Running "Manual" Application¶

1. Leginon/Manual> Open the "Settings" tool and configure the settings:
    
   Important-Use low dose kit option should be set to yes if using the low dose kit on Tecnai. Low Dose Pause Time need to be set to 5 sec or more to complete the mode change.
    
   Recommendations-
   • Acquisition/Camera Configuration- use one of the preconfigured selection for binning and size
      
   • Correct image=yes if dark and bright images of the camera configuration exist.
      
   • Save image to the database=yes.
      
2. Leginon/manual/Settings> Save and close the settings by pressing "OK" button.
    
3. Adjust the exposure time in the setting and/or beam size/spot size on the scope to achieve the desired dose and coverage in exposure mode, if low-dose kit is used.
    
4. Microscope> Search the grid for interested area and focus as normally performed.
    
5. Microscope> If low dose mode is used, leave TEM in Focus model. Leave the screen at up position if "Main Screen/Up before acquire" is not checked in the settings. No need to put on beam blank.
    
6. Leginon/manual> Click on the "Acquire" tool to acquire the image.
    
7. Microscope> If low dose mode is used, Leginon will force the pre-specimen shutter close, switch the scope to exposure mode to acquire the image and then switch back to the original mode.

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