Table 1 |.

Comparison of CODEX tissue imaging for FFPE and FF specimens

	FFPE	FF
Antibodies
Availability	Many clones are not available in purified and carrier-free format	Most flow cytometry antibodies work well
Utilization	Requires optimization of epitope retrieval conditions (i.e., difficult to assemble a panel of ≥50 antibodies that all stain well under the same conditions)	Little protocol optimization required
Cost	Expensive	Reasonable
Tissue specimen
Availability	Widely available (most common type of clinical specimen)	Limited availability
Handling	Easy to handle and store	Difficult to handle and store
Infectious risk	Low to none	Potentially infectious
Morphology	Well-preserved morphology over the course of a multicycle	Deteriorates over the course of many cycles in a multicycle
Applications	Retrospective clinical cohorts, with full clinical annotations; biomarker discovery of cancer or vaccine clinical trials; compatible with large-scale tissue microarrays (e.g., ≤128 samples); enabling all samples/conditions to be stained and imaged in a single multicycle	Requires prospective collection; not compatible with large-scale tissue microarrays; resulting in batch effects over numerous multicycles