IonSpattern

IonSpattern is a software tool for analyzing mass spectrometry imaging (MSI) data. It implements a novel algorithm called the spatial-Dirichlet Gaussian mixture model (spatial-DGMM) to segment ion images and detect components with homogeneous spatial composition. The key features and capabilities of IonSpattern are:

1. Segmentation of single-ion images: IonSpattern can accurately segment individual ion images, accounting for the spatial structure of MSI data.

2. Distinguishing ions based on spatial distribution: The tool can differentiate between ions with homogeneous and heterogeneous spatial distributions within the tissue sample.

3. Downstream analysis support: The spatial information extracted by IonSpattern can be used for various downstream analyses, such as:
- Detecting morphology-specific ions
- Identifying groups of ions with similar spatial patterns
- Detecting changes in the chemical composition of tissues between different conditions.

Topic

Imaging;Proteomics experiment;Metabolomics

Detail

  • Operation: Essential dynamics

  • Software interface: Command-line tool,Library

  • Language: R

  • License: Not stated

  • Cost: Free of charge

  • Version name: -

  • Credit: NSF-BIO/DBI.

  • Input: -

  • Output: -

  • Contact: Olga Vitek o.vitek@neu.edu

  • Collection: -

  • Maturity: -

Publications

  • Unsupervised segmentation of mass spectrometric ion images characterizes morphology of tissues.
  • Guo D, et al. Unsupervised segmentation of mass spectrometric ion images characterizes morphology of tissues. Unsupervised segmentation of mass spectrometric ion images characterizes morphology of tissues. 2019; 35:i208-i217. doi: 10.1093/bioinformatics/btz345
  • https://doi.org/10.1093/BIOINFORMATICS/BTZ345
  • PMID: 31510675
  • PMC: PMC6612871

Download and documentation

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