Thanks for your input Mylenium!
The difficulty in using only jQuery for this is that I need the image map shapes to be quite complex with animated perspective distortions. That's why it would be essential to be able to get the motion tracked shape data from Mocha. JQuery is not capable of motion tracking at the moment.
If there is no simple way to do this then perhaps the best approach would be something like this:
1. Motion track the shape in Mocha
2. Paste shape data into AE
3. Try to develop a script for automatically copying mask shape data from a frame, pasting it to Illustrator, save file as SVG, then go back to AE, go to next frame and repeat process. Not a very easy scripting task I'm afraid, although maybe Autohotkey could handle it.
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Your suggestion of taking it from AE to flash and then use the HTML5 export capabilites of Flash CS6 might indeed be worth investigating.
Let me clarify a little bit why this is more difficult that just a corner pin:
Ps. I understand that the performance might slow down because of handling data on every frame, but in my environment this is not a problem. This application will run only locally and I have already used heavier processing succesfully on a frame by frame basis. I'm just saying that you are right about this being intensive, but just that in my case it doesn't matter.
I see. If you need to follow some contours, then al lthe simple stuff won't work of course. Too bad Flash has been declared evil. This would be so easy to do just with image sequences...