Multiple Record Setup Dialog

This dialog allows you to set parameters for taking multiple Record images with image shift used to center on a series of positions.  The positions can be in a circular pattern around the current position, which would generally be used for taking multiple shots within a hole, or in designated positions relative to the current position, which would generally be used for taking shots in multiple holes.  Both within-hole and between-hole images can be taken.  The parameters are used in two ways: when acquiring the images with the 'MultipleRecords' script command, and when displaying the positions as a pattern of circles representing the beam on an image (e.g., a lower-magnification map).  The latter display occurs when this dialog is open, and also when the 'Show Acquire area' checkbox in the Navigator dialog is turned on and the display is enabled with the Show Shots when Show Acquire option in the Navigator - Montaging & Grids submenu.  When the relevant parameters here are changed, these changes will appear immediately in the display.

It is important to realize that if the image areas are being displayed on a Low Dose View image with a large defocus offset, the positions and sizes may be misleading.

Saving Accurate Image Shift Values for Holes

There are several possible methods of setting the image shift values for the holes, ranging from centering holes in an image where they are all visible (e.g., low dose View), through centering consistent positions at a magnification still lower than the Record mag, to centering positions at the Record mag itself.  Your choice depends on how accurate the positioning needs to be (more accuracy is needed for holes at more distant image shifts or if multiple shots are to be taken inside the holes), and on how well image shift positions correspond between the Record mag and the mag where they are defined (a constant offset is not a problem, scaling or rotation is).  You can try an easier method first and see if it is adequate for your situation.  See the section at the end of this page on how to assess that point .

The goal is the save image shifts at consistent positions, not necessarily the ones at the center of the holes, because only the differences between shifts matter.  It is just as good to save the shift at the edge of each hole, if a corresponding point on the edge can be picked accurately enough.  Here are two methods of positioning along a diagonally oriented part of a hole edge:

All of these methods require the Navigator to be open and suggest that you add a group of points on an image at the locations where you want to save image shift values.  This step is helpful if you have more than a 2x2 pattern of holes, to avoid losing track of which hole you are on. You should add those points in the order in which their positions will be saved (see 'Save Image Shift Values at Holes' below.)  When you press the button to start saving image shift values, the Navigator buttons on the left change, 'Go To XY' and 'Go To Marker' change to 'IS to XY' and 'IS to Marker' respectively.  They can be used to move to marked positions with image instead of stage shift.  The same operation can be done with the 'IS to Nav Pt' button in this dialog.

1) Centering holes at a lower mag.  In order for image shift positions to correspond well enough between this mag and the record mag, this operation must be done near focus (within about 20 microns).  Assuming that you use View images, the steps are:

This method can be accurate to within 1% on a scope with good correspondence between View and Record positions, but can be off by a lot.

2) Picking consistent positions at an intermediate mag where it is still easy to find the hole.  Even if you cannot use the View mag, you will probably get accurate positions at some mag closer to the Record mag (e.g., half the mag), because image shifts are likely to be consistent at higher mags.  You will probably be able to use this method without changing the View defocus offset, but you will need to change the Record mag.  The steps are:

3) Picking consistent positions at the Record mag.  This method is guaranteed to give accurate image shift values, as long as you can define consistent positions.  If you think that you can position edges well enough, then the procedure is the same as just described, except that you do not need to change the Record mag.  However, if you have difficulty finding the holes, you may need to reduce the View defocus offset close to zero.  This will likely throw off the View shift offset, and you might need to adjust that too.

An alternative to positioning edges is to take a Prescan montage at the Record mag big enough to show the whole hole, and center that.  This may be reasonably fast, especially if you use continuous mode with a K2 camera.  The steps are:

The Dialog Controls

Do multiple Records within each hole

Select this checkbox to take images in a circular pattern, with no control over their angles.  The relevant controls will appear when it is selected.

Number of shots around center

Select a value between 2 and 12 for the number of Records taken in off-center positions.

Shot in center

With these radio buttons, you can include a shot in the center of the pattern, which should be possible with 6 or more off-center shots.  The centered shot can be taken either before or after the off-center shots.  Although taking it may involve one more delay for image shift settling, it is reported that this shot will have less drift when taken after the others.

Distance from center to off-center shots

Distance from the center position to the off-center positions, in microns.  This distance must be at least as big as the beam diameter to avoid exposing overlapping areas in more than one Record shot.  If the multi-shot circles are being displayed, press tab or Enter to have the image redrawn after entering a new distance.

Do Records in multiple holes

Select this checkbox to take Records in either a rectangular grid of positions or a series of arbitrary, 'custom' positions around the current center position.  The relevant controls will appear when it is selected.

Multiplier of usual delay after shifting to hole

SerialEM has a built-in settling time after image shift that depends on the size of the shift; it is probably inadequate at high magnification.  The factor entered here increases this settling time when shifting between holes; the extra delay time described below is still added to the settling time.  This separate entrt allows you to have an adequate settling time when moving between holes without having to make the extra delay for shots within a hole bigger than necessary.

Regular pattern of holes: n by n

Use the two spinners to set the number of positions in the rectangular pattern.  These values must be set before recording the image shift values at the corners. Once the spacing of the pattern is defined, the spinners can be changed to acquire more or fewer holes at that spacing.

Use custom pattern

Select this checkbox to take images in an arbitrary set of positions specified by shifting to a center location then to each acquisition position.

Save Image Shift Values at Holes

Press 'For Corners of Regular Pattern' to start setting the image shifts needed for a regular pattern, or 'For custom pattern' to start setting the shifts for arbitrary positions.  After pressing one of these buttons, the label below the next line of buttons will summarize what to do next.

To set the corners of a regular pattern, you will save image shifts at 4 hole positions, even if one of the spinners is set to 1.  Start at one corner of the pattern and save the position.  Then shift by the needed number of holes corresponding to the value of the first spinner (i.e., move by 2 holes if the value is 3) and save that position.  Shift by the number of holes indicated by the second spinner, save, and shift back by the number of holes along the first axis.  If one of the spinners is set to 1, the program will still expect you to shift by one hole along that axis.

To set the positions in a custom pattern, shift to a center position for the pattern and save the shift.  When taking multiple Records, all the shifts will be done relative to this position.  Then shift to the first point to be acquired and save that position.  Repeat until the last point and press 'End Pattern'.

See above for instructions on how to save sufficiently accurate shift values.

IS to Nav Pt

Press this button to move to the location of the current Navigator point with image shift and then select the next point  in the table.  This saves you from pressing 'IS to XY' and selecting the next point in the Navigator window, extra steps where you can lose track of whether you have changed the selection there.  Press this button on first starting the saving operation and immediately after each 'Save Image Shift'.  The first time that you do so, the program looks at how many points are in the current group and which one is selected.  If the first one is selected, or if you are defining a regular pattern and there are 4 points, it will image shift to the first point in the group and select the next one.  Otherwise, it will ask you if you want to start from the beginning and work forward, or start at the end and work backward (which is not going to work for a custom group unless you marked the central point at the end), or simply leave the selected point alone. 

End Pattern

Press this button to end the entries when defining a custom pattern.  It can be pressed either after saving the last position, or without explicitly saving it.  The current image shift will be saved if it is different from that of the last saved point.


Press this button to stop entering shifts and throw away all entries.

Save Record image

Select this option to have the Record image saved in the current file.  The option is disabled and its setting is irrelevant if an early return is selected with no returned image.

Early returns for K2

This group of controls appears when there is a K2 camera available and allows for SerialEM to resume operations as soon as possible after acquiring an image with saved frames, the same as is accomplished with the script command 'EarlyReturnNextShot'.  The radio buttons allow you to select to have an early return only on the last shot, or on all shots.  If post-exposure actions are enabled for the camera (namely, if Post-actions in the Camera menu is not grayed out and is selected), then image shift to the next position will occur soon after the exposure is finished for each shot, regardless of whether early return is selected, and it is slightly more efficient not to do an early return except on the last shot.  If post-actions are not enabled, the early return will allow the program to do the image shift sooner.

In the text box in this group, enter the number of frames in the returned image: 0 for none, a specific number of frames, or -1 for all the frames.

Extra delay after image shift

A standard amount of settling time is imposed after each image shift; the extra delay entered here will be added to this settling time.

Adjust beam tilt to compensate for image shift

This option is enabled if you have calibrated the beam tilt needed for coma-free alignment as a function of image shift with Coma vs. Image Shift in the Calibration - Focus & Tuning submenu.  If so, then beam tilt will be adjusted appropriately for each Record position, and restored at the end.  In addition, the image shift present when starting the routine will also be compensated for, unless the script command 'AdjustBeamTiltforIS' was run or beam tilt was adjusted by any of the image-shift setting commands that provide the adjustment.  The conditions under which the calibration was taken are shown on the following line.  For the adjustment to work accurately, the current beam intensity at least should be close to what it was when the calibration was done.

Diameter of circles to draw

If the multi-shot circles are being displayed, the diameter of the circles is set to the entered value in microns, unless the option described next is selected to use the illuminated area on an FEI Titan.  Press tab or Enter to have the image redrawn after entering a new diameter.

Use Record illuminated area for circles in Low Dose

This option appears on an FEI Titan and allows the multi-shot circle display to take its diameter from the illuminated area setting of the Record area when Low Dose mode is on instead of from the value entered in this dialog.  The display will be updated dynamically as this illuminated area setting is changed.  This update works even while this dialog is option, provided that the scope is in the Record area and 'Continuous update' is check in the Low Dose Control panel before opening the dialog, and illuminated area is changed with microscope controls. 

For this option to be valuable rather than misleading, the illuminated area readout must be fairly accurate in the range of interest, which may not be the case.

Testing Image Location and Coma Adjustment

Once positions are set up in this dialog, the script command 'TestNextMultiShot 1' followed by 'MultipleRecords' can be used to test whether image positions are suitable, and 'TestNextMultiShot 2' can be used to measure the amount of beam tilt adjustment needed at various positions, either with or without an adjustment for image shift.  The details of this operation are as follows: