If the beam is weak the autothreshold doesn't properly work and you get the centroid of the whole chip rather than the area above background. Two possible options
1) subregion the image and only do processing in that region
2) option for manual threshold rather than auto threshold.
Maybe we should implement both in the planned alignment tool gui
If the beam is weak the autothreshold doesn't properly work and you get the centroid of the whole chip rather than the area above background. Two possible options
1) subregion the image and only do processing in that region
2) option for manual threshold rather than auto threshold.
Maybe we should implement both in the planned alignment tool gui