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Hello,
I wanted to know if there's any way of exporting sprites where FFD has been applied separately from every other sprite into the atlas so that we can use trimming on the second set of pieces without altering the uv coordinates for the first set.

Initially our animator used after effects retrieving images directly from a psd, animation which we imported into spine through a script. The problem is that every piece contains the whole whitespace. Thus, every transformation applied is relative to the whole canvas. Whitestripping during export works fine as long as no mesh has been used, so it would be great if we could used a trimmed atlas for every non ffd piece.

Thanks!

Nope. There's currently no way.

Even the AfterEffects script is a third-party thing so what it does is not officially supported. (As a side note, AfterEffects supports importing PSDs where each layer is the size of the trimmed area of that layer, instead of the whole canvas size of the psd.)