Dec 02, 2025

Public workspaceH&E Staining of CODEX slides.

DOI
https://dx.doi.org/10.17504/protocols.io.6qpvrwb8plmk/v1
  • Kyung J Ahn1,
  • Anusha Thadi1,
  • Kai Tan1
  • 1Children's Hospital of Philadelphia
  • Human BioMolecular Atlas Program (HuBMAP) Method Development Community
    Tech. support email: [email protected]
Kyung J Ahn
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DOI: https://dx.doi.org/10.17504/protocols.io.6qpvrwb8plmk/v1
Protocol Citation: Kyung J Ahn, Anusha Thadi, Kai Tan 2025. H&E Staining of CODEX slides.. protocols.io https://dx.doi.org/10.17504/protocols.io.6qpvrwb8plmk/v1
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License,  which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: December 02, 2025
Last Modified: December 02, 2025
Protocol Integer ID: 234034
Keywords: heart, CODEX, H&E, codex slide, codex experiment
Abstract
This protocol describes the method for H&E staining of a CODEX slide after completion of a CODEX experiment.
Troubleshooting
H&E staining of CODEX slides.
On completion of the CODEX procedure, the CODEX slide was incubated in Histochoice clearing agent for 3 days to loosen the flow cell from the slide.
After 3 days, the flow cell was carefully removed from the slide.
The slide with the flow cell removed was incubated in Histochoice clearing agent for 15 minutes.
The slide was than dried overnight at room temperature.
After drying, the slide was H&E stained by The Children's Hospital of Philadelphia Research Institute Pathology Core using the ThermoFisher/Shandon Varistain Gemini slide stainer.
After H&E staining, the slide was imaged at 40X magnification using Akoya Biosciences Phenocycler-Fusion microscope.