Related Experiment Video
Updated: May 22, 2026
Visualization and Quantification of High-Dimensional Cytometry Data using Cytofast and the Upstream Clustering Methods FlowSOM and Cytosplore
Published on: December 12, 2019
CLOVER: An analysis protocol for visualization and identification of cell clusters through cluster overlaying for
Suthicha Kanacharoen1, Sarah M Shin2, Yanyi Sun2
1Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21287, USA; Department of Pathology, Johns Hopkins University, Baltimore, MD 21287, USA.
None:
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.1.
