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Comprehensive Spatial Methods (CSM): a Toolbox for Spatially Analyzing Tissues in Histopathology.

Alvaro Lopez-Janeiro1, Eduardo Miraval-Wong1, Paulo Perez-Dominguez1

  • 1Department of Pathology, Clinica Universidad de Navarra, Pamplona, Spain.

Laboratory Investigation; a Journal of Technical Methods and Pathology
|December 28, 2025
PubMed
Summary

Comprehensive Spatial Methods (CSM) is a new R-based toolbox for analyzing multiplex and high-plex tissue imaging data. CSM offers a complete pipeline for spatial omics analysis, improving cell phenotyping and interaction studies.

Keywords:
computational pathologymultiplex immunofluorescencespatial analysisspatial omics

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Area of Science:

  • Spatial biology
  • Histopathology
  • Computational biology

Background:

  • Multiplex and high-plex tissue imaging enable simultaneous interrogation of multiple proteins with spatial context.
  • Existing analytical pipelines lack comprehensive coverage for the full spectrum of spatial omics analyses.
  • Analytical challenges hinder the full potential of high-resolution spatial platforms.

Purpose of the Study:

  • To present Comprehensive Spatial Methods (CSM), an R-based toolbox for analyzing multiplex and high-plex omics data.
  • To provide a user-friendly, comprehensive analytical pipeline for spatially resolved histopathology data.
  • To address the need for integrated analysis from segmentation to cell interaction determination.

Main Methods:

  • Development of an R-based analysis toolbox named CSM.
  • Implementation of modules for cell and tissue segmentation, protein normalization, cell phenotyping, and spatial analysis.
  • Utilizing top-performing R libraries for a user-friendly experience.
  • Testing CSM on multiplex and high-plex images from various cancer and non-tumoral tissues.

Main Results:

  • CSM demonstrates superior performance in cell phenotyping and quantification compared to state-of-the-art resources.
  • The toolbox effectively assesses cell phenotypes, spatial heterogeneity, cell-to-cell interactions, and cellular neighborhoods.
  • CSM covers a broad range of analytical scenarios for spatially resolved data.
  • Performance validated on diverse tissue types including carcinomas and non-tumoral tissues.

Conclusions:

  • CSM provides a comprehensive, freely available solution for analyzing multiplex and high-plex spatial omics data.
  • The toolbox addresses many analytical needs of researchers working with spatially resolved histopathology.
  • CSM enhances the understanding of biological processes through integrated spatial analysis.