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. Author manuscript; available in PMC: 2022 Feb 1.
Published in final edited form as: Nat Protoc. 2021 Jul 2;16(8):3802–3835. doi: 10.1038/s41596-021-00556-8

Fig. 7 |. Parameters for processing raw microscope images by using the CODEX Uploader.

Fig. 7 |

These include tissue size (i.e., region width and height), degree of tile overlap (0% if only imaging a single tile compared with 30% if the tissue size is greater than one tile) and the optional selection of deconvolution, background subtraction and H&E staining. These parameters will change for each experiment.