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Method Article
Shanina Robbins
Thomas Jefferson University
Corresponding Author
ORCiD: https://orcid.org/0000-0002-7885-743X
Rajanikanth Vadigepalli
Thomas Jefferson University
Corresponding Author
ORCiD: https://orcid.org/0000-0002-8405-1037
License:
This work is licensed under a CC BY 4.0 License. Read Full License
The present protocol describes the process of using the MBF Bioscience Tissue Mapper software to create a 3D reconstructed stack from contouring the block face images of serial cryosections and mark the individual immunolabeled cells onto the contoured images. The stack of aligned, contoured and annotated images can be visualized as a 3D reconstruction that depicts the tissue shape as it was embedded and cryosectioned, relative positions of various tissue features, and locations of individually marked neurons within the tissue, yielding a 3D anatomical map of the distribution of cells of interest with a tissue. This protocol can be used in conjunction with other protocols for sampling spatially-tracked single neurons using laser capture micro-dissection and assessed for molecular profiles using transcriptomics approaches. Such integration extends the present protocol to enable 3D visualization of molecular data in conjunction with the anatomical information for spatial transcriptomic analysis.
Keywords
3D Mapping, Single Cell, tissue reconstruction, MBF, cryosection, Laser Capture Microdissection, LCM
N/A
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Version History
CURRENT STATUS: Posted
Version 1
Posted 26 May, 2021
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Subject Areas
Biological techniques
Associated Publications
A Comprehensive Integrated Anatomical And Molecular Atlas Of Rodent Intrinsic Cardiac Nervous System
by Sirisha Achanta, Jonathan Gorky, Clara Leung, +12
An open repository of community-contributed protocols sponsored by Nature Research.
Learn more about Protocol Exchange
Method Article
Shanina Robbins
Thomas Jefferson University
Corresponding Author
ORCiD: https://orcid.org/0000-0002-7885-743X
Rajanikanth Vadigepalli
Thomas Jefferson University
Corresponding Author
ORCiD: https://orcid.org/0000-0002-8405-1037
Version History
CURRENT STATUS: Posted
Version 1
Posted 26 May, 2021
No community comments so far
Metrics
Comments: 0
HTML Views: ...
Subject Areas
Biological techniques
License:
This work is licensed under a CC BY 4.0 License. Read Full License
The present protocol describes the process of using the MBF Bioscience Tissue Mapper software to create a 3D reconstructed stack from contouring the block face images of serial cryosections and mark the individual immunolabeled cells onto the contoured images. The stack of aligned, contoured and annotated images can be visualized as a 3D reconstruction that depicts the tissue shape as it was embedded and cryosectioned, relative positions of various tissue features, and locations of individually marked neurons within the tissue, yielding a 3D anatomical map of the distribution of cells of interest with a tissue. This protocol can be used in conjunction with other protocols for sampling spatially-tracked single neurons using laser capture micro-dissection and assessed for molecular profiles using transcriptomics approaches. Such integration extends the present protocol to enable 3D visualization of molecular data in conjunction with the anatomical information for spatial transcriptomic analysis.
N/A
This is a list of supplementary files associated with this preprint. Click to download.
Loading...
Associated Publications
A Comprehensive Integrated Anatomical And Molecular Atlas Of Rodent Intrinsic Cardiac Nervous System
by Sirisha Achanta, Jonathan Gorky, Clara Leung, +12