STEM Control Panel

This panel contains options for controlling various aspects of program behavior in STEM mode.


The checkbox can be used to enter and leave STEM mode, and will also be checked when the microscope is put into STEM mode by other means.  After the STEM mode text appears an indicator, which is just OFF or ON on a JEOL, but is OFF, NANO, or MICRO on a Thermo/FEI scope to indicate whether nanoprobe or microprobe mode is selected.  The button will remain checked and the indicator will show the same state even if STEM mode is temporarily suspended by checking the TEM mode when screen down option.  Thus, this button reflects whether the program, not the scope, is in STEM mode.


This button can be used to toggle the beam blanker. When the beam is unblanked, it is labeled 'Blank' and can be used to blank the beam.  Otherwise, it is labeled 'Unblank' and can be used to unblank the beam when it is being maintained in a blanked state by SerialEM.  It will unblank both the blanking imposed by checking BLANK BEAM in STEM mode and the blanking managed by the SerialEM Low Dose module.  It is enabled when the beam is blanked.


This option can be used to keep the beam blanked whenever the microscope itself is in STEM mode.  The beam is, of course, unblanked for image acquisition, and will be unblanked if you press Unblank.  This option would be needed to keep the beam blanked even if the program is in Low Dose mode, unless you keep the screen up or have BLANK BEAM when screen down checked in the Low Dose control panel.

TEM mode when screen down

When this option is checked, the program will place the microscope in TEM mode whenever the screen is down.  The option is cleared by an image acquisition.  This capability could be useful for checking the specimen on the screen, at least on Thermo/FEI scopes.

Invert contrast

When this box is checked, some or all STEM images will have their contrast inverted, which may reduce mental strain when one is used to looking at TEM images.  The behavior, and the text of the button, depends on the setting for the property 'InvertBrightField'.  If the property is 1 (the default value), the button reads Invert contrast of image data and all images will be inverted when the box is checked.  If the property is set to 0 or -1, the text is Invert contrast unless Bright Field and Bright Field images will either never be inverted (for value 0) or be inverted when this option is NOT selected (for value -1).  (More precisely, this behavior applies to images taken with a detector whose name starts with 'Bright'.)

Retract to stop camera blanking

CCD cameras will typically blank the beam unless the screen is down.  There are two ways to defeat this blanking in STEM mode: retracting the camera, and lowering the screen.  This button can be used to specify that camera(s) should be retracted when taking a STEM picture, rather than lowering the screen.  The default is for the program to lower the screen when necessary for taking an image, unless this option is selected.  That behavior is controlled by a property, 'LowerScreenForSTEM', which can be set either to prevent the screen lowering or to make it happen when the scope enters STEM mode. Another property, 'MustUnblankWithScreen', can be set to indicate that camera retraction cannot be used to defeat blanking (e.g., for a nonretractable camera), in which case the option here is disabled.

Match pixel size when switching

Select this option to have the program change magnification when entering or leaving STEM mode so as to maintain approximately the same pixel size for STEM and CCD acquisition.  A camera property, 'PixelMatchFactor', can be set to make binned pixels in one mode match unbinned pixels in the other, e.g., in order to match the field of view instead of the unbinned pixel sizes.

Added STEM rotation

Entering a nonzero angle here will rotate the acquired image (counterclockwise for positive angles).  This field is used during program setup and may be useful for isolated image acquisition.  However, rotating the images will make image and stage shift calibrations inaccurate and move the scan away from parallel to the tilt axis, thus impairing dynamic focusing.

Set Zero of IS (JEOL only)

This button can be used to reset the zero of the image shift on a JEOL, which is actually a beam shift.  It may be needed if the program fails to set the zero correctly the first time it sees STEM mode.  It would also be used if the scope alignment is changed in a way that moves the center of the focused area.