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Board alignment
The first thing to do is to get the board aligned. Rather than painstakingly adjusting the board's position, the camera allows the software to work out the board alignment.
Clicking on the target icon, the board view will show you what point you need to select - it will be the one closest to the centre of the board.
When the camera is centred over this hole, then click on the target icon again. Note that when I make PCBs, I use a technique I first learnt in Eagle PCB, which is something called "Drill Aid", where every drill point is replaced by a small hole (0.25mm). This makes camera alignment very easy.
The machine will move to the next point for alignment purposes - on the assumption that the board is square. It almost certainly isn't, so you'll need to move the board (via the CNC machine) around until it is. The second point is the one nearest the top left.
When it is aligned, click on the target icon again. It will then use these two points to have a better guess as to where the third point is - which will be the one closest to the top centre. Again, move it around (if ncessary), and click on the target to select the next point (which will be the top right).
This continues for a total of 9 alignment points, and then return back to the centre point.
At this point, you can click on any point in the board view, and it'll move the camera to that location. Hopefully it's nicely aligned because I haven't written any code to correct this!
With the 9 points, it'll be able to cope with any stretching of the layout caused when printing onto the sheet, or slight variations in scale.