Tilt Series Scheduled Changes Dialog

This dialog box allows you to specify changes in several parameters during a series: Record exposure time, Record drift settling, target defocus, energy filter settings, and the frame time for Dose Fractionation mode in a K2/K3 camera. Each change is entered independently and appears as a separate line in the table at the bottom of the dialog. The upper section of the dialog contains controls for adjusting the change on the currently selected line of the table. The middle section has controls for adding or removing changes. The dialog may be resized to see more of the table.

Changes can be scheduled to happen on only one side of the tilt series, or a single entry can be used for a change that is to happen at both positive and negative angles. Changes can occur in either discrete steps or continuously, by changing linearly from one specified angle to another.

When changes are in discrete steps, they apply at and above the specified tilt angle. In this case, the value before the tilt series starts is applied below the lowest angle for a scheduled change. For example, suppose two changes are entered for the defocus target,one to set it to -3 at 40° and one to set it to -2 at 20°, both to occur at positive and negative angles. If the target is -1 before the tilt series starts, and the tilt increment is 1°, then the target would have the following values during the series: -3 above and at 40°, -2 from -39° to -20°, -1 from -19° to 19°, -2 from 20° to 39°, and -3 at and above 40°.

When a parameter is set to change linearly in a particular entry, the situation is more complex:

  1. If there is a change set to occur at a higher angle, then the parameter will be changed linearly from the value at the given entry's angle to the value at the higher angle.
  2. If there is no change set to occur at a higher angle, the parameter will be fixed at the value for the given entry. If you want a linear change, you must specify a change at a higher angle, such as the highest angle of the series.
  3. If there is no change specified at a lower angle, the parameter will change linearly from its value before the tilt series starts at 0° to the value at the given entry's angle. If you do not want a linear change, you must specify an entry for 0° with a fixed value.

To apply this to the example, suppose that the defocus target is scheduled to be -3 at 40° and -2 at 20°, but with linear changes in each case. Then the target will be fixed at -3 above 40°, change linearly from -3 to -2 between 40° and 20°, respectively, and change linearly from -2 to -1 from 20° to 0°.

For dose-symmetric tilt series, all changes are imposed at angles relative to the starting angle of the tilt series, under the assumption that this angle is where the specimen itself is near zero tilt.  Thus, if the starting angle is 12, a change scheduled to occur at 20 will actually occur at -8 and 32.  For such series, all changes should be marked as occurring at plus and minus angles.

Setting the properties of a change

The currently selected itme in the table can be modified by entering a tilt angle and a value in the respective text boxes, selecting Change at both plus and minus angles to have the change occur at positive and negative angles, selecting a 'Set' radio button to set the type of parameter to change, and selecting Use fixed value or Change linearly depending on which is desired.

Adding and Removing Items

Press Add Item to add a new row to the table. The item will be a copy of the current item, if any; simply modify the controls in the top section as needed.

Press Remove to delete the currently selected row of the table.

Press Add Series to add a set of changes in Record exposure to the table, replacing any exposure time entries already in the table. The exposures will be proportional to the inverse cosine of the tilt angle to the selected power, just as for beam intensity or exposure control in the Tilt Series Setup dialog.  The powers are the same as the ones available there: 1/1 to 1/5, plus other powers that give an increase in exposure time from 0 to 60 of 1.6, 1.8, 2.2, 2.4, or 2.6.  The exposures will differ by the multiplicative factor given in the Step factor text box, so the number of exposure changes will depend on this factor as well as the highest angle of the tilt series. The changes will be marked as having fixed values, because linear changes would be redundant to what can be achieved using just the settings in the Tilt Series Setup dialog. This feature is intended to allow a hybrid control of specimen exposure, where major changes are accomplished by the scheduled steps in exposure time, while minor changes between steps are achieved with beam intensity changes. The latter intensity changes are limited to be no bigger than the step factor between exposure time changes. Such hybrid control should not be needed if continuously variable exposure times can be used with interpolation of dark references; but if for some reason the interpolation is not available, this hybrid method would require many fewer dark references. 

The hybrid method is also needed when exposure time is constrained to be a multiple of a sizable number.  The program imposes such constraints for all direct detectors and for the Gatan OneView, but the constraints are the most serious with a K2 camera; namely, exposure time must be a multiple of 0.1 sec or 0.5 sec in counting or super-resolution mode without Dose Fractionation, or a multiple of the frame time with Dose Fractionation on.  The program will take the constraints entailed by the current Record parameters into account when picking the exposure times after you press Add Series, and it will find the angles at which those exposure times should be selected.  It is thus important that you select the camera and set the Record parameters prior to entering this dialog, and always check or replace the exposure series here prior to a tilt series if you might have changed parameters.  Note that if the frame time is equal to the exposure time, this dialog knows that the Tilt Series Controller will keep this relationship as it changes exposure time, so it will get rid of any existing scheduled changes in frame time.

If you are doing Dose Fractionation for real, not just to allow fine-grained changes in exposure time, then the Keep # of frames constant checkbox becomes relevant.  If this box is off, then exposure times will be picked that are a multiple of the current frame time.  Since these times will work only if frame time is constant, existing scheduled changes in frame time will be eliminated.  If this box is on, then it will schedule changes in frame time and exposure at each angle, replacing any existing frame times.  The exposure times are generally constrained to be a multiple of a much smaller number in this case, so it should be possible to get relatively fine-grained changes in this way.