Co-Detection by Indexing (CODEX)

CODEX – high parametric imaging of cells in a tissue context


To reveal and understand the collective behaviors of cells in the tissue context, imaging technologies are ideal since they preserve the spatial information. Due to the complexity of cellular phenotypes, their interactions and diversity in function, simultaneous detection of many more markers than allowed with conventional fluorescence microscopes are desired.

Recently a new imaging platform called CODEX – Co-Detection by Indexing was invented, in the lab of Gary Nolan at Stanford. The CODEX technology allows for highly multiplex analysis for up to 40 proteins using cyclic detection of DNA-indexed antibody panels (illustrated in the Figure above). In 2018 the Cell Profiling Facility and the research group of Emma Lundberg at SciLifeLab, was able to purchase one of a few pre-market instruments and since end of 2018 the Cell profiling Facility is developing and integrating this technology to become part of the facility service and make the technology available for its users. Any update of this progress will be presented in this page.


Technology description

The CODEX System is a fluidics control instrument that integrates with an existing fluorescent microscope for the synchronization of the CODEX Assay and image collection.

The overall procedure for a CODEX experiment follows the steps below:

  1. Tissue staining
    The tissue sample is mounted on a glass slide and stained for all targets in parallel. All antibodies are conjugated with a specific oligo barcode developed by the provide – Akoya Biosciences. The targets are then detected using a fluorescently labelled complimentary oligo.
  1. CODEX and microscope set-up
    The stained tissue sample is mounted on the microscope stage and connected to the CODEX module. The CODEX device is set-up with all buffers and the complimentary oligos.
  2. Image acquisition
    Acquisition is done automatically and targets are detected and imaged in cycles of three targets in each cycle. Dapi is used as a counter stain and compensate for drift during image acquisition. Currently, the set-up allows for 24 markers in total.
  1. Image processing
    Images are deconvoluted and stitched.
  1. Image analysis
    This includes cell segmentation and generation of a csv file summarizing signal intensities from the antibodies from each cycle.


Read more about the technology here: https://www.akoyabio.com/codextm/technology

For questions about the CODEX technology contact the Cell Profiling Facility cellpro.facility@scilifelab.se


The CODEX platform is compatible for staining of fresh frozen (FF) and formalin fixed paraffin embedded (FFPE) material from human and mouse, using validated antibody panels provided by Akoya Biosciences. Currently, the panels are focused on immune cell profiling.

Read more about available antibodies and panels here: https://www.akoyabio.com/codextm/codex-antibodies