Well in my research I look at different markers of inflammation in the brain after stroke. I do this by looking at rats brains and staining them with very fancy antibodies for different inflammation markers or cell types. To look at some of these antibodies you need to look through a fluorescent microscope which allows you to see different wavelengths. So you get some very pretty pictures. This is not my work but an example of what it can look like, http://www.nei.nih.gov/eyeonnei/snapshot/archive/0110.asp
I picked this one as it was the clearest on google images so it is of the eye not brain tissue, but you get microglia (green – brain immune cells) and blood vessels (red) in my rat brain samples too. Isn’t this cool! So my favourite microscope is a fluorescent one I take colourful photos of my rat brains on. The one I use at uni is nick-named Ernst (not sure why though).