Low Dose Control Panel

Low Dose Mode

This check box turns low dose mode on or off. When low dose is turned on, the current area is undefined unless the screen is down. When low dose is turned off, the program returns to the Record area.

Electron dose of current area

If electron dose is calibrated, the dose will appear for the current area in the upper right corner of the Low Dose panel. This dose will be updated continuously when the 'Continuous update' option is selected and will also we changed when the exposure time changes for the current area.

Mag & beam settings of current area

The line will show the name of the current area and its magnification, spot size, and brightness setting as given by a condenser lens strength or illuminated area. The line is shown in black when the 'Continuous update' option is selected, to signify that the values can be readily changed. Otherwise the line will be grayed out and be hard to read.

Continuous update (see tooltip)

When this option is selected, any change of magnification, spot size, brightness, diffraction focus in diffraction mode, energy filter settings, probe mode on a Thermo/FEI scope, or alpha on a JEOL scope will immediately change the parameters of the current area. Otherwise, such changes will be lost when a new image is acquired from the given area, except for intensity changes made with Set Intensity or Set Dose Rate in the Tasks menu.  Beam shift, beam tilt, focus settings in imaging mode, and image shift displacements for a particular area are NOT recorded when this option is on, but can be introduced by other options in this panel.

Usually, if you have already changed some microscope settings, those changes will be incorporated into the current area when turning this option on.  However, when the current area is View or Search and either the probe mode has been changed or the magnification has crossed the LM-nonLM boundary, the program needs to reassert the pre-existing area parameters to prevent defocus from getting off.  For these two areas, these kinds of changes can be made only after this option is turned on.

Define position of area

Select Focus or Trial to adjust the position of these areas relative to the Record area. (If 'Keep Focus and Trial identical' is selected, it does not matter which area is selected here.) With one of these options selected, SerialEM will try to display a marker point on the image in buffer A showing the center of the area being defined. On a View image, it will also draw boxes representing the Record area and the area being defined, as well as a circle circumscribing the area being defined. You can adjust the position of the area in 4 ways:

  1. by clicking with the left mouse button in a View image or in an image from the area being defined.  A View image can be in any buffer or even read in from a file; an image of the area being defined must be in buffer A;
  2. by entering a positive or negative distance in the 'Position on tilt axis' text box;
  3. by shifting an image of the area being defined with the right mouse button (although shifting a Record or View will still change image shift as usual);
  4. and even by adjusting image shift through microscope controls when the screen is down.

When you click in a View image, the behavior depends on whether the axis between areas is free to rotate away from the tilt axis, with the 'Rotate interarea axis' option. If that option is off, the marked position will be projected onto the tilt axis and that projection will define the distance of the area along the axis.  If the option is on, the marked position will be used as is, changing both the angle of the axis and the location on the axis.  When you click in an image of the area being defined, the axis rotation is not changed, and the clicked point is projected onto the interarea axis.

You should select 'None' after adjusting the area to avoid inadvertent changes, and to restore the expected behavior when shifting an image with the right mouse button. Note that shifting the area being defined would change its offset until defining is turned off.

Position on Tilt Axis

When the position of the Focus or Trial area is being defined, this text box will show the center-to-center separation between that area and the Record area. You can enter a number to set this distance as desired.

Area separation

When the position of an area is being defined, this line shows the minimum separation between that area and the Record area. This separation is the distance between the edge of a circle drawn just around the outside of the area being defined, as defined by its camera parameters, and the edge of the Record area as defined by its camera parameters. If 'Keep Focus and Trial identical' is selected, the larger of the two areas will be used for this computation.

Go to area buttons

These buttons allow you to go to a particular area without taking an image.  The button for the current area is outlined in green.

Additional beam shift (and possibly tilt)

The controls in this box allow you to impose an independent beam shift for each area relative to Record. You can use this to correct for imperfections in beam centering between the different areas, such as due to mag changes or inadequacy in the coupling between beam shift and image shift. You can also use it to shift the beam in the Trial and Focus areas farther away from the Record area than it would be if it were centered. To set beam shift for an area, first be sure that the beam is centered in the Record area, then go to the area of interest, turn on the 'Set' checkbox, move the beam to the desired position and turn off 'Set'. At this point, if beam shift is calibrated, the value of the shift will appear next to the 'Reset' button. This shift is in microns and in specimen coordinates, where X is along the tilt axis. Press the 'Reset' button to return the shift of the current area to zero. 

If the title line of this group box is Additional beam shift (and tilt), a change in beam tilt is also recorded at the same time as a change in beam shift, and it is applied when changing between areas.  (This feature is enabled by setting the property 'LowDoseBeamTiltShifts' in the properties file; as of SerialEM 3.4, it is no longer restricted to Trial and Focus areas). On Thermo/FEI scopes, the beam tilt recorded in this case would be adjusted by the Rotation Center alignment.  The 'Reset' button will return these beam tilts to 0.

For Thermo/FEI scopes, Dark Field beam tilt provides a better way to adjust beam tilt for the Trial and Focus areas; it is available as of SerialEM  3.6 and the group box title will be Additional beam shift (and DF tilt) unless the 'LowDoseBeamTiltShifts' property is set.  In this case, an absolute setting is stored, not a difference between starting and ending values, so the only the dark field state when 'Set' is turned off matters.  This value is not reset when the 'Reset' button is pressed (should it be?), so to clear it out, just turn Dark Field off and turn 'Set' on then off.  This feature may be useful for allowing larger image shift with a small objective aperture on 300 KV Tecnais and Polaras.

Beam shifts and tilts could be set for the Record area prior to SerialEM 3.6 and can no longer be, to avoid inadvertently setting undesired values for Record and reduce confusion.  Existing values from a previous version will be used until they are cleared out with 'Reset'.

Defocus offset for View or Search

You can use this control to set an additional underfocus for the View or Search area, depending on which radio button is selected. Focus will be changed by this amount when going to the View or Search area (e.g., by taking an image) and then will be restored when going to another area. For example, if you have a focus target of -4 microns, set the offset to -8 to get View images taken at -12 microns defocus.  Be sure to align the View or Search images with the offset feature described next if you use very large defocus values.

The defocus offset is applied after going to the magnification of the area; thus it will be incremental to a focus change imposed by the microscope during the magnification change.  In particular, when going between nonLM and LM, the microscope may restore the last defocus seen in the new magnification range, and the offset is then applied to that.

Defocus offsets are disabled in diffraction mode.  An absolute diffraction focus value is recorded as part of the area settings, and can be modified when continuous update is turned on.  This absolute value is restored whenever going back to an area in diffraction mode.

Shift offset for View or Search

If image features shift when going between the View or Search and Record areas, the Set button allows you to correct for this shift. The are two methods for setting the shift offset: 1) applying a shift with the mouse button to bring the image in buffer A into alignment with a reference image; 2) placing the green marker point at corresponding locations in the images in buffers A and B.   Method 1 is more direct and potentially more accurate, but may be more difficult.  Method 2 is simple but depends on the accuracy of image shift calibrations and may also depend on the accuracy of rotation angle and pixel size calibrations.  The Set button is enabled whenever there is a shift in the A buffer for an image of the type selected with the View or Search radio buttons, or whenever there are marker points on images of appropriate types in buffers A and B. However, the Set button should be pressed only if the shift in A brings the image into alignment with a Record or Preview image, or if the makrers are indeed on corresponding points.

1) Setting shift offset with an alignment shift: The procedure for setting a shift for View is:

  1. In the Image Alignment & Focus panel, turn off 'Move stage for big mouse shifts' if it is on.  (This step is optional if you are making a small adjustment to an existing alignment, or if you shift the image in multiple steps each too small to trigger a stage move.)
  2. Take a Record or Preview image and use the right mouse button to center a feature that will be recognizable in the View image. Take another image to verify that it is centered.
  3. Take a View image. Use the right mouse button to center the feature.  Do not take another image.
  4. Press Set. The shift will be recorded as a correction, and the program will take a new View image, unless you skipped step 1 and your mouse shift triggered a stage move.  (In that case, the offset is correctly recorded, but you will receive a message that you need to reset image shift and start with a new Record image in order to check the offset.)
  5. If the new View image is not centered (such as if you are using a large defocus offset or the image shift calibration is not good), center the feature and press Set again. The new shift will be added to the existing one.  Repeat if necessary.
  6. Turn 'Move stage for big mouse shifts' back on if desired.

The procedure is the same for setting the offset for Search, although here you may want to use a View image instead of Record or Preview as your reference.  If so, be sure to align View with Record first.

2) Setting shift offset with corresponding marker points: The images from a reference area and from the area whose offset is being set can be taken in either order.  To minimize the effect of inaccuracies in the calibrations, try to pick the points near the center of the images, especially for the reference image at higher magnification.

General points: Once an image has been used for setting the offset, it cannot be used again; you need to acquire new images.

If for some reason this shift offset becomes inappropriate, you can set it to zero with the Zero button.  However, do not zero out the shifts after taking images for setting the shift and before setting the shift with them

If the image shift offsets between magnifications are calibrated, this adjustment will work together with that calibration. You can set this adjustment with the option to 'Adjust image shift between mags' either on or off. Once you have set an adjustment, it should work equally well if you turn 'Adjust image shift between mags' on or off.

Blank/Unblank button and blanked indicator

The beam is kept blanked in Low Dose mode when the screen is up.  When the beam is blanked, this button is labeled 'Unblank' and can be used to unblank the beam until the next image acquisition, which will restore blanking when it is done. (Other actions may also turn the blanking back on.)  When the beam is not blanked, the button is labeled 'Blank' and can be used to blank the beam.  The principal use of this button is to unblank the beam before aligning an energy filter. To the right of the button, the text 'Blanked' will appear whenever the beam is blanked, even transiently during exposures when not in low dose mode.

BLANK BEAM when screen downn

This option will prevent specimen exposure while the screen is down. Ctrl-B is a hot key for toggling this setting.

Normalize beam through View / Normalize condenser lenses

This option will appear in one of two forms depending on whether there is an entry for NormCondenserInLowDose in SerialEMproperties.txt. 

When the option is Normalize beam through View and is selected, changes in intensity and spot size when going between some areas will be normalized by passing through the View area intensity and spot size. This initial change will not be done will be done when going to the Search area or going between areas with identical beam settings.  This normalization is intended to compensate for the lens hysteresis that makes the beam position depend on the recent history of intensity changes, a pronounced effect on 300 KeV JEOL scopes. With the option on, the beam position in the Record area, for example, should be the same regardless of whether the program has just come from the View area or has been going back and forth between the Record and Trial/Focus areas. If different areas still have different beam positions, use the option for setting 'Additional beam shift' for some areas. It may be necessary to set the property LowDoseBeamNormDelay to a higher value for maximum effect.

When the option is Normalize Condenser Lenses and is selected, the microscope routine for normalizing condenser lenses will be called when changing areas, except when going to View or Search, or when going between areas with identical beam settings.  Again, the property LowDoseBeamNormDelay may need to be set to a higher value for the best result.

Note that the value of NormCondenserInLowDose can be changed with the SetProperty script command, but the label here will not change.

Keep Focus and Trial identical

When this option is selected, the parameters of the Focus and Trial areas will be kept the same in all respects. It is desirable for these areas to be in the same location because of the large settling time that would be required after moving the beam from one side of the Record area to the other, and because of the limited space inside the objective aperture on the 300 KV Tecnai or Polara. You might want different brightness settings, in which case you would have this option selected while positioning the areas, then unselected to adjust the brightness of one.

Copy current area settings to V - F - T - R - S

These buttons will generally copy all properties except the axis position from the current area to one of the 5 areas: View, Focus, Trial, Record, or Search.  When copying between View and Search, the defocus and shift offsets are copied as well.  When copying to Record, the beam shift and tilt offsets will be set to zero rather than copied, since Record is supposed to be the reference for these offsets.  Copy would be useful mostly when initially setting up the areas. Because they are easily mistaken for the 'Go to area' buttons, a message box will appear asking you to confirm the copy.

Balance Shifts/Center Unshifted

When this button is labeled Balance Shifts, pressing it will make the image shift of the Focus and Trial areas be divided between those areas and the Record area. The Record will be displaced to one side of the center of the viewing area, and the Focus and Trial areas to the other side (assuming they are on the same side). This means that when image shift is reset to zero, there will actually be substantial image shift in the microscope when viewing the Record area.  When shifts are balanced, the button is green and labeled Center Unshifted, and pressing it will restore the unshifted condition: i.e., with Record in the center of the viewing area and Focus and Trial areas displaced by the full amount of their image shifts from the center of the viewing area.  When this button is pressed, the image shift reading in the Scope Status panel will change to reflect the change in the center of image shift coordinates, but the same area will appear if a new picture is taken.

Rotate inter-area axis

Select this option to rotate the axis between the View/Record areas and the Trial/Focus areas away from the tilt axis. Enter the angle of rotation in the text box (CCW positive). All of the features described above for defining the location of the Trial/Focus areas work the same, except that the location is forced to be along this rotated axis instead of along the tilt axis. Although this feature was added to assist with acquisition from multiple locations on an untilted specimen, autofocusing on a tilted specimen should work correctly because it is compensated for the difference in Z height between the focus area and the tilt axis.