MSiReader v0.05 Released!
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MSiReader is a vendor-neutral interface built on the Matlab platform designed to view and perform data analysis of Mass Spectrometry Imaging (MSI) data. A standalone version of MSiReader for which Matlab is not required is also provided. People who are unfamiliar with the Matlab language will have little difficulty navigating the user friendly interface, and users with Matlab programming experience can adapt and customize MSiReader for their own needs.
Because no binning is performed on the imaging data, high resolving power data (small m/z increment) can be viewed and processed as long as the total data cube size does not exceed the memory limit (RAM).
Here are the data processing tools currently available in MSiReader:
All data analysis features are explained in further detail in the User's Manual provided with the application. Different pathways to convert imaging files from vendor's proprietary formats to a format compatible with MSiReader are also presented. Currently, the following formats are supported:
What's new in MSiReader v0.05
What's new in MSiReader v0.04
What's new in MSiReader v0.03
What's new in MSiReader v0.02
MSiReader is an open source application. If you develop a new feature and want to share it with the MSi community we will be more than happy to include it in a later revision of MSiReader. Contributors will be duly mentioned on this website and in the software credits.
MSiReader is optimized for Matlab V2012a and later versions (64-bit). Also please note that the following toolboxes are required: Bioinformatics, Statistics and Image Processing.
The standalone version of MSiReader included in the .zip file does not require Matlab. It is fully functional; however its code source cannot be modified as can the version running with Matlab. The standalone version has been tested on computers running 64-bit Windows 7 and XP. It is not available for Mac or Linux systems. A minimum of 8GB of RAM is recommended (more might be required to process very large data cubes).
If you use MSiReader in published research, please include a citation to the following article:
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
For more information, to report a problem, or to share or request a new feature, please send us an email at firstname.lastname@example.org.
MSiReader is currently released under an open source license (BSD 3).
The authors would like to gratefully acknowledge the financial support received from the National Institutes of Health (R01GM087964).