On clustering for cell-phenotyping in multiplex immunohistochemistry (mIHC) and multiplexed ion beam imaging (MIBI) data

BMC Res Notes. 2022 Jun 20;15(1):215. doi: 10.1186/s13104-022-06097-x.


Objective: Multiplex immunohistochemistry (mIHC) and multiplexed ion beam imaging (MIBI) images are usually phenotyped using a manual thresholding process. The thresholding is prone to biases, especially when examining multiple images with high cellularity.

Results: Unsupervised cell-phenotyping methods including PhenoGraph, flowMeans, and SamSPECTRAL, primarily used in flow cytometry data, often perform poorly or need elaborate tuning to perform well in the context of mIHC and MIBI data. We show that, instead, semi-supervised cell clustering using Random Forests, linear and quadratic discriminant analysis are superior. We test the performance of the methods on two mIHC datasets from the University of Colorado School of Medicine and a publicly available MIBI dataset. Each dataset contains a bunch of highly complex images.

Keywords: Cell phenotyping; MIBI; Multiplex tissue imaging; Semi-supervised Learning; Vectra polaris.

MeSH terms

  • Biomarkers, Tumor*
  • Cluster Analysis
  • Diagnostic Imaging*
  • Flow Cytometry
  • Immunohistochemistry


  • Biomarkers, Tumor