OpenMSI statistics

To access cutting-edge analytics on consensus tools, life science contexts and associated fields, you will need to subscribe to our premium service.

Subscribe
info

Citations per year

Citations chart
info

Popular tool citations

chevron_left Morphometric analysis Image visualization Data management and annotation chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

OpenMSI specifications

Information


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

Maintainer


  • person_outline Ben Bowen <>

Publication for OpenMSI

OpenMSI in publications

 (4)
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 openmsi.nersc.gov 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 […]


To access a full list of publications, you will need to upgrade to our premium service.

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

OpenMSI reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review OpenMSI