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Citations per year

Number of citations per year for the bioinformatics software tool MSiReader

Tool usage distribution map

This map represents all the scientific publications referring to MSiReader per scientific context
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Associated diseases

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chevron_left Image data normalization Image visualization 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


No version available

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
call_split See protocol

[…] ie Atomique et aux Energies Alternatives (CEA, Saclay, France), and the “RAW to imzML” converter developed by Justus Liebig University, respectively. As a result, the imzML files were processed using MSiReader, a free open‐source MSI software. This vendor‐neutral interface was built on Matlab by Robichaud et al. The ion selection bin width (m/z window) of the images generated from the MALDI‐MS dat […]


3D MALDI Mass Spectrometry Imaging of a Single Cell: Spatial Mapping of Lipids in the Embryonic Development of Zebrafish

Sci Rep
PMCID: 5668422
PMID: 29097697
DOI: 10.1038/s41598-017-14949-x

[…] imaging. An isolation width of 2.0 Da and normalized collision energy of 35 were used. Cross-section profiles for MSI were generated by mapping the signal intensity across the zebrafish embryo using MSiReader (v. 0.09; North Carolina State University). […]


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. […]


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
call_split See protocol

[…] alC 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. […]


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

Sci Rep
PMCID: 5177920
PMID: 28004822
DOI: 10.1038/srep39571
call_split See protocol

[…] 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 are […]


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

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

[…] rum. 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 inte […]

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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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