Vesalius: high-resolution in silico anatomization of spatial transcriptomic data using image analysis

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Standard

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.

I: Molecular Systems Biology, Bind 18, Nr. 9, e11080, 2022.

Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › fagfællebedømt

Harvard

Martin, PCN, Kim, H, Lövkvist, C, Hong, BW & Won, KJ 2022, 'Vesalius: high-resolution in silico anatomization of spatial transcriptomic data using image analysis', Molecular Systems Biology, bind 18, nr. 9, e11080. https://doi.org/10.15252/msb.202211080

APA

Martin, P. C. N., Kim, H., Lövkvist, C., Hong, B. W., & Won, K. J. (2022). Vesalius: high-resolution in silico anatomization of spatial transcriptomic data using image analysis. Molecular Systems Biology, 18(9), [e11080]. https://doi.org/10.15252/msb.202211080

Vancouver

Martin PCN, Kim H, Lövkvist C, Hong BW, Won KJ. Vesalius: high-resolution in silico anatomization of spatial transcriptomic data using image analysis. Molecular Systems Biology. 2022;18(9). e11080. https://doi.org/10.15252/msb.202211080

Author

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. I: Molecular Systems Biology. 2022 ; Bind 18, Nr. 9.

Bibtex

@article{93429c0665cb4309a2c2c6f4522742fb,
title = "Vesalius: high-resolution in silico anatomization of spatial transcriptomic data using image analysis",
abstract = "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.",
keywords = "anatomical territories, spatial domains, spatial transcriptomics, tissue architecture, tissue heterogeneity",
author = "Martin, {Patrick C.N.} and Hyobin Kim and Cecilia L{\"o}vkvist and Hong, {Byung Woo} and Won, {Kyoung Jae}",
note = "Publisher Copyright: {\textcopyright} 2022 The Authors. Published under the terms of the CC BY 4.0 license.",
year = "2022",
doi = "10.15252/msb.202211080",
language = "English",
volume = "18",
journal = "Molecular Systems Biology",
issn = "1744-4292",
publisher = "Wiley-Blackwell",
number = "9",

}

RIS

TY - JOUR

T1 - Vesalius

T2 - high-resolution in silico anatomization of spatial transcriptomic data using image analysis

AU - Martin, Patrick C.N.

AU - Kim, Hyobin

AU - Lövkvist, Cecilia

AU - Hong, Byung Woo

AU - Won, Kyoung Jae

N1 - Publisher Copyright: © 2022 The Authors. Published under the terms of the CC BY 4.0 license.

PY - 2022

Y1 - 2022

N2 - 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.

AB - 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.

KW - anatomical territories

KW - spatial domains

KW - spatial transcriptomics

KW - tissue architecture

KW - tissue heterogeneity

U2 - 10.15252/msb.202211080

DO - 10.15252/msb.202211080

M3 - Journal article

C2 - 36065846

AN - SCOPUS:85137192068

VL - 18

JO - Molecular Systems Biology

JF - Molecular Systems Biology

SN - 1744-4292

IS - 9

M1 - e11080

ER -

ID: 319247180