
Undergraduate level reference text that I see in almost every optical engineer's office. It's dense, but it's thorough.
https://edisciplinas.usp.br/pluginfile.php/5054148/mod_resou...
https://www.amazon.com/Optics-5th-Eugene-Hecht/dp/0133977226
That's a good intro into real optics.
It's much more than the optics chapter you'll get in a physics textbook. It goes over the classical ray optics in good detail, does a great job with traditional matrices and that formulation of optics (the one that the design programs like Zemax use), goes well into the real meat-n-potatoes of wave optics (including birefringence, a huge part of biological optics), gives you a good accounting of how lenses and other optical devices are actually Fourier transformers, and also dives into the more esoteric optical devices (a must for practical neuro-optics).
It's an upper-division/graduate level book, fyi. So I'd back-load it in your study course. Though in terms of neuro-optics it's more of a keyhole book.
If you are particularly interested and really want to know what's actually going on with EM, then you need to go through Jackson:
https://www.amazon.com/Classical-Electrodynamics-Third-David...
This is the book on EM, but is very much physics graduate student level. And honestly, I don't think you's need it for BMI stuff. But if you don't go through it, you'll just be trusting other people when they say your ideas won't work and they can't really explain it to you. Just going through Jackson is a bit of a hazing experience and will earn respect.
http://gratings.newport.com/information/handbook/handbook.as...
For a textbook, this one is pretty good:
http://www.amazon.com/Introduction-Spectroscopy-Donald-L-Pav...
For optics, Hecht is the classic text:
http://www.amazon.com/Optics-4th-Edition-Eugene-Hecht/dp/080...
I'd suggest Keating though, since it is a more comprehensive overview and includes things like the human visual system and some basic math review:
http://www.amazon.com/Geometric-Physical-Visual-Optics-2e/dp...
For instrument design in general, these books are outstanding:
http://www.amazon.com/Building-Scientific-Apparatus-John-Moo...
http://www.amazon.com/Optical-System-Design-Second-Fischer/d...
Of course, any understanding of spectroscopy should include some background of the physics behind what you're measuring. Any modern physics book would be fine: Krane, etc.:
http://www.amazon.com/Modern-Physics-Kenneth-S-Krane/dp/1118...
Haven't tried this one, but it looks cool:
http://www.amazon.com/Spectroscopy-Reading-Stellar-Practical...
Camera settings is just a short hand to describe the field of view and depth of focus (at the very least). If you make that implicit you'd still need to give the network the steradians, focal length, circle of confusion, etc. etc. etc. that you want your image to use.
You'd need to understand everything in Hecht's Optics to tweak all the parameters of an AI generated image.