Transparent region on overlay dictated by another image file

I have a page that loads thousands of overlay PNGs (one at a time),
each representing a data contour plot for a time period.

I'd like to make a fixed region of all of these maps transparent, but
don't want to add an Alpha transparency to each PNG..

Can I save one PNG with the same dimensions and correct alpha channel,
and merge the two using js or the google API?

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