Dose Symmetric Tilt Series Parameters Dialog
This dialog allows you to set parameters for acquiring a dose-symmetric tilt series, where images are taken on alternating sides of zero tilt so as to minimize the accumulated electron dose on low-tilt images. More background and details on this tilting method are available in Acquiring Tilt Series. In this dialog, the set of images taken contiguously on one side of the series is referred to as a 'group'.
Initial group size
Use the spinner to select the size of the groups at the start of the series. For example, with a size of 2, images would be take at angles 0, -2, -4, +2, +4, -6, -8, 6, 8, etc.
Increase group size beyond an angle
Select this option to have groups increase in size once the angle specified in the text box is reached. This angle is relative to the initial angle of the tilt series, which need not be zero and is specified in the angle text box for the Run series in two directions from' option of the main tilt series setup dialog. For exmaple, with an initial angle of 10 and an entry of 15 here, the groups would begin to increase in size at -5 and 25 degrees.
Increase group size by n every m degrees
With an increase in group size enabled, use the spinner to set how much the group size should increase when the criterion angle is reached, and the text box to set the angular increment at which the group size should increase by the same amount thereafter. Set the increment to 0 or to a large number to prevent further increases in group size after the first one.
Stop alternating directions beyond an angle
Select this option to convert to unidirectional tilting once the angle in the text box is reached and run to the terminal angle of the series on the first side, then on the second side. This angle is also relative to the initial angle of the series. The unidirectional tilting starts at the end of a group, not necessarily at the angle specified.
Use View anchor if first unidirectional part has >= n tilts
Use this option to use an anchor image to guarantee returning from the end of the first unidirectional segment to the beginning of the final unidirectional segment. Such an anchor image would ordinarily not be needed with dose symmetric tilting, but could be used if the unidirectional segments are sufficiently time-consuming and circumstances are less than ideal (e.g., large sample drift or poor stage performance). Use the spinner to set a minimum size for the unidirectional part below which an anchor will not be used. An anchor will also not be used if the first unidirectional segment is not bigger than the largest alternating group size. Note that only View images can be used for anchors, unlike for regular bidirectional series.
Skip backlash tilt on second side of series
When this option is not selected, the program will do a tilt backlash step on the second side of the series so that the stage is always tilted in one direction, following the original formulation for dose-symmetric tilting by Hagen et al. Backlashing has the advantage of avoiding a discontinuity in tilt angles and also the possibility of a small tilt around the orthogonal axis (referred to as X-axis tilt when analyzing in IMOD). Select this option to skip the backlash step, which would save a little time and wear on the stage. Such a series would need to be aligned like a regular bidirectional series.
Reorder file when finished
SerialEM can produce an image file and associated '.mdoc' file with tilt angles in order from a dose-symmetric series. Unlike a bidirectional series, the tilt series file cannot be rewritten in order until the whole series is done, namely when it is terminated. Whether this reordering takes away from acquisition time depends on two factors: whether saving in the background is disabled in the SerialEM properties file with the property 'BackgroundSaveToFile 0'; and whether frames are being saved and whole tilt series are being aligned in IMOD. If background saving is enabled and the current settings indicate that whole series will not be aligned, the option will be labeled Reorder file in background when finished (allowing other operations), which means that manual and automatic acquisitions can proceed unimpeded. Otherwise, it will be labeled Reorder file synchronously when finished (blocking other operations), which means that nothing else can happen while the program is reading and rewriting the file. Aligning whole tilt series requires that the file be reordered before the command file for the alignment is written.
The first line at the bottom summarizes the tilt strategy, showing the actual angles at which the transition in group size and to unidirectional tilting will occur. Again, these are all relative to the initial angle of the tilt series. The second line shows how many tilt reversals there are, and the total amount of tilting that they involve, which would govern both the additional time and the extra wear imposed on the goniometer by using dose-symmetric tilting.