Hematoxylin and Eosin (H&E) Staining of Tissues following Multiplexed Imaging on Phenocycler-Fusion v1

Phenocycler-Fusion assay enables multiplexed antibody based imaging of FFPE or fresh frozen tissues. Hematoxylin and Eosin (H&E) staining is a gold standard method for observing tissue morphology. Obtaining multiplexed protein expression information and H&E images from the same tissue provides an additional layer of valuable information which can be used to interpret imaging data and used as input novel machine learning algorithms. This protocol details the steps to generate high quality H&E images from both FFPE and fresh frozen (FF) tissues following multiplexed imaging on the Phenocycler-Fusion. This protocol can also be used for H&E staining following multiplexed imaging on other platforms. In that case, skip the 'Flow cell removal' section, perform two washes of each in 1X PBS and proceed directly to Step 5.