Applying to summer research project, should I tell prof about mental health issues to explain poor grades last year? I'm currently a junior undergrad in a mathematics program, and emailed a prof at a different school if I would be able to apply as a candidate for a summer project he advertised on the school's website. I'm interested in attending this school for graduate work, and mentioned that to the prof. 

In his response, he was very excited about my interest in his project (work in ocean sciences) and in the graduate program, and asked if I could send a transcript. I'm very happy about the response, because the prof was very enthusiastic, but due to (what I now know was and is) depression, my grades took a dip, which can be seen in my transcript. For reference, I've done poorly in a mathematics class and computer science class in my sophomore year (2 Cs, and a D in a genetics course, but that's unrelated to this project). Since then, I've gotten Bs in Calc III and Adv Calc (the only other courses relevant so far). 

I know this is not a representation of of my ability, as I've done research projects utilizing the material from classes I've done poorly in, and have done well in the projects. At the same time, I don't want to make excuses for myself, and I don't know if it's fair to disclose that information to the prof to make him choose between a candidate like me, and someone else who is "normal". 

How should I respond to this? Should I tell him I can't do his project because my grades aren't up to par, or should I try and explain myself?
If the lower grades belong to a specific time period, then it might be worthwhile to provide an explanation.  If they are scattered here and there through your first four semesters of college, then maybe not.  Keep in mind that many students have a bumpy start to college, and professors are used to that.

At this stage, perhaps you could leave it rather vague ("health problems") for now.  If you are accepted for the summer project, do mention that recently you were diagnosed and began treatment, so that your professor is aware of the general situation.  Also, if there are any specific accommodations you would find helpful during the summer project, let him know what those are.

Speaking of accommodations, if you are in the U.S., but don't have ADA accommodations (also known as 504 accommodations) set up, this would be something to consider looking into.  If you are interested, you could start by


looking at your college's office for students with disabilities web pages to see what documentation they require;
thinking about what accommodations would be most helpful for you.  Look around on the web at lists of accommodations some people have found helpful, to get some ideas.