Microscope Status Panel

This window displays critical microscope parameters so that a microscope user interface  can be covered over by SerialEM.

Screen current (na) and Float button (FEI and JEOL only)

This readout shows the screen current in nanoamps (na). If the small focusing screen is in, then this is the amount of current that would be measured if the beam uniformly covered the whole large projection screen. If SerialEM thinks the small focusing screen is in it will display the label as na-fs. This readout has some smoothing to prevent jitter, so it may not respond to very small changes in screen current.

The Float button will launch a small window with the screen current readout. This window will stay on top of all other windows, so it can be seen even if other windows are brought on top of SerialEM. Smoothing is optional in this readout, so it may be more suitable for use when aligning gun tilt.

Dose button

The Dose button will launch a small window showing a cumulative dose in electrons per square Angstrom. Dose is added whenever the screen is down, and whenever a picture is taken, except that pictures of the Trial and Focus areas will be ignored in Low Dose mode. No dose is added when the beam intensity is outside a calibrated range. Press the Reset button to zero the cumulative dose.

Magnification (X)

This readout shows the current magnification, or camera length in diffraction mode. On an FEI scope, it changes when the screen is raised, so it should match the readout in the FEI interface.  The X changes to LM in low mag mode, INV in an inverted mag range on a Titan, ST or SL in STEM, or the camera length units in diffraction mode.

Defocus (Def)

This readout shows the same defocus value as appears in an FEI interface. On a JEOL or Hitachi, it is initially a value relative to the defocus when the program was started. It will NOT be the same as the 'measured defocus' reported by the autofocus routine. The defocus value shown here is based on the current objective lens strength, and it is relative to the lens setting when you last selected 'Reset Defocus' in the FEI interface, or did a 'Reset Defocus' operation from within SerialEM. The 'measured defocus' is based on the amount of image displacement that occurs when the beam is tilted, and it should reflect how far the specimen is from zero defocus.

Reset button (JEOL and Hitachi only)

Reset the defocus readout to zero. This does not affect the actual focus setting of the microscope.

Image Shift (IS or PLA)

This readout shows the total image shift in microns. When a montage is being acquired, this value will briefly reflect the image shift of individual pieces. However, in low dose mode, it will show only the image shift used to select the field of view and will not show the additional image shift of the acquisition areas. On JEOL microscopes where projector shift is being used instead of the image shift coils, this field is labeled PLA, but the same kind of shift is referred to everywhere else in the program as image shift.

Objective Lens Strength (Obj)

This readout shows the objective lens strength in percent, and will match the value shown in the microscope interface on an FEI scope.

Vacuum Quality (VAC, FEI only)

This is an indicator of vacuum quality that may alert you to watch the actual vacuum readings in the FEI interface. It should be set up so that green means near perfect, yellow means adequate for working, and red means do not open the column values.

Spot

The numeric readout shows the spot size. Also, the label 'Spot' has a colored background indicating whether the current intensity is calibrated at this spot size: blue if intensity is in the calibrated range, orange if intensity is outside the range of a calibration, or magenta if there is no calibration on the current side of crossover. This feature can be disabled by adding a line 'ShowIntensityCalStatus 0' to SerialEMproperties.txt.

+   Opens an optional section with the following entries:

Stage X, Y and Z

This readout shows the position in microns.

Intensity

This readout shows the percent C2 or C3 value or the illuminated area in microns for a Titan.

Dose rate

This readout appears when the current camera is a direct detector and shows the estimated dose rate incident on the specimen in electrons per unbinned pixel per second. The value is based on a dose calibration plus the change in beam intensity from that at which dose was calibrated, which is estimated from the beam and spot intensity calibrations.