CODEX Technology

Behind-the-scenes of CODEX multiplex imaging technology

CODEX Technology

Behind-the-scenes of CODEX multiplex imaging technology

CO-Detection by indEXing (CODEX)

The CODEX technology, originally developed in the lab of Dr. Garry Nolan at Stanford University, uses antibodies conjugated to a proprietary library of oligonucleotides called Barcodes. This enables customizable panels of up to 40+ CODEX Antibodies to be combined for a single tissue staining reaction.

The CODEX fluidics instrument automates iterative imaging cycles. For each cycle, three CODEX Reporters, each with a spectrally-distinct dye, are applied to the stained tissue to assay the corresponding Antibody Barcodes. This process is repeated until all antibodies have been imaged.

Advantages of CODEX technology:

  • Provides full spatial context and is not limited to just regions of interest (ROI)
  • Provides single-cell resolution down to 600 nm or 250 nm depending on microscope objective used (20X and 40X respectively)
  • Single-step staining and gentle fluorophore removal preserves the sample for ROI analysis
  • Simple, benchtop fluidics system that is cost-effective and simple to implement in any research lab

Behind-the-scenes chemistry



Single-step staining preserves sample integrity and reduces turnaround time. The antibody staining is done before the CODEX instrument runs.

CODEX antibody staining



After staining the tissue with the cocktail of antibodies, the sample is loaded on the CODEX System and Reveal-Image-Remove cycle starts. Three Reporters are added in each cycle.

CODEX reveal step



Each fluorescent reporter is then separately imaged.



After the image is captured, the Reporters are washed away to allow the addition of the next 3 Reporters and the cycle repeats.

Removal of CODEX reporters



The CODEX Fluidics Instrument automates the Reveal-Image-Remove cycles so each run can generate single cell spatial proteomic data of 40+ markers.

Repitition of the CODEX imaging cycle.



Once the multiplex imaging data are acquired, users can analyze the cell phenotypes using the CODEX Software Suite.