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chevron_left Image visualization Image data normalization Baseline correction Image mapping Image signal quantification Image spectra analysis Spectral extraction Image registration Image acquisition chevron_right

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MSiReader specifications


Unique identifier OMICS_05663
Name MSiReader
Software type Package/Module
Interface Command line interface, Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages MATLAB
Computer skills Advanced
Stability Stable
Maintained Yes


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Publication for MSiReader

MSiReader citations


Correlative mass spectrometry imaging, applying time‐of‐flight secondary ion mass spectrometry and atmospheric pressure matrix‐assisted laser desorption/ionization to a single tissue section

Rapid Commun Mass Spectrom
PMCID: 5838509
PMID: 29105220
DOI: 10.1002/rcm.8022

[…] mass spectrometry (ms/ms) capabilities. datasets provided by both mass spectrometers were converted into the open and vendor‐independent imzml file format and processed with the open‐source software msireader., the tof‐sims and ap‐maldi mass spectra show strong signals of fatty acids, cholesterol, phosphatidylcholine and sphingomyelin. we showed a high correlation between the fatty acid ions […]


In vivo neurochemical measurements in cerebral tissues using a droplet based monitoring system

Nat Commun
PMCID: 5665973
PMID: 29093476
DOI: 10.1038/s41467-017-01419-1

[…] imaging was performed on the previously described parylene base plate after the distribution of the brain-fluid samples, as shown in fig. . all data were processed using matlab and visualized using msireader., a standard calibration solution (multi-element 2a, agilent technologies) was used to generate the calibration curves employed for quantifying the metal elements found in the brain-fluid […]


Mass spectrometry imaging identifies palmitoylcarnitine as an immunological mediator during Salmonella Typhimurium infection

Sci Rep
PMCID: 5459799
PMID: 28584281
DOI: 10.1038/s41598-017-03100-5

[…] solubilized in dmso was spotted on a slide and the spot was scanned to collect a spectrum. data was converted into imzml format using imzml converter version and data was visualised using msireader version 0.06. all intensities shown are raw ion intensities and 1st order linear interpolation was used for image generation., palc, solubilised in water was added to the agar plates prior […]


Mass spectrometry imaging of biomarker lipids for phagocytosis and signalling during focal cerebral ischaemia

Sci Rep
PMCID: 5177920
PMID: 28004822
DOI: 10.1038/srep39571

[…] stitched by the image composite editor (microsoft corporation, washington, usa)., the raw-files were converted to imzml by an imzml-converter and loaded into the open-source ms imaging software, msireader. images were generated for the m/z values of interest with a bin width of ±0.1 da for desi imaging and ±5 ppm (±0.002 da to ±0.004 da) for maldi imaging. the images shown in the figures […]


Spatial Quantitation of Drugs in tissues using Liquid Extraction Surface Analysis Mass Spectrometry Imaging

Sci Rep
PMCID: 5121636
PMID: 27883030
DOI: 10.1038/srep37648

[…] individual horizontal line scans were combined into imzml format using the imzml converter v. ( data visualization and region of interest extraction was performed using msireader v0.05. intensity data was extracted for each pixel within a region of interest and subsequently averaged using microsoft excel. all images were created using 0.01 da bin size and linear […]


High resolution MALDI mass spectrometry imaging of gallotannins and monoterpene glucosides in the root of Paeonia lactiflora

Sci Rep
PMCID: 5086847
PMID: 27796322
DOI: 10.1038/srep36074

[…] and root mean square error (rmse) were calculated by using formula (i), (ii) and (iii) respectively, described in . overlaid optical and ion images were generated with the open-source software msireader v0.06. all images were generated using a bin width of ± 5 ppm without any normalization or interpolation., principal component analysis (pca) and image similarity of paeoniflorin […]

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MSiReader institution(s)
W M Keck FT-ICR Mass Spectrometry Laboratory, Department of Chemistry, North Carolina State University, Raleigh, NC, USA

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