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Installation on the microscope computer » History » Version 1

Amber Herold, 04/14/2010 02:51 PM

1 1 Amber Herold
h1. Additional installation on the microscope computer
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The full leginon and its supporting packages need to be installed on the Windows computer
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controlling the microscope. Additional programs are required for communication with the CCD
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and extra functions for Tecnai scripting not supported as default by FEI Tecnai
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microscopes
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h2.  Required supporting programs for the CCD camera from camera makers
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Install and register the following programs for CCD cameras from the two makes:
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|_.Camera Make:|_.File:|
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| Gatan|TecnaiCCD.dll|
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| Tietz|CAMC4.exe*|
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* We have experienced slowness of the CAMC4.exe comes with later version Tecnai TUI/TIA.
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Replacing it with an earlier version of CAMC4.exe resolved the problem.
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h2. Additional Package required from NRAMM for Gatan camera or camera that uses TIA
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For Gatan Camera or FEI Eagle Camera that uses TIA, comarray package need to be install
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with python
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|_.SVN Package Name|_.Installed Python Package Name|_.Reason for update:|
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|comarray|comarray|com module output conversion to array|
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* <link linkend="window_svn">Check out the comarray package</link> from svn
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depository with your SVN client
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<pre>cd Leginon-1.6-ALL
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svn co http://emg.nysbc.org/svn/comarray/branches/leg1.6 comarray</pre>
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* Start a command line Window from Start Menu
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* Install the package with commands such as
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<pre>cd Your_Download_Place\Leginon-1.6-ALL\comarray
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c:\\python25\python.exe setup.py install</pre>
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h2.  Supporting programs for film exposure
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Install the following if you need film exposure on FEI Tecnai TEM through Leginon,
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available through FEI. Please contact Max Otten: <email>mto@feico.com</email> and request
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for adaexp.exe that works with your version of Tecnai user interface program.
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|_.Name:|_.File:|
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| exposure adaptor|adaexp.exe|
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h2.  Register adaexep.exe
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*  From the command prompt:
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<pre>adaexp.exe /regserver</pre>
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*  From the program start menu under pyScope or
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C:\Python25\Lib\site-packages\pyScope\
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<pre>updatecom.py</pre>
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h2. Modify instruments.cfg:
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Sinedon now have full control of database interaction, therefore, the database
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configuration in leginon.cfg is no longer needed.
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* Modify the file instruments.cfg in the installed pyScope directory to that for
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your microscope and camera. For example, if your microscope uses Tecnai Scripting
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Interface and you have a Gatan camera that you interface through
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DigitalMicrograph:
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<pre>[tem]
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class: tecnai.Tecnai
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[camera]
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class: gatan.Gatan</pre>
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The file contains other examples of microscope and camera drivers that we
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distribute from NRAMM.
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h2. Run updatecom.py
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From a command line window:
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<pre>cd C:\python25\Lib\Site-Packages\pyScope
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C:\python25\python.exe updatecom.py</pre>
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This should generate a few files, including tecnaicom.py, gatancom.py and tietzcom.py,
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in the same directory.
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h2. Additional setup on Tietz PXL camera (optional)
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The actual Tietz PXL camera dimension is slightly larger than 2048 x 2048. If you'd like
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to take the images using the maximum of 2048 x 2048 pixels, you may modify the function that
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get camera dimension in tietz.py of pyScope package.
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*  Go to C:\Python25\Lib\site-packages\pyScope\
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*  Edit tietz.py with a plain text editor
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*  Find the lines:
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<pre> def getCameraSize(self):
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# {'type': dict, 'values': {'x': {'type': int}, 'y': {'type': int}}}}
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x = self._getParameterValue('cpTotalDimensionX')
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y = self._getParameterValue('cpTotalDimensionY')
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return {'x': x, 'y': y}
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</pre>
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*  Change the last line to:
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<pre>    return {'x': 2048, 'y': 2048}</pre>
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h2.  Additional Software (Optional):
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TightVNC (http://www.tightvnc.com) if you get tired of going into the microscope room
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just to open the column valves.