Cardinal

Cardinal is an R package designed for the statistical analysis of mass spectrometry-based imaging (MSI) experiments conducted on biological samples, particularly tissues. It accommodates Matrix-Assisted Laser Desorption/Ionization (MALDI) and Desorption Electrospray Ionization-based MSI workflows, handling experiments with multiple tissues and complex designs. Cardinal provides key analytical functionalities, including image segmentation and image classification. Image segmentation partitions tissues into regions of homogeneous chemical composition, determining the number of segments and the subset of informative ions while characterizing associated uncertainty. Image classification assigns locations on the tissue to predefined classes, selects informative ions, and estimates classification error through (cross-validation. The underlying statistical methods leverage mixture modeling and regularization techniques.