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OpenMIMS specifications


Unique identifier OMICS_25923
Name OpenMIMS
Alternative name Open Multi-isotope Imaging Mass Spectrometry
Software type Package/Module, Toolkit/Suite
Interface Graphical user interface
Restrictions to use None
Operating system Windows
Programming languages Java
Computer skills Medium
Stability Stable
Maintained Yes


No version available

Additional information

OpenMIMS citations


The stage of seed development influences iron bioavailability in pea (Pisum sativum L.)

Sci Rep
PMCID: 5932076
PMID: 29720667
DOI: 10.1038/s41598-018-25130-3

[…] prove the counting statistics. The number of images acquired was varied to give the same total dose for each region depending on the beam current. Image processing was conducted with ImageJ using the OpenMIMS plugin (Harvard). […]


Toxicity of Food Grade TiO2 to Commensal Intestinal and Transient Food Borne Bacteria: New Insights Using Nano SIMS and Synchrotron UV Fluorescence Imaging

Front Microbiol
PMCID: 5928251
PMID: 29740421
DOI: 10.3389/fmicb.2018.00794
call_split See protocol

[…] r between 200 and 300 cells was considered (taking into account the aggregated and dispersed TiO2 forms). The signal intensities of the different elements were extracted from image acquisitions using OpenMIMS, a FIJI plugin developed at Harvard at the National Resource for Imaging Mass Spectrometry (). […]


Using Aiptasia as a Model to Study Metabolic Interactions in Cnidarian Symbiodinium Symbioses

Front Physiol
PMCID: 5864895
PMID: 29615919
DOI: 10.3389/fphys.2018.00214
call_split See protocol

[…] ction, the 13C/12C or 15N/14N maps were expressed as a hue-saturation-intensity image (HSI), where the color scale represents the isotope ratio. Image processing was performed using the ImageJ plugin OpenMIMS (National Resource for Imaging Mass Spectrometry, of the isotope labels was quantified for 20 Regions of Interest (ROIs) (circles of 2–10 μ […]


Dissecting the Re Os molybdenite geochronometer

Sci Rep
PMCID: 5700062
PMID: 29167505
DOI: 10.1038/s41598-017-16380-8
call_split See protocol

[…] er size of 45 or 50 μm2, at a resolution of 512 × 512 pixels, with a dwell times of 25 or 30 ms/pixel. Maps were corrected for 44 ns deadtime on each individual pixel. Images were processed using the OpenMIMS plugin for FIJI/ImageJ ( […]


The dynamics of protein body formation in developing wheat grain

Plant Biotechnol J
PMCID: 4988504
PMID: 26898533
DOI: 10.1111/pbi.12549

[…] quired with an image dwell time of 20 ms, while images of the 15N‐labelled samples were acquired with a dwell time of 30 ms and at an image size of 50 ×× 50 μm and 256 by 256 pixels. Image J with the OpenMIMS plugin (Harvard, Cambridge, MA, USA) was used to generate isotope ratio images and extract quantitative data. Hue saturation intensity (HIS) colour maps were used to display the isotopic vari […]


Impact of high CO2 on the geochemistry of the coralline algae Lithothamnion glaciale

Sci Rep
PMCID: 4744931
PMID: 26853562
DOI: 10.1038/srep20572

[…] view were acquired using a 1.3 pA beam (with a nominal probe diameter of approximately 300 nm), at a pixel resolution of 256 × 256, with a count time of 100 ms/pixel. Images were processed using the OpenMIMS plugin for ImageJ, utilising the Hue-Saturation-Intensity scale to display the ratio on a colour scale. Ratios were extracted from images by drawing regions of interest on the images, and cal […]


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