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Installation on the microscope computer » History » Revision 10

Revision 9 (Amber Herold, 05/05/2010 10:42 AM) → Revision 10/86 (Anchi Cheng, 05/18/2010 10:54 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*| 


 *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. 





 h2. Additional installation 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| 






 * [[Windows installation#Check-out-SVN-Source-Files-from-the-depository|Check out the comarray is part of the checkout package you downloaded package]] from our repository svn depository with your SVN client 
 <pre>cd Leginon2.0/comarray 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\Leginon2.0\comarray 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: mto@feico.com 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\ C:\Python25\Lib\site-packages\pyScope\ 
 <pre>updatecom.py</pre> 








 h2. Modify instruments.cfg: 

 



 Sinedon now has 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> 

 The python window appears 



 This should say show the required type libraries it found: 
 <pre> 
 Generating .py files from type libraries... 
 initializing TEM Scripting Error, cannot find typelib for "TEM Scripting" 
 initializing Tecnai Scripting done. 
 initializing TOM Moniker done. 
 initializing Tecnai Low Dose Kit done. 
 initializing Tecnai Exposure Adaptor done. 

 initializing Tietz CCD Camera done. 
 </pre> 
 The output is of course depending on what is available on your microscope computer.    You should have either "Tecnai Scripting" or the pairing of    "TEM Scripting" and "TOM Moniker". 

 The script should generate a few files files, including tecnaicom.py, gatancom.py and tietzcom.py, 
 in C:\\python25\Lib\win32com\gen_py with seemly scrambled names such as BC0A2B03-19FF-11D3-AE00-00A024CBA50Cx0x1x9.py 


 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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 [[Windows Installation|< Windows Installation]] | [[Next Steps|Next Steps >]] 


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