A noise-robust deep clustering of biomolecular ions improves interpretability of mass spectrometric images

MOTIVATION: Mass Spectrometry Imaging (MSI) analyzes complex biological samples such as tissues. It simultaneously characterizes the ions present in the tissue in the form of mass spectra, and the spatial distribution of the ions across the tissue in the form of ion images. Unsupervised clustering of ion images facilitates the interpretation in the spectral domain, by identifying groups of ions with similar spatial distributions. Unfortunately, many current methods for clustering ion images ignore the spatial features of the images, and are therefore unable to learn these features for clustering purposes. Alternative methods extract spatial features using deep neural networks pre-trained on natural image tasks; however, this is often inadequate since ion images are substantially noisier than natural images. RESULTS: We contribute a deep clustering approach for ion images that accounts for both spatial contextual features and noise. In evaluations on a simulated dataset and on four experimental datasets of different tissue types, the proposed method grouped ions from the same source into a same cluster more frequently than existing methods. We further demonstrated that using ion image clustering as a pre-processing step facilitated the interpretation of a subsequent spatial segmentation as compared to using either all the ions or one ion at a time. As a result, the proposed approach facilitated the interpretability of MSI data in both the spectral domain and the spatial domain. AVAILABILITYAND IMPLEMENTATION: The data and code are available at https://github.com/DanGuo1223/mzClustering. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.