Calibration required on FEI microscopes¶

Two calibrations should be done on FEI Tecnai, Polara, and Titan series of microscope for using Leginon MSI applications.

HM Beam Shift/Image Shift Calibration¶

Purpose¶

allow image shift without moving the beam and vice versa.

Procedure¶

1. From TUI Workset look for Alignment tools and start Image/Beam calibration located inside Image HM-TEM. Follow its instruction for the calibration.

TEM Scripting Beam Tilt Calibration¶

Purpose¶

Leginon and its subsystem pyscope uses the property Illumination.RotationCenter in Tecnai/TEM Scripting to set/get beam tilt values. We have noticed that some version of the TEM or Tecnai Scripting defines the function for set/get Ilumination.RotationCenter in units other than the original radians. Since Leginon need the values in radians, a scale factor need to be assigned. We do not not know which version requires non-default scale factors. Therefore, we recommend that all scopes be checked before using Leginon MSI applications with beam-tilt-based autofocusing.

Material¶

1. Gold-shadowed diffraction grating replica for TEM calibration such as Ted Pella's prodoct #606 or #607.

• If such a grid with Gold coating is not available, other material that produces known spacing diffraction in sub nm range can be used. However, the gold <111> spacing 0.236e-9 meters used in get_beamtilt_scale.py need to be replaced.

Procedures¶

1. Put the grating replica grid in a root temperature specimen holder
2. Insert the specimen holder in the microscope
3. From microscope-controlling PC, navigate to the installed myami/pyscope directory. Most likely C:\\Python25\Lib\site-packages\pyscope
4. Find the python file get_beamtilt_scale.py
5. If non-gold grid is used, modify the spacing value with a plain-text editor at the line
   

   gold_diffraction = wavelength/0.236e-9
   

6. Start the script by double-left click on it.
7. Follow the instruction to determine the scale factor.
8. At the end of the script, the beam should be tilted back to the center and the script window closed. If the window does not close, force it to close should not cause any problem.
9. In the same folder, find tecnai.py Open it with a plain-text editor or python's IDLE and look for the following lines close to the beginning of the file.
   

   # This scale convert beam tilt readout in radian to 
   # Tecnai or TEM Scripting Illumination.RotationCenter value
   # Depending on the version,  this may be 1.0 or closer to 6
   rotation_center_scale = 1.0
   

10. replace the number in the last line with the rotation_center_scale determined while running get_beamtilt_scale.py