution across the entire adult mouse brain. We describe the preparation of brain tissue and sample embedding for cell type and vascular STPT imaging and image processing using MATLAB codes. We detail the computational analyses for cell signal detection, vascular tracing, and three-dimensional image registration to anatomical atlases, which can be implemented for brain-wide mapping of different cell types.For complete details on the use and execution of this protocol, please refer to Wu et al. (2022),1 Son et al. (2022),2 Newmaster et al. (2020),3 Kim et al. (2017),4 and Ragan et al. (2012).5 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.http://www.sciencedirect.com/science/article/pii/S2666166723000060BioinformaticsSingle CellHealth SciencesMicroscopyNeuroscienceComputer Sciences |
| spellingShingle | Josephine K. Liwang Hannah C. Bennett Hyun-Jae Pi Yongsoo Kim Protocol for using serial two-photon tomography to map cell types and cerebrovasculature at single-cell resolution in the whole adult mouse brain STAR Protocols Bioinformatics Single Cell Health Sciences Microscopy Neuroscience Computer Sciences |
| title | Protocol for using serial two-photon tomography to map cell types and cerebrovasculature at single-cell resolution in the whole adult mouse brain |
| title_full | Protocol for using serial two-photon tomography to map cell types and cerebrovasculature at single-cell resolution in the whole adult mouse brain |
| title_fullStr | Protocol for using serial two-photon tomography to map cell types and cerebrovasculature at single-cell resolution in the whole adult mouse brain |
| title_full_unstemmed | Protocol for using serial two-photon tomography to map cell types and cerebrovasculature at single-cell resolution in the whole adult mouse brain |
| title_short | Protocol for using serial two-photon tomography to map cell types and cerebrovasculature at single-cell resolution in the whole adult mouse brain |
| title_sort | protocol for using serial two photon tomography to map cell types and cerebrovasculature at single cell resolution in the whole adult mouse brain |
| topic | Bioinformatics Single Cell Health Sciences Microscopy Neuroscience Computer Sciences |
| url | http://www.sciencedirect.com/science/article/pii/S2666166723000060 |
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