So in After Effects, when I import storm clouds as .mov files, the background is black (no transparency and the background is block). I can’t key on the color black as the storm clouds are very dark. I’m guessing that somehow during the import AE isn’t recognizing the alpha channel?
For assets that consist solely of luma (brightness) information (and no color) you can simply substitute the alpha by the luma, if they are shot on black BG.
Load the clip into an AE layer
Add a “Set Channels” effect
Set the “Set Alpha To Source 4’s” to “Luminance”
You can then leave the RGB as is or (most of the time better) add a “Fill” effect and fill the RGB with the color/gray of you choice.
You can then also adjust the Alpha with a Curves effect to make it more opaque/transparent (make sure to only effect the Alpha in the Curves effect for that).