Additional installation on the microscope computer¶

The full leginon and its supporting packages need to be installed on the Windows computer
controlling the microscope. Additional programs are required for communication with the CCD
and extra functions for Tecnai scripting not supported as default by FEI Tecnai
microscopes

Required supporting programs for the CCD camera from camera makers¶

Install and register the following programs for CCD cameras from the two makes:

Camera Make:	File:
Gatan	TecnaiCCD.dll
Tietz	CAMC4.exe*

Note: We have experienced slowness of the CAMC4.exe comes with later version Tecnai TUI/TIA. Replacing it with an earlier version of CAMC4.exe resolved the problem.

Additional Package required from NRAMM for Gatan camera or camera that uses TIA¶

For Gatan Camera or FEI Eagle Camera that uses TIA, comarray package need to be install
with python

SVN Package Name	Installed Python Package Name	Reason for update:
comarray	comarray	com module output conversion to array

• Check out the comarray package from svn
  depository with your SVN client

cd Leginon-1.6-ALL
svn co http://emg.nysbc.org/svn/comarray/branches/leg1.6 comarray

• Start a command line Window from Start Menu

• Install the package with commands such as
  

  cd Your_Download_Place\Leginon-1.6-ALL\comarray
  c:\\python25\python.exe setup.py install

Supporting programs for film exposure¶

Install the following if you need film exposure on FEI Tecnai TEM through Leginon,
available through FEI. Please contact Max Otten: <email>mto@feico.com</email> and request
for adaexp.exe that works with your version of Tecnai user interface program.

Name:	File:
exposure adaptor	adaexp.exe

Register adaexep.exe¶

• From the command prompt:

adaexp.exe /regserver

• From the program start menu under pyScope or
  C:\Python25\Lib\site-packages\pyScope\

updatecom.py

Modify instruments.cfg:¶

Sinedon now have full control of database interaction, therefore, the database
configuration in leginon.cfg is no longer needed.

• Modify the file instruments.cfg in the installed pyScope directory to that for
  your microscope and camera. For example, if your microscope uses Tecnai Scripting
  Interface and you have a Gatan camera that you interface through
  DigitalMicrograph:

[tem]
class: tecnai.Tecnai
[camera]
class: gatan.Gatan

The file contains other examples of microscope and camera drivers that we
distribute from NRAMM.

Run updatecom.py¶

From a command line window:

cd C:\python25\Lib\Site-Packages\pyScope
C:\python25\python.exe updatecom.py

This should generate a few files, including tecnaicom.py, gatancom.py and tietzcom.py,
in the same directory.

Additional setup on Tietz PXL camera (optional)¶

The actual Tietz PXL camera dimension is slightly larger than 2048 x 2048. If you'd like
to take the images using the maximum of 2048 x 2048 pixels, you may modify the function that
get camera dimension in tietz.py of pyScope package.

• Go to C:\Python25\Lib\site-packages\pyScope\

• Edit tietz.py with a plain text editor

• Find the lines:

 def getCameraSize(self):
# {'type': dict, 'values': {'x': {'type': int}, 'y': {'type': int}}}}
x = self._getParameterValue('cpTotalDimensionX')
y = self._getParameterValue('cpTotalDimensionY')
return {'x': x, 'y': y}

• Change the last line to:

    return {'x': 2048, 'y': 2048}

Additional Software (Optional):¶

TightVNC (http://www.tightvnc.com) if you get tired of going into the microscope room
just to open the column valves.

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