msIQuant 2.x is a novel software for mass spectrometry imaging based on the input format imzML, enabling fast access, visualization, and analysis of large data sets

The software provides many tools for image visualization including multiple interpolation methods, low intensity transparency display, and image sharpening. It also has a quantitation function that automatically generates calibration standard curves from series of standards that can be used to determine the concentrations of specific analytes. Regions-of-interest in a tissue section can be analyzed based on a number of parameters, including the number of pixels, average intensity, standard deviation of intensity, and median and quartile intensities. Moreover, the suite’s export functions enable simplified postprocessing of data and report creation. The msIQuant suite is a powerful tool for accessing and evaluating very large data sets, quantifying drugs and endogenous compounds in tissue areas of interest, and for processing mass spectra and images.

If this software is used for publication, please cite the following article:

Källback P, Nilsson A, Shariatgorji M, Andrén PE. Quantitation Software for Mass Spectrometry Imaging Enabling Fast Access, Visualization, and Analysis of Large Data Sets.

Anal. Chem., 2016, 88 (8), pp 4346–4353. DOI: 10.1021/acs.analchem.5b04603

Supported MSI Format imzML
Requirements Windows 7 (64 bit) and higher
Output Format Images can be saved as jpg, png or tiff format. ROI results can be copied via “Evaluation” to the clipboard and copied to any software.
Origin, Copyright Copyright © 2016 Biomolecular Imaging and Proteomics, Dept. of Pharmaceutical Biosciences, Uppsala University. All rights reserved.
Software Developer Patrik Källback, Biomolecular Imaging and Proteomics
Download (7.5 MB)
Manual msIQuant Quick Startup Guide (included in the installation zip file).
Registration 7 days trail version. A license key for msIQuant is required on every installed computer. The license key is required to run msIQuant, and is generated for free after applying a license key request.
Acknowledgements This study was sponsored by grants from the Swedish Research Council (Medicine and Health #2013-3105, Natural and Engineering Science #2014-6215, Research Infrastructure #2009-6050) and National Institution of Drug Abuse (NIDA), grant R21 DA027548-01, to Per E. Andrén.


The msIQuant software was developed to be instrument- and manufacturer-independent quantitative MSI software suite using imzML as the only input data format. The imzML data is converted to msIQuant data format which structure enables rapid image display and analysis of very large data sets (>50 GB) without any data reduction.



Below is a screenshot of msIQuant displaying a coronal rat brain tissue section and the distribution of endogenous dopamine derivatized by DPP-TFB.




Unzip the installation file and follow the instructions in the included Installation Guide.