title: MANTiS: a program for the analysis of X-ray spectromicroscopy data.
abstract: Spectromicroscopy combines spectral data with microscopy, where typical datasets consist of a stack of images taken across a range of energies over a microscopic region of the sample. Manual analysis of these complex datasets can be time-consuming, and can miss the important traits in the data. With this in mind we have developed MANTiS, an open-source tool developed in Python for spectromicroscopy data analysis. The backbone of the package involves principal component analysis and cluster analysis, classifying pixels according to spectral similarity. Our goal is to provide a data analysis tool which is comprehensive, yet intuitive and easy to use. MANTiS is designed to lead the user through the analysis using story boards that describe each step in detail so that both experienced users and beginners are able to analyze their own data independently. These capabilities are illustrated through analysis of hard X-ray imaging of iron in Roman ceramics, and soft X-ray imaging of a malaria-infected red blood cell.
authors.affiliation: 2nd Look Consulting, Room 1702, 17/F, Tung Hip Commercial Building, 248 Des Voeux Road, Hong Kong.
authors.forename: Mirna
authors.initials: M
authors.lastname: Lerotic
authors.affiliation: Department of  Physics and Astronomy, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208-3112, USA.
authors.forename: Rachel
authors.initials: R
authors.lastname: Mak
authors.affiliation: Center for Advanced Radiation Sources, University of Chicago, 5640 South Ellis Avenue, Chicago, IL 60637, USA.
authors.forename: Sue
authors.initials: S
authors.lastname: Wirick
authors.affiliation: Inorganic Chemistry and Catalysis, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands.
authors.forename: Florian
authors.initials: F
authors.lastname: Meirer
authors.affiliation: Department of  Physics and Astronomy, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208-3112, USA.
authors.forename: Chris
authors.initials: C
authors.lastname: Jacobsen
mesh_terms: D002516:Ceramics / Q000737:chemistry; D004912:Erythrocytes / Q000000981:diagnostic imaging / Q000469:parasitology; D007091:Image Processing, Computer-Assisted / Q000295:instrumentation*; D007501:Iron / Q000737:chemistry; D011859:Radiography; D012984:Software; D013052:Spectrometry, X-Ray Emission
chemical_list: D007501:Iron
keywords: NEXAFS; X-ray microscopy; X-ray spectromicroscopy; XANES