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Related Experiment Video

Updated: May 26, 2026

Integrated Cell Manipulation Platform Coupled with the Single-probe for Mass Spectrometry Analysis of Drugs and Metabolites in Single Suspension Cells
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OpenIMC: an open-source platform for analyzing single-cell and spatial proteomics by imaging mass cytometry.

Dean Tessone1,2, Mohamed Kamal1, Valerie Hennes1

  • 1Convergent Science Institute in Cancer, University of Southern California, Los Angeles, CA, 90089, USA.

Research Square
|May 25, 2026
PubMed
Summary

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OpenIMC is a new open-source platform that simplifies data analysis for imaging mass cytometry (IMC), a technique for single-cell proteomics. This tool enhances reproducibility and accessibility for spatial proteomics research.

Area of Science:

  • Biotechnology
  • Proteomics
  • Computational Biology

Background:

  • Imaging Mass Cytometry (IMC) offers high-plex, spatially resolved single-cell proteomic analysis.
  • Current IMC data analysis relies on fragmented tools, hindering reproducibility and scalability.
  • A unified, open-source platform is needed to streamline IMC workflows.

Purpose of the Study:

  • To introduce OpenIMC, an integrated, open-source software platform for Imaging Mass Cytometry data analysis.
  • To consolidate diverse IMC analysis steps, including visualization, preprocessing, segmentation, feature extraction, phenotyping, and spatial analysis.
  • To enhance reproducibility, scalability, and accessibility in spatial proteomics research.

Main Methods:

  • Development of OpenIMC, an open-source platform with integrated graphical and command-line interfaces.
Keywords:
Batch correctionImage analysisImaging Mass CytometryMultiplexed imagingOpen-source softwareSingle-cell proteomicsSpatial proteomics

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  • Implementation of automated parameter recording and session sharing for enhanced reproducibility.
  • Validation using case studies on blood-derived cells and tissue slices.

    • Main Results:

    • OpenIMC successfully integrates multiple IMC data analysis modules into a cohesive environment.
    • The platform ensures consistent execution through a shared backend for both interface types.
    • Validation studies demonstrated the recovery of known cell phenotypes and tissue organization, confirming the software's efficacy.

    Conclusions:

    • OpenIMC addresses the limitations of fragmented analysis tools in Imaging Mass Cytometry.
    • The platform lowers technical barriers, promoting rigorous and scalable single-cell and spatial proteomics.
    • OpenIMC facilitates reproducible and accessible spatial proteomics research through its integrated and user-friendly design.