CLOVER: An analysis protocol for visualization and identification of cell clusters through cluster overlaying for imaging mass cytometry.

Suthicha Kanacharoen, Sarah M Shin, Yanyi Sun, Courtney D Cannon, Laura D Wood, Won Jin Ho

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Article in STAR protocols, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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5 · Who and what money

Authors and funding

6 authors.

Suthicha KanacharoenSidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21287, USA; Department of Pathology, Johns Hopkins University, Baltimore, MD 21287, USA.

Sarah M ShinSidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21287, USA.

Yanyi SunSidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21287, USA.

Courtney D CannonSidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21287, USA; Mass Cytometry Facility at Johns Hopkins University, Baltimore, MD 21287, USA.

Laura D WoodSidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21287, USA; Convergence Institute, Johns Hopkins University, Baltimore, MD 21287, USA; Sol Goldman Pancreatic Cancer Research Center at Johns Hopkins University, Baltimore, MD 21287, USA; Department of Pathology, Johns Hopkins University, Baltimore, MD 21287, USA.

Won Jin HoSidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21287, USA; Mass Cytometry Facility at Johns Hopkins University, Baltimore, MD 21287, USA; Convergence Institute, Johns Hopkins University, Baltimore, MD 21287, USA. Electronic address: wjho@jhmi.edu.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Imaging mass cytometry (IMC) enables spatial single-cell analysis on formalin-fixed paraffin-embedded (FFPE) sections. Here, we present a protocol for visualizing and identifying cell clusters through cluster overlaying of IMC data. We outline steps to source and preprocess images, compile and format data frames, and generate cluster-specific overlays in a high-throughput manner. We then describe procedures to composite these overlays onto corresponding reference images and export finalized visualizations. This workflow integrates high-dimensional data with ground-truth tissue images to support more accurate cell-type classification within tissue microenvironments. For complete details on the sample data used for the execution of this protocol, please refer to Bever et al.

Indexed as

Image CytometryImage Processing, Computer-AssistedSingle-Cell AnalysisAnimalsCluster AnalysisFlow CytometryHumansParaffin EmbeddingSoftwareCancerImmunologyMass CytometryMicroscopySingle Cell

Identifiers

PMID42160172

DOI10.1016/j.xpro.2026.104557

PMCPMC13213774

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LicenceCC BY-NC-ND

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.