Running "Manual" Application¶

• 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.

Recommandations-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.

• Leginon/manual/Settings> Save and close the settings by pressing "OK" button.

• 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.

• Microscope> Search the grid for interested area and focus as normally performed.

• 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.

• Leginon/manual> Click on the "Acquire" tool to acquire the image.

• 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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