Power your hardware on at least 2 hours before you set up your focus map and make sure that there is no hot or cold air blowing on it.
There were not enough focus sites.
Try adding more focus sites to the focus map (see step 9. Define focus map).
Verify that the focus sites are consistently dispersed throughout the contour or grid.
If stage drift is the issue (and you allowed your microscope to warm up prior to starting the side scan), include manual Focus Adjustments at relatively frequent intervals.
We recommend first adding a manual focus 3-4 times throughout the image and see if it helps (e.g., if the image has 2000 tiles, add a manual focus every 500 sites).
In our experience, this occurs with extremely “wavy” tissue with drastic differences in z-depth between focus sites. The focus map interpolation cannot account for these large differences resulting in out-of-focus tiles.
Try increasing the number of focus sites in the focus map to create a tighter triangulation grid (see Step 9: 9. Define focus map).
You may need to include manual Focus Adjustments at relatively frequent intervals.
The image is dark or there are bright specks consistently spaced throughout the image 
