NC State


MSiReader is a vendor-neutral Matlab application to view and perform data analysis of Mass Spectrometry Imaging (MSI) data. MSiReader is distributed as a standalone Windows application that does not require a Matlab license.

Because binning is not performed on the imaging data until requested by the user, high resolving power data (small m/z increment) can be viewed and processed as long as the data set size does not exceed memory resources (RAM).


Data Processing

Below is a summary of the processing and visualization tools available in MSiReader:

• Automatic peak detection
• Peak normalization (8 methods available)
• Polarity switching and filtering
• Absolute quantification
• Baseline correction
• Background subtraction
• Partial data set loading using an ROI location file
• Filtering by m/z range and abundance magnitude
• Bespoke scan filtering
• Spectral extraction (single or average)
• Save figure, image, and data (single or batch)
• Customizable centroid calculation
• Customizable abundance calculation
• Customizable colormaps, logarithmic color scaling
• Colocalization of 3 images, plus an image overlay
• Multiple pixel interpolation schemes
• Image mosaic for a folder of data sets
• Multiple normalization strategies, including custom
• Spectrum browsing tool
• Isotopic distribution and adduct calculator
• Percent isotope enrichment (PIE) tool
• Peak exclusion filter
• Support for METASPACE annotation files

• Save and restore ROIs
• Data extraction from ROI
• Export data set, ROI and all results
• Data set or ROI binned export for MVA
• Batch processing of a list of m/z peaks
• Rapid image correlation
• Principal component analysis
• TIC, m/z rank and peak density,plots
• Abundance threshold plots
• 4D visualization with MSiSlicer
• Overlay and co-registration of a 2nd image
• Lipid maps plots with exported peak markers
• Mass measurement accuracy plots
• Spectral accuracy plots
• Annotation of putative peaks from user database
• User-written external function support
• External calibration
• 3D colocalization plots
• Sequential paired covariance
• Scan scrubber
• Summary statistics for QC
• More . . .


All data analysis features are explained in further detail in the User’s Manual provided with the application. The release notes summarize the changes since the last release. Different pathways to convert imaging files from vendor’s proprietary formats to a format compatible with MSiReader are also presented. The following formats can be read directly:

• imzML (processed or continuous, single or multiple files)
• mzXML (single or multiple files)
• IMG (Analyze 7.5)
• ASCII (one file per scan)