I do a lot of IF, and frequently need to count the number of cells in a given frame quickly - so naturally, I just stain the nucleus and have a few lines of code in my Fiji processing macro to automate counting inline with my analysis.
I have issues when using DAPI with green fluorophores (alexa488, GFP fusions, etc) in that DAPI's huge emission spectrum overlaps with those fluorophores' excitation. I avoid this by using A568 or rhodamine whenever possible, and when I *must* have a green fluorophore, I scan the green channel first. This doesn't always help, though, especially if I need to scan the same slide in both channels multiple times.
I plan to start doing some more complicated IF experiments with 3 or 4 dyes, and I won't be able to avoid using A488. Are there any good nuclear stains (preferably either blue or far-red) that have a narrower emission spectrum, one that will minimally overlap common green excitation? I'd like to avoid having to invest in new filters, so preferably something that excites in the UV range and emits around 450.