COBI-GRINE: A Tool for Visualization and Advanced Evaluation of Communities in Mass Channel Similarity Graphs

TL;DR

COBI-GRINE is an interactive web tool that visualizes mass spectrometry imaging data as graphs to identify molecular communities and link them to histopathological features, aiding biologists and pathologists.

Contribution

It introduces COBI-GRINE, an advanced visualization and community detection tool that integrates expert knowledge for improved molecular clustering analysis.

Findings

Enables visualization of MSI data as graphs with community detection.

Supports manual optimization of clusters using graph statistics.

Links molecular co-localization to histopathological features.

Abstract

The detection of groups of molecules that co-localize with histopathological patterns or sub-structures is an important step to combine the rich high-dimensional content of mass spectrometry imaging (MSI) with classic histopathological staining. Here we present the evolution of GRINE to COBI-GRINE, an interactive web tool that maps MSI data onto a graph structure to detect communities of laterally similar distributed molecules and co-visualizes the communities with Hematoxylin and Eosin (HE) stained images. Thereby the tool enables biologists and pathologists to examine the MSI image graph in a target-oriented manner and links molecular co-localization to pathology. Another feature is the manual optimization of cluster results with the assist of graph statistics in order to improve the community results. As the graphs can become very complex, those statistics provide good heuristics to support and accelerate the detection of sub-clusters and misclusterings. This kind of edited cluster optimization allows the integration of expert background knowledge into the clustering result and a more precise analysis of links between molecular co-localization and pathology.