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Vesalius: high‐resolution in silico anatomization of spatial transcriptomic data using image analysis
Characterization of tissue architecture promises to deliver insights into development, cell communication, and disease. In silico spatial domain retrieval methods have been developed for spatial transcriptomics (ST) data assuming transcriptional similarity of neighboring barcodes. However, domain re...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
John Wiley and Sons Inc.
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9446088/ https://www.ncbi.nlm.nih.gov/pubmed/36065846 http://dx.doi.org/10.15252/msb.202211080 |
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author | Martin, Patrick C N Kim, Hyobin Lövkvist, Cecilia Hong, Byung‐Woo Won, Kyoung Jae |
author_facet | Martin, Patrick C N Kim, Hyobin Lövkvist, Cecilia Hong, Byung‐Woo Won, Kyoung Jae |
author_sort | Martin, Patrick C N |
collection | PubMed |
description | Characterization of tissue architecture promises to deliver insights into development, cell communication, and disease. In silico spatial domain retrieval methods have been developed for spatial transcriptomics (ST) data assuming transcriptional similarity of neighboring barcodes. However, domain retrieval approaches with this assumption cannot work in complex tissues composed of multiple cell types. This task becomes especially challenging in cellular resolution ST methods. We developed Vesalius to decipher tissue anatomy from ST data by applying image processing technology. Vesalius uniquely detected territories composed of multiple cell types and successfully recovered tissue structures in high‐resolution ST data including in mouse brain, embryo, liver, and colon. Utilizing this tissue architecture, Vesalius identified tissue morphology‐specific gene expression and regional specific gene expression changes for astrocytes, interneuron, oligodendrocytes, and entorhinal cells in the mouse brain. |
format | Online Article Text |
id | pubmed-9446088 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | John Wiley and Sons Inc. |
record_format | MEDLINE/PubMed |
spelling | pubmed-94460882022-09-09 Vesalius: high‐resolution in silico anatomization of spatial transcriptomic data using image analysis Martin, Patrick C N Kim, Hyobin Lövkvist, Cecilia Hong, Byung‐Woo Won, Kyoung Jae Mol Syst Biol Methods Characterization of tissue architecture promises to deliver insights into development, cell communication, and disease. In silico spatial domain retrieval methods have been developed for spatial transcriptomics (ST) data assuming transcriptional similarity of neighboring barcodes. However, domain retrieval approaches with this assumption cannot work in complex tissues composed of multiple cell types. This task becomes especially challenging in cellular resolution ST methods. We developed Vesalius to decipher tissue anatomy from ST data by applying image processing technology. Vesalius uniquely detected territories composed of multiple cell types and successfully recovered tissue structures in high‐resolution ST data including in mouse brain, embryo, liver, and colon. Utilizing this tissue architecture, Vesalius identified tissue morphology‐specific gene expression and regional specific gene expression changes for astrocytes, interneuron, oligodendrocytes, and entorhinal cells in the mouse brain. John Wiley and Sons Inc. 2022-09-06 /pmc/articles/PMC9446088/ /pubmed/36065846 http://dx.doi.org/10.15252/msb.202211080 Text en © 2022 The Authors. Published under the terms of the CC BY 4.0 license. https://creativecommons.org/licenses/by/4.0/This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Methods Martin, Patrick C N Kim, Hyobin Lövkvist, Cecilia Hong, Byung‐Woo Won, Kyoung Jae Vesalius: high‐resolution in silico anatomization of spatial transcriptomic data using image analysis |
title | Vesalius: high‐resolution in silico anatomization of spatial transcriptomic data using image analysis |
title_full | Vesalius: high‐resolution in silico anatomization of spatial transcriptomic data using image analysis |
title_fullStr | Vesalius: high‐resolution in silico anatomization of spatial transcriptomic data using image analysis |
title_full_unstemmed | Vesalius: high‐resolution in silico anatomization of spatial transcriptomic data using image analysis |
title_short | Vesalius: high‐resolution in silico anatomization of spatial transcriptomic data using image analysis |
title_sort | vesalius: high‐resolution in silico anatomization of spatial transcriptomic data using image analysis |
topic | Methods |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9446088/ https://www.ncbi.nlm.nih.gov/pubmed/36065846 http://dx.doi.org/10.15252/msb.202211080 |
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