Falcon Orius combo installation and setup¶

Falcon/Orius combo unique installation and setup¶

Falcon/Orius is controlled by the same computer as the microscope¶

Currently working configuration uses TIA and TIA Scripting to control Falcon and Gatan Digital Micrograph Scripting to control Orius.

Extra Package and Installation¶

• Use all 32-bit version of Windows installer

  program/package	notes
  TecnaiCCD.dll
  Tia.dll	(Should come with the microscope)

Program	package web site	local copy of win32 installer
comtypes 0.6.2	http://sourceforge.net/projects/comtypes"	comtypes-0.6.2.win32.exe

Register TecnaiCCD.dll (It may have been registered already)¶

• From the command prompt, run the following commands. You may need to enter the full path of the dll:
  

  REGSVR32 TecnaiCCD.dll

Run updatecom.py¶

• From a command line window:
  

  cd C:\python27\Lib\site-packages\pyscope
  C:\python27\python.exe updatecom.py

• The output sould contain this output for DM scripting
  

  initializing Gatan CCD Camera done.
  

and one of these outputs for TIA scripting

initializing ES Vision 3.0 done.
initializing ES Vision 3.1 done.

instruments.cfg¶

[Falcon Camera]
class:tia.TIA_Falcon
zplane: 50
width: 4096
height: 4096

[Orius]
class:gatan.Gatan
zplane:49
width: 2048
height: 2048

• Note that the class name for Gatan DM controlled camera depends on the number of cameras. Ask us if you have more than one and need to find out which is which.

Setup¶

• Set camera configuration to give the standard Leginon orientation. For example, we need 270 degree rotation and flip around the vertical axis on FEI F20. Note that the rotation required is different if it is installed post-GIF and/or on Krios.
• Set the shutter configuration in DM to protect the specimen when camera is not taking images.
• Create the folder to store the dose fractionation raw frames. Frames are saved as unsigned 16-bit mrc image stack in K2 computer under D:\frames by default as set in the code inside pyscope/dmsem.py in the function calculateFileSavingParams. You must create the frames directory first. Leginon will not do that for you. You may change where the frames are saved here but will need to make corresponding changes when setting up raw frame file transfer
• Setup raw frame file transfer from a network data server.
• Unless you want to develop your own frame alignment program. We recommend that you use Appion to do frame gain correction and alignment. These are parallelized by images so it cam almost keep up with the acquisition.

Testing with pyscope¶

Testing Orius¶

from pyscope import tia
g = gatan.Gatan()
g.setExposureTime(100)
g.getImage()

Testing Falcon¶

from pyscope import tia
g = tia.TIA_Falcon()
g.setExposureTime(1000)
g.getImage()

Programs to open before Leginon Client: Digital Micrograph and then TIA¶

See more about K2 implementation in Using_Gatan_K2_Summit_in_Leginon¶