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Segmentation of Multi-Isotope Imaging Mass Spectrometry Data for Semi-Automatic Detection of Regions of Interest

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  • Philipp Gormanns
  • Stefan Reckow
  • J Collin Poczatek
  • Christoph W Turck
  • Claude Lechene

Abstract

Multi-isotope imaging mass spectrometry (MIMS) associates secondary ion mass spectrometry (SIMS) with detection of several atomic masses, the use of stable isotopes as labels, and affiliated quantitative image-analysis software. By associating image and measure, MIMS allows one to obtain quantitative information about biological processes in sub-cellular domains. MIMS can be applied to a wide range of biomedical problems, in particular metabolism and cell fate [1], [2], [3]. In order to obtain morphologically pertinent data from MIMS images, we have to define regions of interest (ROIs). ROIs are drawn by hand, a tedious and time-consuming process. We have developed and successfully applied a support vector machine (SVM) for segmentation of MIMS images that allows fast, semi-automatic boundary detection of regions of interests. Using the SVM, high-quality ROIs (as compared to an expert's manual delineation) were obtained for 2 types of images derived from unrelated data sets. This automation simplifies, accelerates and improves the post-processing analysis of MIMS images. This approach has been integrated into “Open MIMS,” an ImageJ-plugin for comprehensive analysis of MIMS images that is available online at http://www.nrims.hms.harvard.edu/NRIMS_ImageJ.php.

Suggested Citation

  • Philipp Gormanns & Stefan Reckow & J Collin Poczatek & Christoph W Turck & Claude Lechene, 2012. "Segmentation of Multi-Isotope Imaging Mass Spectrometry Data for Semi-Automatic Detection of Regions of Interest," PLOS ONE, Public Library of Science, vol. 7(2), pages 1-12, February.
    • Handle: RePEc:plo:pone00:0030576
    DOI: 10.1371/journal.pone.0030576
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    Cited by:

    1. Gabrijel Ondrasek & Peta L. Clode & Matt R. Kilburn & Paul Guagliardo & Davor Romić & Zed Rengel, 2019. "Zinc and Cadmium Mapping in the Apical Shoot and Hypocotyl Tissues of Radish by High-Resolution Secondary Ion Mass Spectrometry (NanoSIMS) after Short-Term Exposure to Metal Contamination," IJERPH, MDPI, vol. 16(3), pages 1-13, January.

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