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Updated: Jun 10, 2025

Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection
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Vispro improves imaging analysis for Visium spatial transcriptomics.

Huifang Ma1, Yilong Qu1, Anru R Zhang1,2

  • 1Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, USA.

Biorxiv : the Preprint Server for Biology
|October 17, 2024
PubMed
Summary
This summary is machine-generated.

Vispro is a new automated tool that enhances spatial transcriptomics (ST) image quality by removing fiducial markers and improving tissue segmentation. This leads to better downstream analyses for ST data.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Spatial transcriptomics (ST) integrates gene expression with tissue spatial context.
  • Histological images in ST data offer crucial spatial information but are often obscured by fiducial markers and background noise.
  • Analyzing these images is complex and hinders downstream applications.

Purpose of the Study:

  • To develop an automated image processing tool, Vispro, for 10x Visium spatial transcriptomics data.
  • To address challenges posed by fiducial markers and background regions in histological images.
  • To improve the quality of ST images and enhance subsequent analyses.

Main Methods:

  • Vispro is an end-to-end, automated tool with four integrated modules.
  • Modules include: fiducial marker detection, marker removal and image restoration, tissue region detection, and segmentation of disconnected tissue areas.
  • The tool is specifically tailored for 10x Visium data.

Main Results:

  • Vispro successfully enhances the quality of spatial transcriptomics images.
  • The tool improves performance in downstream analyses such as tissue and cell segmentation.
  • Enhanced image quality also benefits image registration and histology-based gene imputation.

Conclusions:

  • Vispro provides a robust solution for preprocessing spatial transcriptomics histological images.
  • The automated nature of Vispro simplifies and improves the analysis of ST data.
  • By enhancing image quality, Vispro facilitates more accurate and comprehensive biological insights from spatial transcriptomics.