Tasks menu commands

The Tasks menu offers the following commands:

Set Intensity Sets beam intensity based on current image mean.
Set Dose Rate Set beam intensity for a desired dose rate in electrons/unbinned pixel/sec
Move Beam Moves beam based on center marked by display point.
Center Beam Analyzes image for beam edges and tries to center beam.
Autocenter Beam Takes an image with condensed beam and uses it to center beam
Setup Autocenter Opens dialog to set up beam for autocentering
Eucentric - Rough Finds eucentric point using coarse search only.
Eucentric - Fine Refines eucentricity with pictures at a series of tilts.
Eucentric - Both Finds eucentric point with coarse search then refines it.
Refine & Realign Refines eucentricity and realign to original position.
Set Tilt Axis Offset Set offset to center image shift on tilt axis
Use Trial in LD Refine Use Trial area in Low Dose mode for Refine Eucentricity
Walk Up Goes to high tilt in steps, tracking current position.
Walk Up & Anchor Goes to high tilt in steps, leaving an image at intermediate tilt.
Use View in LD Use View area in Low Dose mode for Walkup operation.
Set Increments Set minimum and maximum tilt increment for Walkup
Setup Cooker Opens dialog to set conditions for pre-exposing specimen prior to tilt series
Cook Specimen Pre-exposes specimen for desired dose or time
Assess Angle Range Opens dialog to acquire small series of images at high tilt
Assess Interset Shifts Measure shifts between Record and other acquisition types in STEM mode
Revise/Cancel Shifts Adjust the shift for the image in A relative to Record or disable use of interset shifts
Reset IS & Realign Resets Image Shift and realigns image position.
Set Iteration Limit Set minimum Image Shift for reiterating Reset & Realign
Use Trial In LD Use Trial area in Low Dose mode for Reset & Realign
Reverse Tilt Reverses tilt direction and realigns image position.
Verbose Outputs progress and results of tasks to Log Window.
Special Options Specialized and experimental options for tasks, tilt series, Navigator, or Low Dose
  Skip Beam Shift in TS  Skip beam shift when autoaligning with image shift in tilt series
  Piezo for LD Axis Shift  Use piezo-driven stage movement for on-axis shift between Low Dose areas
  Disable Dark Trim in Align Disable automatic trimming of dark borders in Autoalign in some cases
  Allow Continuous in TS  Permit continuous mode acquisitions to be started during tilt series
  Normalize Via View for Autofocus  In Low Dose mode, go through View mode to normalize before autofocus
  Adjust Focus on Probe Mode Change   Maintain constant focus difference when switching between microprobe and nanoprobe

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.

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 unbinned 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.

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.

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.

Eucentric - Rough command (Tasks menu)

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 area). 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.

Eucentric - Fine command (Tasks menu)

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). 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.

Eucentric - Both command (Tasks menu)

Use this command to run the rough eucentricity procedure followed immediately by the fine eucentricity procedure. This sequence does make any attempt to keep the starting specimen location in the field of view.

Refine & Realign command (Tasks menu)

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 area. It is not necessary to be at zero tilt to run this command.

Set Tilt Axis Offset command (Tasks menu)

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 menu)

Use this command to select whether the Trial area rather than the View area will be used for the tilted images that are taken when refining eucentricity. The View 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.

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 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. 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 parameters.

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 and Trial areas for the Reset IS & Realign procedure. The View area 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.

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 parameters.

Verbose command (Tasks menu)

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

Skip Beam Shift in TS command (Tasks - Special Option 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  - Special Option 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.

Disable Dark Trim in Align command (Tasks  - Special Option 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 when the Navigator does Realign to Item.  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.

Allow Continuous in TS command (Tasks  - Special Option 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.

Normalize Via View for Autofocus command (Tasks  - Special Option 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.

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

When changing between microprobe and nanoprobe TEM modes on 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.  However, in Low Dose mode, focus differences are always applied when changing between Low Dose areas and changing probe modes at the same time, regardless of this setting.  To focus independently in the two modes while in Low Dose mode, change the probe mode first with a script or in the microscope interface, then change Low Dose mode.

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.