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Updated: Jan 14, 2026
Visualization, Quantification, and Mapping of Immune Cell Populations in the Tumor Microenvironment
Published on: March 25, 2020
Imaging mass cytometry-derived single cell extraction, transformation and phenotyping to analyze immune tumor
Zoe X Malchiodi1, Louis M Weiner1
1Department of Oncology, Georgetown Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, United States.
Insights
Spatial proteomics using imaging mass cytometry (IMC) reveals cellular interactions in tissues. This guide simplifies extracting single-cell data and spatial information from IMC images for researchers.
Area of Science:
- Spatial biology and proteomics
- Computational pathology and bioinformatics
Background:
- Spatial technologies enable deep investigation of cellular interactions within intact tissues.
- Conventional single-cell methods lack spatial context.
- Imaging mass cytometry (IMC) is a powerful spatial proteomics platform.
Purpose of the Study:
- To provide a practical guide for extracting single-cell data and spatial information from IMC images.
- To assist basic scientists in performing spatial analyses and cell clustering on IMC data.
- To overcome technical challenges in analyzing multiplex IMC images.
Main Methods:
- Detailed step-by-step protocol for single-cell data extraction from IMC multiplex images.
- Methodology for obtaining spatial information from intact tissue samples analyzed by IMC.
- Guidance on cell clustering and spatial analysis techniques for IMC datasets.
Main Results:
- Successful extraction of single-cell data and spatial information from complex IMC images.
- Demonstration of effective cell clustering and spatial analysis workflows.
- Simplified approach to analyzing spatial proteomics data for basic scientists.
Conclusions:
- This chapter demystifies the analysis of imaging mass cytometry data.
- Enables researchers without extensive bioinformatics expertise to perform advanced spatial analyses.
- Facilitates deeper understanding of cellular spatial interactions in tissues.
Abstract:
Spatial technologies have been revolutionary in the analysis of intact tissue samples as they allow for in depth investigation of cellular spatial interactions that cannot be elucidated through conventional single-cell methodologies. Imaging mass cytometry (IMC) is a unique and novel spatial proteomics platform that utilizes metal-conjugated antibodies to generate multi-plex images where spatial information of single cells can be extracted from intact tissue samples, allowing for in depth spatial analyses. However, extracting single cells data and spatial information from IMC multi-plex images can be technically challenging for basic scientists without experience in bioinformatics or computational sciences. In this chapter, we describe how steps on how to extract single cell data and spatial information from multi-plex IMC images of intact tissue samples and tips on performing cell clustering and spatial analyses.
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