How to prepare SerialEM

There are a few steps that are requied within SerialEM prior to running SmartScope.

  1. Load the SmartScope settings file that contains the Low-dose presets and imaging conditions. Guidelines on how to set up this file are found in the setup section.

  2. Align beam and correct astigmatism and coma, as per your usual procedures.

  3. Align your Record -> View -> Search image-shifts.

    This is the same way as for any SerialEM experiment. It applies image shift to keep the registration between the magnification levels. This ensures proper targeting.

  4. Open a navigator and the imaging states.

    You should have a mont-map imaging state pre-saved. Double-click it to enable it.

  5. Go to file -> setup montage

    In the dialog, click the use montage mapping, not record option.

    Click ok until prompted to save a file. Don’t save any file and cancel. The options in the dialog will be saved.


    We are aware that this is an odd procedure but it avoids many errors and warnings.

  6. You’re all set!

    Refer on how to prepare the SmartScope run from the web page.