New Extension: MassVision

Amoon
Sun, 21 Sep 2025 02:28:12 +0000
Support

Happy to announce the official release of MassVision extension v 1.0, now available through the 3D Slicer Extension Manager (compatible with the latest stable release, v5.8.1).

MassVision is an end-to-end platform for AI-driven exploration and analysis of mass spectrometry imaging (MSI) data.

Key Features:

Data compatibility: imzML, structured CSV, hierarchical HDF5, DESI TXT images

Visualization: targeted (single-ion heatmap, multi-ion colormap), untargeted (global/local contrast PCA, UMAP, t-SNE), multi-pixel spectrum plotting

Exploration: clustering, segmentation, correlation analysis

Dataset generation: spatial co-localization with pathology annotations, pathology-guided spatial annotation, spectrum labeling and extraction

Multi-slide merge: feature alignment, peak matching

Preprocessing: normalization (TIC, TSC, single-ion, mean, median, RMS), spectral filtering, spatial pixel aggregation

Statistical analysis: ANOVA, volcano plots, boxplots

AI model training/validation:

Feature ranking (PLS-DA, Linear SVC, LDA)

Feature selection (automated, manual)

Data stratification (random, patient-based, cross-validation)

Data balancing (oversampling, undersampling)

Model training (PCA-LDA, Linear SVM, Random Forest, PLS-DA)

Whole-slide AI deployment: feature matching, global or masked deployment

Useful Links:

Codebase

User Manual

Publication

Demonstrations:

Visualization and exploration

Spatial colocalization

https://raw.githubusercontent.com/jamzad/SlicerMassVision/refs/heads/main/docs/source/Images/colocalization.gif

Pathology guided ROI dataset curation

https://raw.githubusercontent.com/jamzad/SlicerMassVision/refs/heads/main/docs/source/Images/roi.gif

Statustucal analysis

Citation

Please use the following citations if you use MassVision in your research

A Jamzad, J Warren, A Syeda, M Kaufmann, N Iaboni, C JB Nicol, J F Rudan, K YM Ren, D Hurlbut, S Varma, G Fichtinger, and P Mousavi; "MassVision: An Open-Source End-to-End Platform for AI-Driven Mass Spectrometry Imaging Analysis, Analytical Chemistry 2025, DOI: 10.1021/acs.analchem.5c04018.

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