The CODEX system is made up of a bench-top fluidics platform and a widefield microscope equipped with a 20X objective, to automate high parameter image acquisitions. Along with barcoded antibodies (antibodies tagged with unique oligonucleotide sequences) and reporters (fluorescent dyes conjugated to complementary oligos), users can image 40+ protein markers in tissue samples at single cell resolution. 

​

In CODEX experiments, users have to first stain a tissue section with their antibodies of interest, all at once and manually. Next, they have to transfer the sample to the CODEX system for a CODEX run, where reporters are dispensed onto the tissue and revealed via fluorescence imaging automatically.

​

CODEX runs are comprised of multiple cycles. In each cycle, the sample is incubated with up to three different reporters (plus DAPI), imaged and then gently washed to remove the reporters. The repetition of these cycles using different sets of reporters allows the revealing of more than 40 protein markers in a single sample!