Stage does not rotate back to zero after doing z-height measurements
Added by @Maria Janssen over 8 years ago
Hi Anchi,
I was wondering if I have a microscope problem or a problem within Leginon... During z-height measurements (in z-focus node) the stage is rotated to -1.0 degree and then to +1.0 degree. It then should go back to 0 degrees, but it doesn't. It goes back to 0.02 degrees. Then after moving to the next square, and doing another z-height measurement, the stage gets stuck at 0.05 degrees, then 0.08 degrees, 0.11 degrees, etc etc. So, every additional z-height measurement results in incremental alpha rotations of the stage. I just re-did part of the modeled stage calibration for one magnification only, but did not think this could cause it?
Thank you,
Mandy
Replies (5)
RE: Stage does not rotate back to zero after doing z-height measurements - Added by Anchi Cheng over 8 years ago
Hi, Mandy,
None of Leginon stage calibration does anything to the tilt.
This is a problem we have seen on JEOL microscope often but not on FEI scope since the latter supposed to have an internal sensor to check if the stage has arrived to its requested position. It looks like your sensor is not doing its job. Did the stage-tilt focusing went up correspondingly to 1.02 and then 1.05 and so on ? If not, we might be able to add a software confirmation step. If the slipping of tilt angle is also shown in the tilted state, then there is nothing I can do since that indicates that there is an increasing offset between the value we get from and control through scripting and the value displayed in TUI.
RE: Stage does not rotate back to zero after doing z-height measurements - Added by @Maria Janssen over 8 years ago
Hi Anchi,
That's what I thought... however when we ask FEI software to move to 0, it rotates exactly back to 0. Strange. There is no slipping of the tilt angle at the tilted state, so a software confirmation step would be helpful. We will ask FEI about the sensor.
Thank you!
Mandy
RE: Stage does not rotate back to zero after doing z-height measurements - Added by Anchi Cheng over 8 years ago
add this to pyscope/tecnai.py on your scope PC at the installation location (likely C:\Python27\Lib\site-packages).
Look for
def setStagePosition
change
return self._setStagePosition(value)
to
if 'a' in value.keys(): self._setStagePosition(value) time.sleep(0.1) return self._setStagePosition(value)
Be careful with indentation. Make sure it matches the original file in tabs. If you have trouble with this instruction , let me know your exact Leginon version, or attach your tecnai.py so that I can modify it for you.
RE: Stage does not rotate back to zero after doing z-height measurements - Added by @Maria Janssen over 8 years ago
Thanks, an FEI engineer looked at it today and according to him the microscope stage is tilting perfectly to exactly where where it is asked to go every time. There is no hysteresis that they can measure. They also tried serialEM to do the tilting to see if there’s something in the scripting that’s wrong. From SerialEM it’s again perfect. I am wondering, does Leginon tell the microscope to go to a certain value (0 degrees) or does it tell the microscope to increment a degree?
In any case, I hope to be able to add this to tecnai.py before Monday.
Thanks for your help!
Mandy
RE: Stage does not rotate back to zero after doing z-height measurements - Added by Anchi Cheng over 8 years ago
Leginon tells the microscope to go to an absolute value. At the end it returns to the original a value it read from TEM Scripting before the tilt. If something is wrong in the original read, then it could create your problem. I don't know how that could be, I can look into possibility of read delay.