We have Cameca Peak Sight 4, and loading offline images into there reliably is a pain (input the center and then the image dimensions and size in microns), so in addition to the thin-section scanning via flatbed scanning, I made some checkerboard images that are 2,500x4000 pixels, and I just told the cameca software to load that in 4 different times, and put a different center coordinate in for each one (25,000/2 x 40000/2, changing the signs for the specific quadrant). I saved those in the impDat file and now I have generic navigation aids for any given thin-section, and we can use an image editor to overlay the scan on the checkerboard image, line it up based on where things are in the probe, and you have an accurate navigation aid. If you have close-ups from microphotography you can layer those in as well.
I divided the image about 10x in the X direction for the checkerboard pattern. Plus, after you've lined things up between the scan and checkerboard, you can save that and import it back into Peak Sight with the exact same settings you loaded the plain checkerboard into, and it will be accurate enough until you remove the section. And can just adjust when you load a slide back in if the lack of accuracy drives you crazy.
Cheers,
Nick
[I'm pretty sure PfE just does all this automatically with far less work]