Thank you for the fish pump link. We have looked at pump based systems as a way to create controlled measurement environments. You get consistent lighting, predictable fish orientation, and the fish are already moving through a constrained path. The challenge is you are still dealing with water turbidity, particulates, and bubbles in the flow which can mess with imaging. It is better than open water but not a free pass on the vision problems.
We have also been looking at pescalators which use an Archimedes screw design to lift fish out of the water. Some setups combine this with anesthetization for operations that require handling. The tradeoff is you are adding stress and complexity but you get a much cleaner imaging environment. There is no single right answer here and the best approach depends on the species, life stage, and what you are trying to measure. This is definitely technology that will develop over time as the industry matures.
What species are you working with in your aquaponics setup?
The pescalators sound great. There are so many tools like that where the application specifics ( species, system, life stage ) could make room for a scalpel-precise optimization of some tool, but the benefits would have to come from scale, and there just haven't been many first-movers ( or they keep quiet and defend the moat ) who seem poised to raise the tide for the whole industry. It is very ripe for the work you are doing to help the downstream gains over generations of stocks.
Cheers to you guys!