This window displays critical microscope parameters so that a microscope user interface can be covered over by SerialEM.
Current button (Thermo/FEI and JEOL only)
The readout of screen current was eliminated from this panel in SerialEM 4.1.
This button will launch a small window with the screen current readout 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. There is an option for smoothing to prevent jitter, in which case it may not respond to very small changes in screen current. Turning this option off may make it easier to judge small changes in current, e.g., when aligning gun tilt. 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.
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.
Microscope imaging mode
There is a text indicator of whether the microscope is in TEM, EFTEM, STEM, or diffraction.
Vacuum Quality (VAC, Thermo/FEI and JEOL)
This is an indicator of vacuum quality that may alert you to watch the actual vacuum readings in the microscope 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. On a JEOL configured to access a vacuum gauge during updates of the microscope state, the color will show up here if there is no alpha, or on the imaging mode indicator if there is.
Magnification (X)
This readout shows the current magnification, or camera length in diffraction mode. On a Thermo/FEI scope, it changes when the screen is raised, so it should match the readout in the Thermo/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.
Reset button
Reset the defocus readout to zero. This does not affect the actual focus setting of the microscope, but on a Thermo/FEI scope, it will zero its defocus readout.
Defocus (Def)
This readout shows the same defocus value as appears in a Thermo/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 Thermo/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.
Image Shift (IS, PLA, or CLA)
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. On a JEOL, it will be relabeled CLA in STEM mode.
Illumination mode
On a Thermo/FEI scope, this indicator will show the probe mode as uP or nP. On a JEOL scope with alpha, the alpha value is shown after the letter 'a'.
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 directly calibrated range, light cyan if it is in the region outside that range where the calibration is extrapolated, orange if it is completely 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.
Intensity
This readout shows the percent C2 or C3 value or the illuminated area in microns for a Titan.
+ Opens an optional section with the following entries:
Stage X, Y and Z
This readout shows the position in microns.
Objective Lens Strength (Obj)
This readout shows the objective lens strength in percent, and will match the value shown in the microscope interface on a Thermo/FEI scope.
Dose rate and S/C buttons
This readout appears when electron dose is calibrated and shows the estimated dose rate incident on either the specimen (in electrons per square Angstrom per second) or the camera (in electrons per physical 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. If any of the cameras are direct detectors, the S and C buttons will appear for switching between specimen and camera dose rates. They are enabled only when the current camera is a direct detector and an image has been taken that provides a scaling between specimen and camera doses. In Low Dose mode, the camera dose rate is based on the current magnification, spot size, and intensity, unlike in the camera setup dialog, where it depends on the defined properties of each Low Dose area.