Biology would be a lot easier if we could see what we were doing. This maybe isn’t so much a problem for ecologists, but for many of the rest of us our objects of attraction are not just very, very small, but also pretty similar to everything else around them. We have to use fancy tricks to distinguish sub-cellular structures; either specific stains or polarized light for example.
Things get really complicated once you move out of the realms of visible light. Magnetic resonance imaging (MRI) depends on measuring changes in electromagnetic signals, and to image structures in biological specimens (which tend to be mostly water, as you know) you need to add ‘contrast’; a chemical that improves visibility by altering the relaxation times