title: Cardinal: an R package for statistical analysis of mass spectrometry-based imaging experiments.
abstract: Cardinal is an R package for statistical analysis of mass spectrometry-based imaging (MSI) experiments of biological samples such as tissues. Cardinal supports both Matrix-Assisted Laser Desorption/Ionization (MALDI) and Desorption Electrospray Ionization-based MSI workflows, and experiments with multiple tissues and complex designs. The main analytical functionalities include (1) image segmentation, which partitions a tissue into regions of homogeneous chemical composition, selects the number of segments and the subset of informative ions, and characterizes the associated uncertainty and (2) image classification, which assigns locations on the tissue to pre-defined classes, selects the subset of informative ions, and estimates the resulting classification error by (cross-) validation. The statistical methods are based on mixture modeling and regularization.
authors.affiliation: Department of Statistics and.
authors.forename: Kyle D
authors.initials: KD
authors.lastname: Bemis
authors.affiliation: Department of Statistics and.
authors.forename: April
authors.initials: A
authors.lastname: Harry
authors.affiliation: Department of Chemistry, Purdue University, West Lafayette, IN 47907 USA.
authors.forename: Livia S
authors.initials: LS
authors.lastname: Eberlin
authors.affiliation: Department of Chemistry, Purdue University, West Lafayette, IN 47907 USA.
authors.forename: Christina
authors.initials: C
authors.lastname: Ferreira
authors.affiliation: Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine, Palo Alto, CA 94304 USA.
authors.forename: Stephanie M
authors.initials: SM
authors.lastname: van de Ven
authors.affiliation: Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine, Palo Alto, CA 94304 USA.
authors.forename: Parag
authors.initials: P
authors.lastname: Mallick
authors.affiliation: Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine, Palo Alto, CA 94304 USA.
authors.forename: Mark
authors.initials: M
authors.lastname: Stolowitz
authors.affiliation: College of Science and College of Computer and Information Science, Northeastern University, Boston, MA 02115 USA.
authors.forename: Olga
authors.initials: O
authors.lastname: Vitek
mesh_terms: D000818:Animals; D003627:Data Interpretation, Statistical; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D012984:Software; D021241:Spectrometry, Mass, Electrospray Ionization / Q000379:methods*; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization / Q000379:methods*; D013552:Swine