Do I need to Koehler the microscope when I am doing only epi fluorescence?
Yes!. Epifluorescence does not make use of the condenser, and therefore an unaligned condenser won’t influence your image quality. Nevertheless, the objective is itself acts as the condensor in Epi-illumination and most microscopes have a field diaphragma and in some cases aperture diaphragmas that need to aligned. Aligning the lightsource is absolutly critical in Epi-illumination.