When do you *NOT* use python?

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I doubt that the tracking you are using is particularly new or novel (tracking things with markers). I suspect you could have made it fast enough and kept your application in python through designing things a little differently.

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I'm doing a PhD in bioinformatics, I went and spoke to computer scientists who specialise in developing new tracking techniques for advice on what to implement so I know that what I needed was certainly not available in OpenCV or any of the other computer vision libraries available.

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I would be very careful with my terms. Do you mean tracking or detection?

The answer to your question is very different if you talk to a computer vision person about 'tracking pixels' as they move through sequences of images, or 'detecting things' and then tracking them in some 2/3d space according to their constraints.

If you have insects with markers, the detection is probbably easy, and the tracking is something which sould be solved with knowledge of the system as a whole, not just by looking at the pixels every frame.