Spatial Segmentation of Mass Spectrometry Imaging Data by Combining Multivariate Clustering and Univariate Thresholding

Spatial segmentation partitions mass spectrometry imaging (MSI) data into distinct regions, providing a concise visualization of the vast amount of data and identifying regions of interest (ROIs) for downstream statistical analysis. Unsupervised approaches are particularly attractive, as they may be used to discover the underlying subpopulations present in the high-dimensional MSI data without prior knowledge of the properties of the sample. Herein, we introduce an unsupervised spatial segmentation approach, which combines multivariate clustering and univariate thresholding to generate comprehensive spatial segmentation maps of the MSI data. This approach combines matrix factorization and manifold learning to enable high-quality image segmentation without an extensive hyperparameter search. In parallel, some ion images inadequately represented in the multivariate analysis were treated using univariate thresholding to generate complementary spatial segments. The final spatial segmentation map was assembled from segment candidates that were generated using both techniques. We demonstrate the performance and robustness of this approach for two MSI data sets of mouse uterine and kidney tissue sections that were acquired with different spatial resolutions. The resulting segmentation maps are easy to interpret and project onto the known anatomical regions of the tissue.