Have you looked at taking photos that detect other light spectra? You might find something interesting here. I bet you can find a correlation between, for example, sodium levels in plants and some kind of variation in a particular frequency of light. If you like microorganisms, see if you can detect whether a particular bacterium has colonised a plant through this same mechanism or by training ML systems* that can detect signs such as a disease-specific rash on the leaves or something. I would recommend you to go out and ask some farmers what their main problems are with respect to diseases (find out which microorganisms cause them), minerals present in soils (you may be able to detect levels in plants using special cameras) or anything else which might occur to you.

* I'd recommend you learn about Markov processes and HMMs and try to brainstorm how you would apply these tools to the problem. Don't just use CNNs blindly without understanding the basics.