Fine tuning positioning accuracy

The procedure for using a grid to derive the number of microns per pixel is described here. This is sufficient to get the system working pretty well. You will likely need to conduct this measurement for each image resolution that you plan on using. The number of microns per pixel can vary by about 1% between different image sizes.

After conducting this procedure (and aligning the stages) you may still see errors in tile placement. These errors should be consistent and larger for larger tiles. One way of eliminating them is to tweak the number of microns per pixel in the recipe file and re-stitch with chessboard stitching. This way it's possible to get near-perfect stitching. Then tweak the objective resolution in ScanImage to reflect this new value.

The following image shows the effect of fine-tuning stitching accuracy. On the left is the stitching accuracy using the number of microns per pixel obtained by measuring with a grid (1.316 microns per pixel) on the right is the with this number manually over-ridden to 1.323 microns per pixel. So that's a tiny difference: only 7 nm per pixel!