The CODEX® Software Suite

Visualize spatial relationships between different cellular phenotypes

The CODEX® Software Suite

Visualize spatial relationships between different cellular phenotypes

CODEX Software Analysis Suite

CODEX® technology 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 CODEX 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 CODEX System
The CODEX Analysis Suite has three core components:
CODEX instrument manager for data collection
CODEX Instrument Manager (CIM)

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
CODEX Processor

Data processing

  • Formats raw images for downstream analysis
  • Drift compensation, background subtraction, deconvolution, cell segmentation and clustering
Data interpretation and visualization with the CODEX multiplex analysis viewer
Multiplex Analysis Viewer (MAV)

Data interpretation

  • Visualize different markers in situ
  • Cluster cell types using tSNE plots
  • Gate cells
  • Generate spatial network maps
CODEX Data Visualization offers you a deeper look into the tissue microenvironment:

The CODEX 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