"Looking down the microscope at a slide you get a largely 2D view of the object and rarely use binocular microscopes."
That's an interesting point. I started off as a pollen analyst. Pollen grains are very definitely 3D objects but mostly grains were very easy to recognise whatever their orientation. This was because human perception has evolved to understand 3D objects and I think combines 3 things - a 3D model, the 2D image and an understanding of viewpoint. Maybe the last is what's missing in AI and being substituted by pattern.
Perhaps pollen grains (optical images, not SEM) would be a useful training set for AI as shape, size and texture are all significant.
One of the problems with AI is that you can't ask it how it comes by its decisions nor explain to it how to reach them. One could at least explain to students "I'm focussing up and down through the grain to look for pores" or "try moving the cover slip gently to roll the grain over", these being useful techniques to deal with edge cases.