Multispectral imaging on the PhenoImager HT can be applied across a whole slide using, multiplex immunohistochemistry slides, but also fluorescently stained slides, HE stained slides, chromogenic stained slides, etc. Multiplex immunohistochemistry stained slides enables the biology to be explored at multiple scales, from cell-to-cell interactions to the macroscopic tissue architecture. When using IF or IHC stains, multiple proteins can be measured on a per tissue, per cell, or per cell compartment (e.g. nuclear, cytoplasmic) basis.