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I would look hard at a remote camera mounted to a remote control glider. There are tons of pages on the internet talking about ROV or RTV( Real time View) model airplanes. In effect a small drone.
the reason I'd think about a glider is they are a lot quieter than a helicopter, or even a remote control helicopter, which will make the birds fly, making the counting harder.
that's also a lot cheaper than a full scale airplane.
if this is scientific only, I'd mount a GoPro HD on the belly of a 6" or 8" RC glider, and fly that thing back and forth over the area, then download the footage and make stills to count from.