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What program did you use for stitching your photoset? You can get transparency to work better if you upload a PNG with a transparency layer to mapknitter.
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I tried two ways: a demo of agisoft and opendronemap suite. The problem i have is that i cannot (don't know how) resize my huge PNG/TIF to be under 10mb but i can do this with a jpeg, that's why there's no transparency.
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