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

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 https://github.com/koellenspergerlab/mexpose under the MIT license. Additional test data are available at https://doi.org/10.5281/zenodo.20287869.