Raf Van de Plas

IsoMobil: Resolving Molecular Ambiguity in Mass Spectrometry-based Spatial Omics Through Ion Mobility

IsoMobil reduces high-dimensional ion mobility mass spectrometry data by grouping isotopologues, improving interpretation at the molecular-species level.

Multimodal Molecular Mapping of the Vasculature in Human Cortex Reveals Lipid Markers of Cerebral Amyloid Angiopathy

The paper maps lipid microenvironments in human brain vasculature using multimodal imaging and identifies lipid markers associated with cerebral amyloid angiopathy.

Elucidating Molecular Features of White Matter Hyperintensities in Alzheimer’s Disease through Multimodal Imaging and SHAP Analysis

This study identifies region-specific lipid alterations in Alzheimer’s disease white matter hyperintensities using multimodal imaging and SHAP analysis.

Signal Strength Aware Latent Spaces Reveal Molecularly Distinct Substructures within Human Kidney Tissue

The paper introduces a method to uncover molecular substructures in human kidney tissue using signal strength-aware latent spaces, revealing previously unknown lipid species and biological subdivisions.

IsoSpace: Chemistry-Informed Dimensionality Reduction and Automated Isotope Candidate Detection in Imaging Mass Spectrometry

IsoSpace provides a chemistry-informed dimensionality reduction method for imaging mass spectrometry that identifies isotopic patterns without prior assumptions.

Unmixing of Imaging Mass Spectrometry Measurements Using Microscopy-Informed Constraints

This paper introduces TULIP, a method to unmix IMS data using microscopy constraints, improving analysis of tissue structures in synthetic and kidney datasets.

Spatial Dependence and Heterogeneity in Molecular Imaging: Moran Quadrant Maps Enable Advanced Spatial-Statistical Analysis

The paper introduces Moran quadrant maps and workflows for spatial-statistical analysis of molecular imaging data, enabling scalable exploration of spatial dependence and heterogeneity.

Integrative Spatial Omics for Systems-Level Mapping of Pathological Niches

This paper introduces a multimodal pipeline for spatiomolecular analysis of tissue samples, demonstrating its application in Alzheimer's disease and type 2 diabetes.

Preserving Full Spectrum Information in ImagingMass Spectrometry Data Reduction

The paper introduces a data reduction method for imaging mass spectrometry that preserves full spectrum information while achieving size reduction comparable to traditional methods.

A Multimodal Imaging Pipeline for the Discovery of Molecular Markers of Cellular Neighborhoods

The paper develops a multimodal imaging pipeline to identify molecular markers of cellular neighborhoods in human kidney tissue by integrating imaging mass spectrometry and immunofluorescence data.

msiFlow: Automated Workflows for Reproducible and Scalable Multimodal Mass Spectrometry Imaging and Immunofluorescence Microscopy Data Processing and Analysis

msiFlow automates and streamlines multimodal mass spectrometry imaging and immunofluorescence data analysis to enhance reproducibility and scalability in biological research.

Automated Segmentation of Kidney Nephron Structures by Deep Learning Models on Label-free Autofluorescence Microscopy for Spatial Multi-omics Data Acquisition and Mining

Automated Biomarker Candidate Discovery in Imaging Mass Spectrometry Data Through Spatially Localized Shapley Additive Explanations

This paper introduces an automated workflow using SHAP to identify biomarker candidates in imaging mass spectrometry data by ranking molecular species based on their predictive importance for biological class recognition.