Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Search research articles

Related Experiment Video

Updated: Jul 2, 2026

Integrated Cell Manipulation Platform Coupled with the Single-probe for Mass Spectrometry Analysis of Drugs and Metabolites in Single Suspension Cells

Integrated Cell Manipulation Platform Coupled with the Single-probe for Mass Spectrometry Analysis of Drugs and Metabolites in Single Suspension Cells

Published on: June 21, 2019

OpenIMC: an open-source platform for analyzing single-cell and spatial proteomics by imaging mass cytometry.

Dean Tessone^1,2, Mohamed Kamal¹, Valerie Hennes¹

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

BMC Bioinformatics

|July 1, 2026

Summary

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

Integrated Molecular and Clinical Analysis of Thymic Epithelial Tumors.

JCO precision oncology·2026

Same author

Dietary and Lifestyle Patterns Among Young Patients with Lung Cancer: Analysis of Mutation-Specific Phenotypes.

Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology·2026

Same author

OpenIMC: an open-source platform for analyzing single-cell and spatial proteomics by imaging mass cytometry.

Research square·2026

Same author

Augmenting Performance Status: A Preliminary Study of Objective Kinematic Assessment Using Motion Capture.

Oncology and therapy·2026

Same author

Copper isotope fractionation and copper-to-zinc ratios reveal altered metal homeostasis in prostate cancer.

Scientific reports·2026

Same author

Eligibility criteria and study phase limit racial/ethnic enrollment in oncology clinical trials.

BMC cancer·2026

OpenIMC is a new open-source platform that unifies Imaging Mass Cytometry (IMC) data analysis. This integrated framework simplifies complex single-cell and spatial proteomics workflows, enhancing reproducibility and accessibility for researchers.

Area of Science:

Proteomics
Single-cell analysis
Spatial biology

Background:

Imaging Mass Cytometry (IMC) offers powerful single-cell proteomics with spatial context.
Current IMC data analysis is fragmented across multiple tools, hindering reproducibility and accessibility.
Researchers face technical barriers due to the complexity of integrating diverse analysis software.

Purpose of the Study:

To develop a unified, open-source platform for integrated Imaging Mass Cytometry (IMC) data analysis.
To reduce the technical barriers and improve reproducibility in IMC workflows.
To provide a comprehensive framework for visualization, preprocessing, phenotyping, and spatial analysis of IMC data.

Main Methods:

Developed OpenIMC, an integrated graphical and command-line platform for IMC analysis.

Keywords:

Batch correction Image analysis Imaging mass cytometry Multiplexed imaging Open-source software Single-cell proteomics Spatial proteomics

More Related Videos

Single-cell Analysis of Immunophenotype and Cytokine Production in Peripheral Whole Blood via Mass Cytometry

Single-cell Analysis of Immunophenotype and Cytokine Production in Peripheral Whole Blood via Mass Cytometry

Published on: June 26, 2018

Related Experiment Videos

Last Updated: Jul 2, 2026

Integrated Cell Manipulation Platform Coupled with the Single-probe for Mass Spectrometry Analysis of Drugs and Metabolites in Single Suspension Cells

Integrated Cell Manipulation Platform Coupled with the Single-probe for Mass Spectrometry Analysis of Drugs and Metabolites in Single Suspension Cells

Published on: June 21, 2019

Single-cell Analysis of Immunophenotype and Cytokine Production in Peripheral Whole Blood via Mass Cytometry

Single-cell Analysis of Immunophenotype and Cytokine Production in Peripheral Whole Blood via Mass Cytometry

Published on: June 26, 2018

Incorporated modules for image visualization, quality control, preprocessing, segmentation, feature extraction, dimensionality reduction, batch correction, clustering, phenotyping, and spatial analysis.

Implemented automated provenance tracking and ensured interoperability with existing community tools.

Main Results:

OpenIMC successfully integrates major IMC analysis stages into a unified framework.
Benchmarking confirmed deterministic behavior, concordance between workflows, and agreement with established pipelines.
The platform supports high-resolution IMC workflows, including signal attenuation modeling and image deconvolution.
Demonstrated integrated single-cell and spatial proteomics analysis on circulating cells and breast tissue datasets.

Conclusions:

OpenIMC simplifies IMC data analysis by providing a unified, reproducible, and extensible framework.
The platform lowers technical barriers through interactive visualization and scalable computational analysis.
Facilitates reproducible single-cell and spatial proteomics research by integrating diverse analytical steps.