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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 citations


Ecosystem Fabrication (EcoFAB) Protocols for The Construction of Laboratory Ecosystems Designed to Study Plant microbe Interactions

PMCID: 5933423
PMID: 29708529
DOI: 10.3791/57170

[…] g moving 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). […]


From chromatogram to analyte to metabolite. How to pick horses for courses from the massive web resources for mass spectral plant metabolomics

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

[…] onversion Tool; MUSCLE: Multi-Platform Unbiased Optimization of Spectrometry via Closed-Loop Experimentation; NaDH: Nicotiana attenuata Data Hub; NIST: National Institute of Standards and Technology; OpenMSI: Open Mass Spectrometry Imaging; PCA: principal component analysis; PlantMAT: Plant Metabolite Annotation Toolbox; PLS-DA: partial least squares discriminant analysis; PMR: Plant/Eukaryotic an […]


Methods for Specifying Scientific Data Standards and Modeling Relationships with Applications to Neuroscience

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

[…] trometry imaging (MSI) dataset of the left coronal hemisphere of a mouse brain and a derived, monochrome image. For the example we use an MSI dataset made available by Louie et al. (Lee et al., ) via OpenMSI (Rübel et al., ). The MSI dataset has a size of (120 × 122 × 80, 339) and has been processed via peak detection and integration, principle component analysis, and interpolation to generate a ( […]


Development of a High Throughput Platform for Screening Glycoside Hydrolases Based on Oxime NIMS

Front Bioeng Biotechnol
PMCID: 4603251
PMID: 26528471
DOI: 10.3389/fbioe.2015.00153

[…] 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 products. […]


Mass spectrometry imaging for plant biology: a review

PMCID: 4870303
PMID: 27340381
DOI: 10.1007/s11101-015-9440-2

[…] n (PREMIER Biosoft), Metabolite Imager (University of Texas) (Horn and Chapman ), MIRION (Justus Liebig University) (Paschke et al. ), MSiReader (North Carolina State University) (Robichaud et al. ), OpenMSI (Lawrence Berkeley National Lab, CA, USA, (Rübel et al. ), SCiLS Lab (SCiLS Bremen, Germany) and TissueView (AB Sciex, based on BioMap). The website, op […]

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

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