Leginon

h1. TEM Scripting Beam Tilt Calibration

* Recommended for all FEI scopes

h2. 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.  Known versions with this problem are Tecnai 3.1.1 are Titan 1.0.0. We also know that it is fixed in Tecnai 3.1.2 and Titan 1.0.2 (Thanks to Wim Hagen for the information).  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.

* The most likely values are 1.0 and ~6 and it does not need to be very accurate.  Please let Leginon team knows if yours is very different from these.

h2. Material

#  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.

h2. Procedures

* Do this calibration at one of the high tension values you plan to use Leginon at.

# Insert the specimen holder with the grid in the microscope

# From microscope-controlling PC, navigate to the installed myami/pyscope directory.  Most likely *C:\\Python25\Lib\site-packages\pyscope*

# Find the python file *get_beamtilt_scale.py*

# If non-gold grid is used, modify the spacing value with a plain-text editor at the line

<pre>

gold_diffraction = wavelength/0.236e-9

</pre>

# Start the script by double-left click on it.

# Follow the instruction to determine the scale factor.

# 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.

# 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.

<pre>

# 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

</pre>

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