Tasks menu commands

The Tasks menu offers the following commands:

A Note on Tasks in Low Dose Mode

Tasks that use lower magnification tracking will generally use View images in Low Dose mode, although some have menu entries to control which area is used.  However, each such task has a required minimum field of view when run outside of Low Dose, which sets a minimum magnification at which it should be run.  When the View magnification is higher than that minimum, and the Search magnification is lower than View and not in LM mode, the program will use Search instead to minimize the risk of excessive shifts between images.

Rough Eucentricity command (Tasks - Eucentricity submenu)

This command can be used to adjust the Z height to the eucentric point when the Z height might be off by more than 5-10 microns, which can often be the case when the specimen rod has just been inserted. This procedure will find eucentricity to within about 0.5 micron. This is good enough for tuning the microscope but not as accurate as the adjustment provided by the Eucentric - Fine command, which should be run before starting a tilt series.

This procedure does not make any attempt to keep the starting specimen location in the field of view.

The rough eucentricity procedure first switches to a low magnification (or, in Low Dose mode, it uses the parameters of the View or Search area, as described above). It takes pictures to determine how far the specimen moves laterally upon tilting, starting with a very small tilt increment and working up to a total increment of 8 degrees. It may adjust the Z height more than once before finishing.

Fine Eucentricity command (Tasks - Eucentricity submenu)

This command can be used to adjust the Z height to the eucentric point when it is already within 5-10 microns. It is thus a suitable procedure to use if you have moved to a new location on the specimen grid since the last time eucentricity was adjusted. It is recommended that you run this command before starting a tilt series.

This procedure does not make any attempt to keep the starting specimen location in the field of view. It can be run when not at zero tilt, and the program will return the stage to your pre-existing tilt at the end.

The fine eucentricity procedure first switches to a low magnification (or, in Low Dose mode, it uses the parameters of the View area or Search area, as described above). It then takes pictures at a set of tilts between -24 and +24 degrees. From the image displacements during this series, it can compute both the distance in Z from the eucentric point and the lateral displacement of the tilt axis from the optical axis. If image displacements become too large, the program will adjust Z height then repeat the procedure from the beginning.

For specialized uses it may be desirable to change the maximum angle or tilt increment.  These parameters can be changed with the properties 'EucentricityMaxFineAngle' and 'EucentricityFineIntervalAtZero'.

Both Rough and Fine command (Tasks - Eucentricity submenu)

Use this command to run the rough eucentricity procedure followed immediately by the fine eucentricity procedure. This sequence not does make any attempt to keep the starting specimen location in the field of view.

Refine & Realign command (Tasks - Eucentricity submenu)

Use this command to run the fine eucentricity procedure while retaining an item of interest centered in the field of view. The program will first take a low-magnification reference picture, then do the fine eucentricity procedure, then take another picture at the original tilt angle and use that to restore the alignment. In Low Dose mode, the reference picture will be taken of the View or Search area, as described above. It is not necessary to be at zero tilt to run this command.

Set Tilt Axis Offset command (Tasks - Eucentricity submenu)

Use this command to set the offset of the tilt axis from the optical axis, which is used to keep image shift centered on the optical axis. If the tilt axis is more than a micron from the optic axis, it is desirable to set this offset to minimize specimen movements in Y and Z during tilting. The offset should be set as a system-wide property. However, if this property setting is not adequate, or if the offset varies significantly from place to place, this command can be used to set the offset. It is placed in this menu because the lateral offset from the Refine Eucentricity procedure indicates how much the offset should be changed. When the command is selected, a dialog box comes up informing you of the current tilt axis offset, and the total offset implied by the lateral displacement reported in the last run of Refine Eucentricity, if any. The default value in the box is the implied total offset (or just the current offset, if Refine Eucentricity has not been run.) A tilt axis offset has an effect only if you have selected 'Center image shift on tilt axis' in the Image Alignment and Focus control panel.

Use Trial in LD Refine command (Tasks - Eucentricity submenu)

Use this command to select whether the Trial area rather than the View or Search area will be used for the tilted images that are taken when refining eucentricity. The View or Search area will still be used for the initial and final tracking images when the Refine and Realign procedure is used, and for the rough eucentricity procedure when both rough and fine procedures are run together. Using the Trial area will save a little dose but will reduce the range of Z heights over which the procedure can run reliably. Also, if the specimen is not relatively flat along the tilt axis, the Trial area rather than the Record area will be brought to the eucentric height.

Rough Use Search if in LM command (Tasks - Eucentricity submenu)

Toggle this entry to switch between using the View or Search area (as described above) for the rough eucentricity procedure in Low Dose mode and using the Search area, if it is defined as being in low magnification and if the microscope is already in low magnification.  Running this procedure in LM may be accurate enough for some purposes, so this option allows it to be run with the Search area without losing the time involved in leaving low magnification just for this purpose.

Eucentricity by Focus command (Tasks - Eucentricity submenu)

Use this command to set the Z height to the eucentric point with a procedure that sets an absolute focus value then measures the defocus and adjusts Z until the measured defocus matches the appropriate value.  Both the absolute focus and the measured defocus are recorded with a calibration procedure run from the Eucentricity by Focus Setup dialog opened by the next menu item.  Defocus can be measured with either Focus or View images in Low Dose mode, with a desired amount of defocus offset.

Setup Eucentricity by Focus command (Tasks - Eucentricity submenu)

Use this command to open the Eucentricity by Focus Setup dialog and calibrate the focus targets for the Eucentricity by Focus command as well as set a few parameters controlling how it operates.

Set Intensity command (Tasks menu)

Use this command to change the beam intensity so as to achieve a desired mean level in images taken with Record parameters. When you select this command, the program first computes the zero-tilt mean (mean of the tilt-foreshortened area) of the image in buffer A. It then takes account of the exposure time and binning of that image to determine what the zero-tilt mean of a Record image would have been at the current beam intensity. The program presents a dialog box in which you can enter the new intensity; the default value in this box is the computed mean for a Record image at the current intensity. This value will give you some idea of how big a change you are requesting. If you accept this default, nothing will change. Enter the desired mean level.

Since the program changes intensity by condensing the beam, it is possible that the beam will become too small to cover the camera area. If you increase the intensity by a substantial amount, you should check whether the beam still covers the area before going on to tasks that rely on full exposures.

In Low Dose mode, this command will change the intensity setting for the Low Dose area from which the image was acquired, regardless of whether 'Continuous update' is on in the Low Dose control panel.

Set Dose Rate command (Tasks menu)

Use this command to change the beam intensity to give a desired dose rate on the camera, in electrons per physical pixel per second, based on the counts in the image in buffer A.  The mean of the tilt-foreshortened area will be used, as for the Set Intensity command.  The programs presents a dialog box showing the dose rate in that image and asking for the new value.  In Low Dose mode, this command will also change the intensity setting for the Low Dose area from which the image was acquired.

Electron Dose command (Tasks menu)

Use this command to calibrate electron dose for a particular spot size. This calibration is also specific to the probe mode for Thermo/FEI scopes. It is automatically saved in a special short-term calibration file and is only good for a limited period of time (1 day by default, but this time can be set with the property 'DoseLifetimeInHours'). The calibration requires that beam intensity be calibrated and that the SerialEMproperties.txt file contain an entry for CountsPerElectron for the camera.

Before activating the command, take an image of the blank beam with a reliable exposure time (e.g., 0.2 or more seconds) and with the beam in the calibrated range for the current spot size.  Specifically, the intensity has to be within the directly calibrated range, not in the range where the calibration can be extrapolated, so the 'SPOT' label in the microscope status panel should be darker blue, not light cyan. Select the command and press OK. The program will report the dose rate (electrons per square Angstroms per second) of the beam intensity at which that image was taken.  Or, if intensity was not in the directly calibrated range, there will be a message telling you what that range is.

The dose calibration will be most accurate if the spot size is normalized (on a Thermo/FEI scope). To do this, open the Normalizations panel in the Microscope User Interface, select TEM Spotsize, and check Spotsize. Then change spot size to get a normalized beam, take a picture, and calibrate the dose with it. By the same token, the actual measurement of dose at a particular beam setting will be more accurate if the spot size is normalized whenever you change spot sizes. Hysteresis in the second condenser lens will also reduce the accuracy of a dose measurement, but this is more difficult to control for.

The dose calibration is specific to the side of beam crossover on which the calibration image was taken. Once a calibration is present, the program can compute the dose for any image acquisition when beam intensity is within the calibrated range, taking into account drift settling time as well as CCD exposure time. If relative spot intensities have been calibrated, then a calibration at a single spot size will allow dose to be computed at any spot size. Note that dose is automatically calibrated when you take a gain reference, unless you deselect this option in the Gain Reference dialog .

When there is an electron dose calibration, the estimated dose at the specimen will be displayed in several places:

1. The dose for a low dose acquisition area will appear in the upper right of the Low Dose control panel, with a continuous readout if 'Continuous update' is selected.
2. The dose for the current camera exposure time, in the lower right of the Camera Setup dialog .
3. When a direct electron detector is the selected camera, the dose rate at the specimen, per unbinned pixel per second, will appear in the Options portion of the Microscope Status panel.

Purge Old Calibs command (Tasks menu)

This command will remove any dose calibrations done before the current instance of the program was started. You would use this if you do a dose calibration (or take a gain reference) and then want to remove any earlier calibrations. Dose calibrations older than 24 hours are ignored when the program starts. Also, when dose is calibrated, other calibrations older than 12 hours are then removed.

Move Beam command (Tasks menu)

Use this command to move the beam by a controlled amount. You can use it to center the beam by first taking a picture with the beam condensed enough to show much of its boundaries. Then click the left mouse button to set a display marker point in the center of the beam. Next, select this command, and the center of the beam will be moved to the center of the field. In general, the beam will be moved by the amount that would move the marker point to the center of the field.

After you use this command, you need to take another picture to see the position of the beam.

Center Beam command (Tasks menu)

You can use this command to center the beam if the edge of the beam is fairly sharp and appears in the currently active image. The program will analyze the image to find the beam edge then solve for a circle that fits the edge. It will then move the beam to move the center of that circle toward or to the center of the image. The solution will be most accurate if the beam edge appears in 3 or 4 corners of the image, and will be fairly accurate when there is beam edge in two corners of the image. With an edge in only one quadrant, the program will be increasingly conservative in how much it moves the beam, the smaller the piece of edge is. When the edge occupies less than 20 degrees, the beam will simply be moved enough to get the edge out of the field, so do not expect the beam to be centered in such situations. This command will not work if the beam edge is not relatively sharp, so it will not work with some non-FEG scopes.

If the log says 'No beam edges detectable in this image' for an image with clear edges, check the counts in the region otside the beam compared to inside the beam.  The program requires that the counts outside fall below 15% of the mean inside.  If the background counts outside the beam are too high, set the property 'FindBeamOutsideFrac' to an appropriate value above 0.15.

Autocenter Beam command (Tasks menu)

You can use this command to center the beam automatically by taking an image with the beam condensed so that its position can be detected reliably either from the edges of the beam or from the average location of the beam in the image. You must first set up the beam intensity at the current or a nearby magnification and spot size, using the Beam Autocenter Setup dialog box . The program will condense the beam, take one or two images depending on the centering method, and restore the beam.

Setup Autocenter command (Tasks menu)

Use this command to open the Beam Autocenter Setup dialog box and set the beam intensity that will be used for autocentering.

Walk Up command (Tasks menu)

Use this command to go from one tilt angle to another while retaining an item of interest centered in the field of view. Typically this would be used to go from zero tilt to a high tilt angle. After you select the command, you will encounter a dialog box in which to enter the destination tilt angle. This destination angle will be saved and will appear as the default angle the next time you invoke the command.

This procedure involves taking alignment pictures at a series of tilt angles, with a tilt interval that is quite coarse at low angles and finer at high angles. Image shift will be reset whenever it gets too high, but no autofocusing is done. The pictures are taken with the Trial parameter set and, if in Low Dose mode, the pictures are of the Trial area. If the magnification is too high for reliable tracking, the pictures will be taken at a lower magnification.

If you choose a destination angle that is in the opposite direction from the last direction of tilt, the routine will run the Reverse Tilt procedure first to avoid losing the area of interest.

Walk Up & Anchor command (Tasks menu)

Use this command to do the same operation as in the Walk Up command but also leave an image behind at a specified intermediate tilt angle. The image will be left in the last image buffer and can be used as an 'anchor' for alignment during a tilt series. The angle for the anchor image will be saved as the default for the next use of this command and is the same as the angle that appears for an anchor image in the Tilt Series Setup dialog box .

Use View in LD command (Tasks menu)

Use this command to select whether the Walk Up routine will be run with the View or Search area (as described above) instead of the Trial area when in Low Dose mode.

Set Increments command (Tasks menu)

Use this command to set the minimum and maximum tilt increments for the Walk Up operation. The maximum increment is used at zero tilt, and the increment at any tilt angle is either this maximum times the cosine of the angle, or the minimum increment, whichever is greater. In STEM mode, you can also set the tilt interval between autofocusing during a Walk Up.  Your settings for these values are retained between sessions of SerialEM.

Setup Cooker command (Tasks menu)

Use this command to open the Specimen Cooking Setup dialog box and set the magnification, spot size, and intensity to use for pre-exposing the specimen.

Cook Specimen command (Tasks menu)

Use this command to pre-expose the specimen for the desired electron dose or time, using the parameters set in the Specimen Cooking Setup dialog box . The program will lower the screen to expose the specimen, report in the log window as each tenth of the exposure is finished, and continually update the status bar with the expected time remaining.

Assess Angle Range command (Tasks menu)

Use this command to acquire a small series of images at high tilt in order to determine the limits of the tilt range for a tilt series. There are options that allow a series to be acquired as quickly as possible, or more slowly and carefully, depending on what you wish to see in the high tilt images. These options are set in the Tilt Series Range Finder dialog box.

Assess Interset Shifts command (Tasks menu)

In STEM mode, use this command to measure the shifts between Record and other images with current camera parameters.  These shifts are compensated during tilt series acquisition to make sure that tracking and focusing images are centered on the Record area.  The shifts are specific to the magnification and the image size and binning, and also depend on exposure time when the scan rate is relatively high.  The shifts are not saved for different conditions, so this command needs to be run as part of the routine tasks before starting a tilt series, after camera parameters have been set up.  The Record exposure time can be varied during the tilt series, but the other exposure times should be kept constant, or else the shifts will not be considered valid.

When not in Low Dose mode, the routine will measure the shift for a Trial image and for a Focus image relative to Record.  When in Low Dose mode, the routine will always measure a shift for a Preview image.  It will then measure a shift for a Trial if Trial area is centered on Record, and a shift for Focus if the Focus area is centered on Record.  At the end, you should scroll through the images to make sure they are well-enough aligned.  If the image in A is not aligned, you can align it with the right mouse button then use the Revise/Cancel Shifts command.  If a different image is not aligned, you can try the command again with a new image area, or eliminate the shifts with the Revise/Cancel Shifts command.

Revise/Cancel Shifts command (Tasks menu)

Use this command either to indicate that an interset shift should be taken from the alignment of the image in buffer A, or to eliminate the last measured interset shifts.  You will first be asked if you want the revise a shift based on the alignment of the image in A.  If you answer No, you will then be asked if you want to eliminate the interset shifts.

Reset IS & Realign command (Tasks menu)

Use this command to reset the microscope image shift (IS) while retaining an item of interest centered in the field of view. The program will take a reference picture, reset the image shift to zero and move the stage to compensate, then take another picture and align it to the reference picture. At the end, image shift will no longer be zero because of this alignment; in fact, it can be as much as one-quarter of the original image shift because of inaccuracy in stage movement. The reference picture will be taken at low magnification or, if in Low Dose mode, with the View or Search parameters, as described above.

If you just want to reset image shift without having a feature stay centered, use the Reset Shifts button in the Image Alignment & Focus panel .

Set Iteration Limit command (Tasks menu)

Use this command to change the criterion that the Reset IS & Realign procedure uses to decide whether to reset the shift and realign a second time. After resetting the shift, the program takes an image and aligns it to image taken before the reset. If image shift is still greater than this criterion, it will be reset again, and another image taken and aligned.

Use Trial in LD command (Tasks menu)

Toggle this entry to switch between using the View or Search area versus the Trial area for the Reset IS & Realign procedure. The View or Search area (as described above) is the default because the stage movement involved in resetting the shift is unpredictable, and the larger field of view of the View area is assumed to be needed to do the reset reliably. It may be safe to use the trial area if your limit for resetting image shift is small (~1 micron), if the field of view of the trial area is fairly large (2 microns), and if your stage is adjusted so that stage movements are reliable at high tilt for the holder being used.

Setup VPP Conditioning command (Tasks menu)

Use this command to open the Phase Plate Conditioning Setup dialog box and set parameters for conditioning a Volta phase plate. The dialog allows one to start the conditioning operation, which can also be run with the ConditionPhasePlate script command.

Setup Wait for Drift command (Tasks menu)

Use this command to open the Wait for Drift Setup dialog box and set parameters for the Wait for Drift task, which can be run from tilt series and with the script command DriftWaitTask to measure drift and wait until it reaches a selected level.

Reverse Tilt command (Tasks menu)

Use this command to reverse the direction of tilting while retaining an item of interest centered in the field of view. For example, if you tilt up to a high angle, center your item of interest, then try to start a tilt series by just tilting back down, the specimen may move considerably because of backlash in the stage. This problem can be avoided by using this command. The program will take a reference picture, tilt far enough in the current direction to work out the backlash, tilt back to the starting angle, then take another picture and align it to the reference picture. The reference picture will be taken at low magnification or, if in Low Dose mode, with the View or Search parameters, as described above.

Setup Scope Management command (Tasks menu)

Use this command to open the Dewar and Vacuum Management dialog, which allows you to set parameters for a routine that can manage periodic operations on the microscope that might interfere with data collection, either vacuum pumps running on a Thermo/FEI scope, or nitrogen dewar filling on various scopes.  The routine can check whether some events have begun and wait until they are done, or start some events proactively and wait until completion.

Verbose command (Tasks menu)

Use this command to toggle diagnostic output to the Log window from the various procedures run from the Tasks menu.

Disable Dark Trim in Align command (Tasks  - Specialized Options submenu)

Even when 'Trim dark borders in Autoalign' is not selected in the Image Alignment & Focus control panel, this trimming happens automatically in three cases: when in Low Dose mode, when doing a task at a lower magnification and not in Low Dose mode, and in the first round of Realign to Item or alignments after resetting image shift in Align to Template.  This option allows the automatic trimming to be disabled in selected cases.  Three dialog boxes will come up.  The first controls the trimming in Low Dose mode; enter 1 if you want to disable it just when doing a tilt series, or 2 if you want to disable it always.  The second entry controls the trimming when doing tasks; again, enter 1 if you want to disable it just when doing a tilt series, or 2 if you want to disable it always.  The third entry allows you to disable the trimming when running Realign to Item or Align to Template.  Note that the 'AlignTo' script command also has an optional entry to prevent trimming.  The decision to trim is made as follows:

• Trimming is not done if 'AlignTo' is run with that option set to prevent trimming
• Otherwise, if doing Realign to Item or Align to Template, trimming is determined by the option set here for those operations
• Or, if in low mag for another task and not in Low Dose, trimming is determined by the option set here for tasks
• Or if in Low Dose mode, not doing a Realign or  Template Align, trimming is determined by the option set here for Low Dose
• If not in Low Dose mode or doing Realign or Template Align or a task, trimming is controlled by the choice in the control panel

Adjust Focus on Probe Mode Change command (Tasks  - Special Option submenu)

When changing between microprobe and nanoprobe TEM modes on Thermo/FEI scopes, the scope will restore the defocus last seen in a mode when returning to that mode.  With this option turned on, the program will try to maintain a constant difference between the focus levels in the two modes. It does this by tracking how much defocus changes during the time spent in one mode and imposing that focus change on the scope's restored focus value when switching to the other mode.  This means that you can use autofocus in one mode and have the required focus change applied when returning to the other mode. 

The option needs to be turned off in order to impose a needed focus difference between the modes.  As of SerialEM 3.7, focus differences are always applied in Low Dose mode only when this option is on.

If you want to "Reset Defocus" while this option is on and have that change in focus readout ignored, use the entry in the Focus menu instead of a button in the microscope interface.

Normalize All on Mag Change command (Tasks  - Specialized Options submenu)

This option controls when all lenses are normalized after changing magnification on a Thermo/FEI or Hitachi scope.  Normally, the program will always normalize the projector lenses, and normalize condenser and objective lenses in addition when changing between LM and nonLM magnifications.  With this option, you can enter a 1 to normalize all lenses after all mag changes within LM, or a 2 to normalize all lenses after all mag changes.

Turn Off Beam After Long Inactivity command (Tasks  - Specialized Options submenu)

With this option, you can enable the program to close valves or turn off the filament if it is left idle for longer than a specified length of time.  After selecting the option, enter the number of minutes of inactivity after which the program should turn off the beam, or 0 to disable this feature.  The option appears checked in the menu when a positive time has been entered.

Normalize Via View for Autofocus command (Tasks  - Specialized Options submenu)

When this option is selected, the program will switch to the View area in Low Dose before going to the Focus area for autofocusing, unless it is currently in Focus and arrived there from View.  When 'Keep Focus and Trial identical' is selected in the Low Dose Control Panel, Trial and Focus are considered equivalent for the purpose of deciding whether this normalization needs to be done.

This option controls whether the beam is kept blanked except when acquiring images when the screen is up in Low Dose mode.   This blanking protects the specimen from being exposed when there is no camera inserted that would cause shuttering to keep the beam blanked. When there is a camera inserted, it also protects the specimen when the screen is lowered during the interval between the camera opening its shutter and SerialEM discovering that the screen is down.  Select this option to prevent the blanking if it is problematic for some reason.

Keep Focus & Trial at Same Position (Tasks  - Specialized Options submenu)

Keep the Focus and Trial areas in Low Dose mode at the same position even when the Keep Focus and Trial identical option in the Low Dose control panel is not selected. 

Tasks Use View Even if Search Better command (Tasks  - Specialized Options submenu)

When a task is run in low dose mode and needs to take tracking images at a lower magnification, it will generally use the View area.  As of SerialEM 4.0, January 16, 2022, the Search area will be used instead if it provides a better field of view for reliable tracking, namely, if the View magnification exceeds the maximum magnification for that particular task when run outside of low dose while the Search magnification is less than that of View but not in LM mode.  The list of tasks where this will occur is: Reset Shift and Realign, Walk Up with 'Use View in LD' selected or when getting an anchor image, Reverse Tilt, Rough and Fine Eucentricity, Tilt after Stage Move, Adjust Backlash, Assess Angle Range, and Condition Phase Plate.  This option can be used to disable this new behavior and use the View area regardless of how unsuitable it is.

Skip Beam Shift in TS command (Tasks - Specialized Options submenu)

When using a phase plate on a JEOL microscope, the beam shift that accompanies every image shift operation will change the centering of the phase plate.  Turn on this entry to suppress the beam shift for the alignment operations involving image shift during a tilt series.

Piezo for LD Axis Shift command (Tasks  - Specialized Options submenu)

If there is a piezo plugin loaded that can provide stage movement along the tilt axis, and the properties file contains both an entry 'UsePiezoForLDAxis' specifying this piezo and an entry 'PiezoScale' defining the range and scaling of this piezo, this option can be turned on to use this piezo movement as a substitute for on-axis image shift between Record/View and Trial/Focus areas in Low Dose mode.  The option can be toggled only when Low Dose mode is off.  When Low Dose is turned on with this option enabled, the piezo is moved to the end of its range appropriate for the Record area.  Several restrictions are also enforced: Focus and Trial are constrained to the same properties; 'Balance Shifts' is turned off; rotation of the interarea axis away from the tilt axis is turned off.  The 'Position on tilt axis' entry can be negative or positive as needed, but the stage will be moved to the other end of its range when the sign is changed.

Allow Continuous in TS command (Tasks  - Specialized Options submenu)

Ordinarily, the program will acquire images in single-frame mode for almost all automated operations, even when using a camera parameter set that has continuous mode set.  If this option is selected, images acquired directly by the Tilt Series Controller will be allowed to be taken in continuous mode if that mode is set in the camera parameters.  Such continuous acquisitions must be stopped manually by the user before the tilt series can go on.  This exception does not apply to images taken when autofocusing or doing other tasks; all tasks enforce single-frame mode.  Thus, it applies to Trial and Record, as well as to View and Preview images taken in Low Dose mode.