OpenMSI statistics

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Citations per year

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Popular tool citations

chevron_left Morphometric analysis Image visualization Data management and annotation chevron_right
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Associated diseases

Associated diseases

OpenMSI specifications


Unique identifier OMICS_05669
Name OpenMSI
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes


  • person_outline Ben Bowen <>

Publication for OpenMSI

OpenMSI in publications

PMCID: 5933423
PMID: 29708529
DOI: 10.3791/57170

[…] the root across the nims surface. return the plant to the clamp if desired., attach the nims chip onto a custom maldi plate and load the plate into a maldi spectrometer for mass imaging ()., use openmsi program to generate the nims image of root metabolites (-g)., each ecofab system includes an ecofab device and a plant sized transparent plastic container. one ecofab device has a plant […]

PMCID: 5499862
PMID: 28520864
DOI: 10.1093/gigascience/gix037

[…] in molecular histology []. few tools have been developed so far, namely exploring imaging mass spectrometry data (exims) [] for data processing and analysis and open mass spectrometry imaging (openmsi) [], a web-based visualization, analysis, and management tool., lipidomics data require a very specialized pipeline, and therefore many tools were developed exclusively for this kind […]

PMCID: 5095137
PMID: 27867355
DOI: 10.3389/fninf.2016.00048

[…] of storage object names, locations, and descriptions. many application formats build on existing self-describing formats, e.g., nexus (klosowski et al., ) (neutron, x-ray, and muon data), openmsi (mass spectrometry imaging) (rübel et al., ), cxidb (maia, ) (coherent x-ray imaging), or netcdf (rew and davis, ) in combination with cf and coards metadata conventions for climate data, […]

PMCID: 4603251
PMID: 26528471
DOI: 10.3389/fbioe.2015.00153

[…] at 2,550 and 15 shots per sub-spectrum. the detector voltage multiplier was set as 0.77. for imaging, the step size was set up at 50 μm for both x and y direction., the imaging file was uploaded to by globus connect personal. the converted file was analyzed by a draggable points notebook written in python. signal intensities were identified for the ions of the tagging […]

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OpenMSI institution(s)
Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA, USA

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