Leginon

h1. Calibration required on FEI microscopes

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

h2. HM Beam Shift/Image Shift Calibration

h3. Purpose

allow image shift without moving the beam and _vice versa_.

h3. Procedure

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

!TUIAlignmnet.png!

h2. TEM Scripting Beam Tilt Calibration

h3. 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.

* 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.

h3. 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.

h3. Procedures

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

# Put the grating replica grid in a root temperature specimen holder

# Insert the specimen holder 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*