Multiplexed protein imaging
PhenoCycler (CODEX) data analysis
High-plex protein imaging turned into reliable cell phenotypes and spatial insight.
What PhenoCycler (CODEX) measures
PhenoCycler, originally CODEX, images dozens of protein markers on a single tissue section by cycling DNA-barcoded antibodies. Panels commonly reach 40 to 100 or more markers across whole slides at single-cell resolution, which enables deep cell phenotyping and analysis of tissue organization.
Strengths
- High-plex protein imaging, often 40+ markers, at single-cell resolution
- Whole-slide imaging rather than small regions
- Standard FFPE and fresh frozen tissue
- Detailed phenotyping of immune and tumour microenvironments
How we can help with PhenoCycler (CODEX) data
Image QC
Channel quality, background and artifact checks before analysis.
Segmentation
Deep learning cell segmentation with tools such as StarDist or Cellpose.
Phenotyping
Marker thresholding, clustering and hierarchical gating to define cell types.
Spatial analysis
Cellular neighbourhoods, proximity and interaction analysis across regions.
Cohort statistics
Comparing patients, regions and conditions with appropriate statistics.
QuPath workflows
Reproducible QuPath projects and scripts your team can rerun.
Related technologies
Working with PhenoCycler (CODEX) data?
Tell us about your samples, panel and question. The first consultation is free.