Step 4Rescue the holes
Depending on the individual circuit board, you may have to find a different technique that works for you.
It may be easiest to just paint them in. Create a new transparent layer (Layer > New Layer) and ensure it is active. Choose a brush about the same size as the pads, and dot over each one in some colour you like.
If the pads are copper coloured on a green board, as in the example, open the channels dialogue, and turn off the green and blue channels. With a little bit of luck, you will be looking at just the pads. If not, you have a bit more work to do - see next paragraph for details. Go to Layer > New from Visible. Turn the blue and green channels back on. Add a new layer and fill it with red, and change the red layer's mode to Darken Only. You might want to repeat the process with another red layer. Delete any layers you are no longer using, such as the red layer(s) and the first New from Visible if you created more than one.
If turning off the green and blue channels did not make the holes/pads clear enough, go to colours > components > decompose... Select HSV and click OK. When the new image appears, copy the "hue" layer and paste it as a new layer (edit > paste as > new layer) into the image you are working on. It should be the top layer. Set it's mode to "subtract". With a bit of luck, you should now have clearly visible, if a bit dim, holes. Resume the procedure above. Again, the exact result will vary depending on the board you are working on. Try different decompose modes/layers if "hue" does not work you.
With the New from Visible layer active, use the select by colour tool (toolbox, top row, second from right) to select the pads, adjusting the threshold as necessary. Copy the selection. Create a new transparent layer, set it active, and paste the selection. (You will need to "anchor floating selection" in the layers window). You can now delete everything except the layer with the holes/pads in it.
If this method does not work well for you, experiment with layers consisting of grayscale and inverted copies of the background, different coloured layers, turning channels on and off, and layer blend modes.
You may find that if the lighting is too uneven, you need to use one method on one part of the board, and a different method on another. Make a selection of the part you want to work on, create a new transparent layer, and paste the selection into it. All the parts will be visible through the transparency as you build up the layers. If you find all this is taking too much time, manually dotting the holes is probably quicker.
Find any bits of track or other artefacts that are showing through and erase them. The dots that are left are now your place-holders for every through connection on the board. Copy the alignment marks to the layer if you are using them, and save a copy to a new .png file. Call it something meaningful, like solder-side-holes.png. Finally, delete all the layers in the original file except the one showing the holes you rescued.
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