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Updated: Aug 29, 2025

Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection

Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection

Published on: July 6, 2022

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

Patrick C N Martin^1,2, Hyobin Kim^1,2, Cecilia Lövkvist²

¹Department of Computational Biomedicine, Cedars-Sinai Medical Center, Hollywood, CA, USA.

Molecular Systems Biology

|September 6, 2022

Summary

This summary is machine-generated.

Vesalius deciphers tissue anatomy from spatial transcriptomics data by using image processing. This method identifies complex tissue structures and reveals morphology-specific gene expression in various organs.

Keywords:

anatomical territories spatial domains spatial transcriptomics tissue architecture tissue heterogeneity

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Last Updated: Aug 29, 2025

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Published on: July 6, 2022

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High-resolution In Vivo Manual Segmentation Protocol for Human Hippocampal Subfields Using 3T Magnetic Resonance Imaging

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Published on: November 10, 2015

Area of Science:

Computational biology
Bioinformatics
Genomics

Background:

Spatial transcriptomics (ST) enables mapping gene expression within tissues.
Current ST domain retrieval methods assume transcriptional similarity, limiting application in complex tissues.
Accurate tissue architecture characterization is crucial for understanding biological processes and diseases.

Purpose of the Study:

To develop a novel computational method for deciphering tissue anatomy from ST data.
To overcome limitations of existing methods in complex, multi-cellular tissues.
To enable the identification of tissue morphology-specific gene expression.

Main Methods:

Developed Vesalius, a novel computational tool applying image processing techniques to ST data.
Vesalius detects territories composed of multiple cell types, unlike previous methods.
Applied Vesalius to high-resolution ST data from mouse brain, embryo, liver, and colon.

Main Results:

Vesalius successfully recovered tissue structures in diverse high-resolution ST datasets.
The method uniquely identified territories comprising multiple cell types.
Discovered tissue morphology-specific and regionally specific gene expression changes in the mouse brain.

Conclusions:

Vesalius accurately reconstructs tissue anatomy from ST data, even in complex tissues.
The tool enables novel insights into cell communication and disease mechanisms by linking gene expression to tissue architecture.
Vesalius advances the analysis of spatial transcriptomics for biological discovery.