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Separate Alpha Channel File Types
Alpha channel files are themselves black and white files: their own alpha channel is ignored and should be omitted. Ideally they can be monochrome images.
Since SynthEyes is intended for processing RGB imagery, support for reading gray-scale formats is limited (currently PNG or TIFF or JPEG, but don’t use JPEG for alphas!). You can write an alpha channel as RGB if necessary (many apps won't give you a monochrome output option). SynthEyes will use the green channel of an RGB image for alpha.
Alpha channels have a lot of redundancy, so you want to make sure that the format do a good job compressing the alpha channel, without introducing artifacts. Run- length or ZIP compression are good choices (not JPEG, which will create slight transparency and incomplete opacity around sharp edges!). Due to compression, an RGB image will probably not be much larger than a gray-scale image.
For most usage, PNG is the recommended alpha-file format.
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