How to Update from v21 (Microscope Windows Computer)¶

Instruction is similar to How to Update from v20 (Microscope Windows Computer)

• If you have done TEM_Scripting Beam Tilt Calibration and have changed the scale factor in tecnai.py, you should copy the value to your new installation.
• If you want to avoid copying cfg files to new installation in the future, copy it to the global config directory

Locate global configuration directory following standard on Windows¶

Saving cfg files in a global location reduces future need for copying old configuration to updated installation. The location is different for different versions of Windows. To locate the one for your Windows version:

1. go to C:\\python27\Lib\site-packages\leginon
2. run configcheck.py

The script gives the three search directories of the cfg files and the loaded file if present. Note the first search directory that with a name most likely start with C:\\Programs and ends with \myami. This is the global configuration directory we will use.

Modify pyscope/instruments.cfg¶

Starting from 2.2, Cs values are saved with the scope in instruments.cfg that need to match the value saved in the database. Also a z-plane needs to be assigned to each camera

TEM¶

cs is the coefficient of spherical aberration in meters. Find out from TEM manufacture the proper value for your tem.
For example

[tem]
class: fei.Tecnai
cs: 2.0e-3

Camera¶

height and width are number of pixels based on the orientation presented in Leginon image viewer

• Some Tietz camera may have an odd physical dimension. Use TCL/EMMenu program to find out the good dimension used in Tietz's own software and entered in this configuration.

For example

[camera]
class: gatan.Gatan
zplane: 50
height: 4096
width: 4096

zplane is a number that gives the order of camera. If a camera with low zplane value is going to acquire an image, Leginon will attempt to retract all cameras at higher zplane values.

HEIGHT and WIDTH are not shown in these examples for simplicity

• One computer for both tem and digital camera:
  

  [tem]
  class: fei.Tecnai
  cs: 2.0e-3
  [camera]
  class: gatan.Gatan
  zplane: 50
  

• Separate computers for the two instruments: configure only the instrument reside on the particular computer
  • On the computer that controls the tem:
    

    [tem]
    class: fei.Tecnai
    cs: 2.0e-3
    

  • On the computer that controls the digital camera:
    

    [camera]
    class: gatan.Gatan
    zplane: 50
    

• Two camera at the same plane:
  • On the computer that controls the digital camera:

    DE12 and DE Survey camera are retract/extend together, with the survey camera at off-axis. Therefore zplane should be set at the same value
    For example,
    

    [camera1]
    class: de.DE12
    zplane: 50
    
    [camera2]
    class: de.DESurvey
    zplane: 50
    

• Gatan Orius camera that is installed typically with Gatan K2/Falcon camera is technically on the same plane but is not capable of insertion unless K2 is retracted. On the other hand, K2 camera insertion includes a retraction of Orius at lower level of the function call in DM. Therefore, Orius is considered as a camera at lower zplane.
  

  [camera1]
  class: dmsem.GatanK2Base
  zplane: 50
  
  [camera2]
  class: dmsem.GatanOrius
  zplane: 49
  

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