Spatial segmentation of mass spectrometry imaging data featuring selected principal components

Spatial segmentation aims to find homogeneous/heterogeneous subgroups of spectra or ion images in mass spectrometry imaging (MSI) data. The maps it generated inform researchers of vital characteristics of the data and thus provide the basis for strategizing further biological analysis. Dimensional reduction and clustering are two basic steps of segmentation. Due to the variations in the quality, resolution, density of spectral information, and sizes, not all datasets could be segmented ideally with combinations of different dimensional reduction and clustering algorithms. Here, we proposed a segmentation pipeline that utilized pattern compression by principal component analysis (PCA) and represented by principal components. Instead of preprocessed or raw MSI data, normalized principal components were used for the segmentation process. Multiple datasets of rat brains and mouse kidneys were tested, and the proposed segmentation pipeline presented the obvious advantage of easy-to-use and can be readily intergraded with other existing innovative pipelines.