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Scanned lineart for dummies (layers & colouring)
You need:
+ A lineart scan, doesn't have to be good. Pencil sketches are okay, we'll see why later.
+ Crappy old image editing program/painting program. We'll use Photoshop 5.5 to demonstrate the oldness.
DISCLAIMER! The screenshots are in Danish. That sucks for you, but you don't really need to read those.
1: Load your picture.
This picture has pretty clean lines, but it's pale, there's crap from nearby drawings, and other such mess. Erase what you can see. And crop some more. Now see if you have a Levels tool (sometimes called Curves or Histogram Adjustment):
This graph is trying to represent the distribution ("histogram") of darkness in your image, I think!
Moving the leftmost slider makes relatively darker pixels totally black, moving the rightmost slider makes light pixels totally white. Moving the middle shifts a threshold of sorts. Shift around and see what looks good, the "bumps" in the histogram usually indicate good places to put the sliders. You should be able to make your stuff look a lot crisper. New smudges may show up, so just erase those.
Some programs only have simpler tools to fix things like "Brightness and Contrast", but sometimes that's good enough - Levels just gives you more control.
2: Transparant whites - how?
Grab whatever excuse your program has for a Layer Manager, and duplicate your drawing to a layer above the background. Wipe the background (Select All + Delete), and fill it with a colour because it's time to experiment.
Now, how would you go about getting the lineart transparant? Erase the white? I suppose we could do that! So grab your magic wand, kick up the tolerance to 30-50, enable the anti-alias, and delete those whites:
Oh that just looks like crap. The truth is, no matter how you set your tolerances, you'll end up with whites in your lineart, or end up erasing the finer lines. Unless you lineart is super pixel-sharp clean. Damn, huh?
Undo that crap.
3: Magic: Layers!
Grab the layer manager again, and see if you have any "blending modes". It's the box that says 'normal' or 'standard' by default. See if there's one called Multiply, Multiple, Darken or something along those lines. This merely refers to how it adds up the pixel colours when they're stacked on top of each other.
Thusly, by magic, our lines are now transparent, with no pixellation. So go ahead and fix up the last couple of stray lines, and colour all you want. All layers will show through the lineart, and any darkness on them will merely enhance the line darkness!
This also allows you to colour in quite messy pencil sketches where you have zero chance of cleaning them with simple tools like the magic wand.