MeXpose 2.0: A Comprehensive Toolkit for Single-Cell Spatial (Metall-)omics-Covering All Steps from Image Reconstruction to Integrative Analysis

Gabriel Braun; Lyndsey Hendriks; Claude Molitor; Hoang Anh Nguyenova; Elisabeth Foels; Martin Schaier; Gunda Koellensperger

doi:10.1021/cbmi.6c00070

MeXpose 2.0: A Comprehensive Toolkit for Single-Cell Spatial (Metall-)omics-Covering All Steps from Image Reconstruction to Integrative Analysis

Gabriel Braun (Corresponding author)
, Lyndsey Hendriks (Corresponding author)
, Claude Molitor
, Hoang Anh Nguyenova
, Elisabeth Foels
, Martin Schaier
, Gunda Koellensperger (Corresponding author)

Publications: Contribution to journal › Article › Peer Reviewed

Abstract

MeXpose 2.0 is a major update to our interactive workflow for comprehensive analysis of multiplexed imaging data, optimized for spatial metallomics. This release streamlined the existing pipeline by replacing third-party software with custom Jupyter notebooks for image reconstruction, preprocessing, and data extraction. Additional features such as limit-of-detection calculations, interactive region-of-interest annotations, cytometry-style gating, and integrated spatial statistics enhance both exploratory and quantitative analyses within a single, compact environment. MeXpose 2.0 is free and open-source, available at under the MIT license. Additional test data are available at .

Original language	English
Journal	Chemical & biomedical imaging
DOIs	https://doi.org/10.1021/cbmi.6c00070
Publication status	Published - 1 Oct 2026

Funding

Funders	Funder number
Fonds zur Förderung der wissenschaftlichen Forschung (FWF)	10.55776/FG3

Austrian Fields of Science 2012

104002 Analytical chemistry
104027 Computational chemistry
301305 Medical chemistry

Keywords

image processing
bioinformatics
metallomics
open-source
single-cell

Access to Document

10.1021/cbmi.6c00070

Cite this

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AU - Nguyenova, Hoang Anh

AU - Foels, Elisabeth

AU - Schaier, Martin

AU - Koellensperger, Gunda

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