Abstract: An electrophoresis apparatus with minimal autofluorescence to enable gel processing in situ, and methods of making and using the electrophoresis apparatus. An exemplary electrophoresis apparatus may comprise a cassette defining a cavity between a first pane and a second pane of a double-paned viewing window, and also may comprise a slab gel located in the cavity. The viewing window may be transparent to ultraviolet light that drives a derivatization reaction in the slab gel, and, absent the slab gel, may define a window autofluorescence inducible by irradiation with the ultraviolet light. The window autofluorescence, per unit area, may be less than five-fold a gel autofluorescence of the slab gel, per the same unit area and under the same irradiation with the ultraviolet light.