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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

Information


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 in publications

 (12)
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 […]

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 […]

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 1.1.4.5 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 […]

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 […]

PMCID: 5121636
PMID: 27883030
DOI: 10.1038/srep37648

[…] individual horizontal line scans were combined into imzml format using the imzml converter v.1.1.4.5 (www.maldi-msi.org). 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 […]


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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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