no Stage position matrix
Added by Bob Grassucci over 10 years ago
I am getting the error failed tilt correction. no stage position matrix... and it lists the correct microscope and camera. When I look at all of the presets they all have a calibration listed. There seems to be a disconnect between the program and the database where the calibrations are. Any way we can check this? Somehow the stage was left at 2.0 degrees likely after a x height correction. Once I but the stage back to 0 degrees the problem went away but I am curious what happened?
Replies (1)
RE: no Stage position matrix - Added by Anchi Cheng over 10 years ago
From the code for tiltcorrector.py:
The TiltCorrector class implements the methods of the following paper: Correction of autofocusing errors due to specimen tilt for automated electron tomography. Journal of Microscopy, Vol 211, Pt 2, August 2003, pp. 179-185 It is useful if you need to cross correlate two images that are at different beam tilts, and you are on a tilted specimen.
To do the correction, it needs to know which direction the tilt axis is parallel to on the image. The assumption in Leginon is that it is the y-axis of the compustage (Holds for FEI and JEOL scopes). Since most image shift-involved beam-tilt-based autofocus is at "fa" preset mag at highest mag used, and it is not required for moving the targets in the view in general. It is likely that it is not calibrated. It should say one way or the other in Presets Manager Node when you select "fa" preset. Often time, stage position calibration at "fa" preset is beyond good reproducibility of the computage as the whole imaging area may be ~< 0.5 um, and may produce 20% or more error during calibration. However, all this tilt correction needs is a rough estimate of the direction, so it is not a problem.