Hi Anna,

I do not think so there are any specific checklist to screen Zebrafish embryo in order to find malformations (I can be wrong). I was using olympus and zeiss fluorescence microscope to track them. In the microinjection time you can separate some eggs and can compare with the morpholino injected eggs. Or you can use specific transgenic zebrafish line who express fluorescence color in eye, it will be more easy to track.

I spent half of my PhD trying to interpret MO artefacts, and I always warn people to be careful when assessing phenotypes produced by MO injections. Morpholinos can have plenty of off-target side effects. Most common off-target phenotypes are developmental delay and cell death (particularly in the eyes and the brain). I will recommend you doing some Control MO injections and/or co-injections of p53 MO to block non-specific cell death (unless the gene you are knocking down is part of the p53-induced apoptosis pathway, in which case you don't use the p53 MO). See the attached paper for more information. 

Article p53 Activation by Knockdown Technologies