The PhenoCycler
Software Suite

Spatial Visualization of Cell Phenotypes and Populations

We’ve rebranded some of our products, learn more ›

CODEX is now PhenoCycler
Phenoptics is now Phenolmager

PhenoCycler Software Analysis Suite

The PhenoCycler™ System (formerly CODEX®) provides unparalleled levels of highly multiplexed tissue imaging data.

In order to unlock the true complexity of the tissue microenvironment, we offer a suite of analysis tools to rapidly enable researchers to move from multiplexed imaging data to easily interpretable visualization of spatially resolved cellular structure and cell phenotypes.

Features include:

  • Synchronized control of the PhenoCycler assay fluidics and microscope image capture
  • Spatial visualization of cell phenotypes and populations

Complement your single-cell genomics data with spatially resolved, proteomic data from the PhenoCycler System​

Watch how the Multiplex Analysis Viewer (MAV) allows you to cluster single cell data and spatially map dozens of cell phenotypes.

The PhenoCycler Analysis Suite has three core components

CODEX instrument manager for data collection
PhenoCycler Instrument Software
Data collection
  • Installed on the microscope control PC
  • Controls fluidics instrument
  • Integrates with microscope control software for image acquisition
Cell segmentation with the CODEX analysis suite
PhenoCycler Processor
Data collection
  • Formats raw images for downstream analysis
  • Controls fluidics instrument
  • Drift compensation, background subtraction, deconvolution, cell segmentation and clustering
Data interpretation and visualization with the CODEX multiplex analysis viewer
Multiplex Analysis Viewer (MAV)
Data collection
  • Visualize different markers in situ
  • Cluster cell types using tSNE plots
  • Gate cells
  • Generate spatial network maps

PhenoCycler data visualization offers you a deeper look into the tissue microenvironment

The PhenoCycler MAV software is a robust visualization solution encompassing image navigation, cell segmentation and biomarker quantification for sophisticated algorithmic clustering of cellular phenotypes. The intuitive interface enables spatial overlay for the easy interpretation of tissue substructures such as tumor and stromal boundaries.

Load and display experiment image data, including its various regions, markers and Z-slices

Provides an interface for hierarchical biaxial gating and KNN/FLANN clustering (dimensionality reduction plots)

Visualize populations on region images and marker expressions in an intuitive heatmap

Save, import and export annotated populations and analysis states in .fcs or .csv formats for easy retrieval and analysis by third-party pipelines