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Test Leginon on the Computer Controlling the Microscope » History » Revision 4

Revision 3 (Anchi Cheng, 05/22/2010 10:39 PM) → Revision 4/28 (Anchi Cheng, 05/22/2010 10:42 PM)

h1. Test Leginon on the Computer Controlling the Microscope 



 h2. Using a Gatan Camera 





 *    Open Digital Micrograph (or check that the Tietz software is closed). 


 *    insert the Gatan CCD in Digital Micrograph. 









 h2. Using a Tietz Camera 





 *    Close Tietz TCL program 


 *    Put camera switch box to select CCD. 

 h2. Make sure that you have [[Installation on the microscope computer|Leginon Leginon installed and configured ]] configured. 

 h2. Start Leginon on the Microscope computer & Import Magnifications 





 *    scope> Start Leginon (Either with the shortcut on the Desktop or follow the 
 Start Menu-\Start\Programs\Leginon>Leginon) 


 *    Leginon Setup Wizard> select "Create session" in session type. Even though you 
 have created a session for simulation test, if the other machine uses linux os, it is 
 better to create a new session so that the path mapping difference betwee Windows and 
 Linux does not cause confusion. 




 *    Fill in session name and comments. Comments will appear in Viewers 


 *    Select instrument and project, if project database is used. Image path is 
 automatically selected. 


 *    Image path is automatically selected based on your leginon.cfg file. 






 *    Choose "Finish" in the set up wizard to start the session. 


 *    Leginon/Main menu/Application> select "Run...." and choose the application 
 named "Manual", both "main" and "scope" launchers will be set to the scope computer, 
 and then launch the application. 


 *    Leginon/Node Selector> select Instrument node. 


 *    Leginon/Instrument> check that TEM is selected to display the 
 parameters. 


 *    Left-click on the tool "Get Magnification". 



 !http://emg.nysbc.org/software/leginon/images/icons/calculate.png! 



 This will import the valid TEM magnification from the microscope into the 
 database. 






 * During Leginon run an Application Error Message may pop up saying 

 <blockquote> 

 _"Exception EAccessViolation in module adaExp.exe at ...._ 


 _Access violation at address xxxx in module 'adaExp.exe'. Read of address 
 xxxx"_ 

 </blockquote> 

 Do NOT touch this message box, or leginon client will need restarting. 





 h2. Acquiring the first real image 





 *    scope> make sure you have beam and something other than a blank to image on 
 the CCD. 


 *    Leginon/Application/Run> select Manual Application. 


 *    Leginon> From the list of nodes on the left panel, select Manual node. 


 *    Leginon/Manual> Open the "Setting" tool and configure the settings: 


 Your TEM and CCDCamera should be available for selection. 


 Acquisition/Camera Configuration- use one of the preconfigured selection for 
 binning and size such 512x8. 


 Save image to the database=yes. 


 Leave the rest of the configuration to default. 


 *    You should see your first real image acquired through Leginon in the image 
 display panel. 









 h2. Check on the Web viewer 



 Follow the <link linkend="AppManual_webviewer">instruction in Manual Application 
 Chapter</link>. 





 h2. Closing Leginon program on Windows 



 The best way to close Leginon program is to close the python command window (normally 
 black) that shows up when the Leginon GUI appears since Leginon GUI window on Windows is 
 controlled through the python command window 


 If you first close the GUI window, the python process is not ended. Therefore, the 
 latter become frozen and you will have to wait for TaskManager to ask you to close the 
 broken process. 





 h2. Problem solving for the first mircoscope test 



 Most common problem at this point is that your TEM or CCDCamera does not show up in 
 Leginon for use. It is caused by lack of proper functioning or non-communicating microscope 
 scripting or CCD drivers to Leginon system's python wrapper in pyScope package. See <link 
 linkend="InstT_testrun">Installation Troubleshooting</link> and    "pyScope Bulletin Board regarding 
 "testing if pyScope is working"":http://emg.nysbc.org/bb/viewforum.php?t=246    for more. 


 If everything goes smoothly, test the network connection as in the next section and then 
 do the same above image acquisition test through from the remote computer. 

 ______ 

 [[Test Leginon with Simulator|< Test Leginon with Simulator]] | [[Test Network Connection Between Remote and Microscope Computers|Test Network Connection Between Remote and Microscope Computers >]] 

 ______