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Installation on the microscope computer » History » Revision 3

Revision 2 (Amber Herold, 04/16/2010 10:20 AM) → Revision 3/86 (Amber Herold, 04/23/2010 01:26 PM)

h1. 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 



 h2.    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*| 




 * 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. 





 h2. 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| 






 * <link linkend="window_svn">Check out the comarray package</link> from svn 
 depository with your SVN client 

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

 * Start a command line Window from Start Menu 


 * Install the package with commands such as 
 <pre>cd Your_Download_Place\Leginon-1.6-ALL\comarray 
 c:\\python25\python.exe setup.py install</pre> 









 h2.    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| 







 h2.    Register adaexep.exe 



 *    From the command prompt: 

 <pre>adaexp.exe /regserver</pre> 

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

 <pre>updatecom.py</pre> 








 h2. 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: 



 <pre>[tem] 
 class: tecnai.Tecnai 
 [camera] 
 class: gatan.Gatan</pre> 



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









 h2. Run updatecom.py 



 From a command line window: 



 <pre>cd C:\python25\Lib\Site-Packages\pyScope 
 C:\python25\python.exe updatecom.py</pre> 



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





 h2. 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: 



 <pre> 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} 
 </pre> 



 *    Change the last line to: 



 <pre>      return {'x': 2048, 'y': 2048}</pre> 








 h2.    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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