MSiReader is an open source Matlab GUI and function library for visualization and analysis of Mass Spectrometry Imaging data sets.
A variety of popular data formats are supported, including imzML, mzXML, IMG (Analyze7.5) and ASCII. Data processing functions include peak detection, absolute quantification, polarity switching, graphical ROI selection tools, spectrum export, binned data export, customizable colormaps, normalization, background subtraction, image overlay, image colocalization, peak annotation, mass measurement accuracy and spectral calculation and plots. Recent additions include a rapid image correlation and batch processing tool and principal component analysis.
No compression or reduction algorithms are performed until requested by the user. This allows high resolving power data (small m/z increment) to be accurately viewed and processed as long as the total data cube size does not exceed the available RAM.
MSiReader is available for free under the BSD-3 license. The open source version requires a Matlab installation (R2012b or later) with the image processing, statistics and bioinformatics toolboxes. A standalone 64-bit version that uses the 2017a release of the Matlab MCR is also available.
Robichaud, G.; Garrard, KP; Barry, JA; Muddiman, DC. MSiReader: An Open-Source Interface to View and Analyze High Resolving Power MS Imaging Files on Matlab Platform, J. Am. Soc. Mass. Spectrom, 2013, 24(5), 718-721. DOI: 10.1007/s13361-013-0607-z Bokhart, M.; Nazari, M.; Garrard, K.; Muddiman, D. MSiReader v1.0: Evolving Open-Source Mass Spectrometry Imaging Software for Targeted and Untargeted Analyses. J. Am. Soc. Mass Spectrom., 2017, DOI: 10.1007/s13361-017-1809-6
Added MSiCorrelation and MSiPCA GUIs