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Here is our resulting layer:
Only clean islands of colors. No anti-aliasing and the little areas respecting the neutral grey of the "Flag Area".
This layer is ready to import back into Krita ( drag and drop on the canvas, then in the dialog "insert as new layer" ).
Gallery of my results on episode 12 with the same method
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Shading the potions
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Before painting all the shadows one by one with a brush, one tip is to duplicate the lineart and put a Gaussian blur on it, then contrast the result with a hard curve, It will create a shadow zone around every objects.
In the design of my curve, I added subtle variations ( spikes / noises ). This create little highlight in the shadows.
This shadow with stripes on it can simulate the ambiant occlusion between objects and a bit of the reflection of the glass and will helps to read the volume of each potion.