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In this (zoomed) picture you can see white artifacts at the edges of the coloured sides.

A coloured cube.

This is caused by me selecting the white area of each face, and using that selection to limit the colouring-in.

The problem is that the "magic wand" selection tool gives a selection with hard edges.

Feathering the selection almost solves the problem, but the fill gets noticeably lighter near the edges.

I am happy to use Gimp or Krita (or anything else available for Linux which supports Wacom Intuos tablets).

I think that what I want is a magic-wand tool which creates a selection with opacity equivalent to the difference between the white background and the current pixel.

Is there a way that I can draw lines and colour-in within those lines?

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Yes, there are several possible ways to mitigate this problem which is caused by anti-aliasing. Here's one fairly simple method.

  1. On a new transparent layer. Draw shapes as you normally would, with the Paint Brush tool set to black, to get nice smooth hand drawn lines.

  2. Create a new transparent layer under that. Select the bucket tool and choose a foreground colour. In the Tool Options change the Threshold until you get a good result. Also you may get better results if you choose the Fill by: Blue option. Click inside the shape to fill it.

Here are the settings I used for the Tool Options, for the image I made below. Your threshold value may be different from mine. You will need to experiment to get it just right.

enter image description here

  1. If you made a good Threshold adjustment when applying the Bucket Fill in step 2, then you should get an almost perfect result. If you don't get a good result, undo it (Ctrl+Z), and readjust the Threshold until it's as good as you can get it.

Example: Zoomed in (left), and at 100% zoom (middle), and the arrangement of layers (right)

enter image description here

  1. With this fill colour layer selected, hit the Lock Alpha Channel icon in the layers panel. Now you can paint additional colours on it, and these will stay within the lines.

Finished example

enter image description here

Obviously you can repeat this process for other colours you want to add, just make sure to have each fill on its own layer so you can easily draw on it using the Lock Alpha trick.

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1

Your black edges are blurry. They have partially transparent or partially with background mixed pixels. That's used commonly for anti-aliasing i.e. to avoid jaggy look and it comes without asking if you scale objects or use drawing tools without preventing anti-aliasing.

When you draw with so low resolution that pixels can be seen you very likely expect pixel perfect selections. You get them if you do not use anti-aliasing.

Here's an example. At first a frame is drawn with 1 pixel wide pencil. The interiors are selected with magic wand (=the fuzzy selection tool) and the selected areas are painted with a half-transparent brush. See the tool options for the selection tool!

enter image description here

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0

In Gimp 2.10:

Paint the lines on a transparent layer:

enter image description here

Set the bucket-fill tool mode to Behind (selector at top of Tool options) and the "affected areas" to Fill by line art detection.

Then click in the middle of the area to paint.

enter image description here

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