The dithering is pretty easy. He's basically just using a single line with a certain arc. And when you get closer to the middle he makes it fade away more like real clouds, it's not that hard, zoom in!
The line-based dithering was actually a fair bit of trial and error - it was originally done in a shader but once we decided we didn't want dithering over the whole game (it made the text hard to read), i ended up doing it semi-manually
The "trick" in this case is a patterned overlay layer and then palettising the image automatically, and then following it up with some clean up in any problem spots. This means you can start from high-res clouds and get your levels right, which is much less fragile if you decide to change the colours a lot.
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