In order to efficiently couple to a high Numerical Aperture (NA) objective lens, as required for epi-fluorescence measurements, it is crucial that the light is well collimated as it enters the back aperture of the lens.  In order to achieve this with the appropriate magnification the light must come from a small point, historically an arc lamp which is a reasonable approxiamtion of a point source.  Intense LEDs with emitters of approximately 1mm square work very well for this application.

For transmitted light applications the light passes through a microscope condenser which is designed to work with a relatively large emitter, typically a halogen lamp.  In our experience it is possible to make use of the extra output of larger LEDs in this application and this makes it easier to fill the appropriate aperture and field stops (essential for modalities such as phase contrast).  The problem with using these larger LEDs for fluorescence is that they have a lower point intensity (flux per unit area) than single emitters so are inferior rather than just being wasteful.