The general consensus in the imaging field when it comes to capturing quality images is simply  

Rubbish in = rubbish out. 


What that means in practice is in order to obtain the best quality images, a number of key steps need to be kept at the front of researcher's minds. These include dye selection and sample prep, choosing the right microscopy method, performing the correct pre-capture alignments and using the right settings for acquisition. 


Important Reading 


Other important information can be found in the following presentation: