Tilt Series Batch Policies Dialog

This dialog is used to set how the tilt series controller responds to an error during a tilt series that is run in batch mode from the Navigator. It also has other settings particularly relevant running in the batch mode. An error is any condition in which the program would stop with a message. The first choice is the most critical one:

General response to error during the series

Here there are two choices:

  1. The program can stop with the usual message box, which requires you to confirm the message box, take appropriate action, and resume or terminate the tilt series. If you have chosen to have emails sent when tilt series stop, then an email will generally be sent as well. Choose this option if you want to be sure to get through every selected tilt series, or if you are able to check progress periodically or respond to an email and intervene in a timely fashion. The one exception to stopping is given in the radio buttons immediately below this choice, the rest of the settings in this dialog are irrelevant.
  2. The program can automatically terminate the tilt series and go on to the next. Choose this option if you are running a long sequence of unattended series and want to continue the data collection even if some series fail. If you choose this option, then other choices in this dialog govern how the program responds when there is an error that would ordinarily require you to make a choice between several responses.

After 3 images too dim or one dim Record in Low Dose Mode

If you have chosen to have the program stop with a message box, this option allows you to have automatic termination of the tilt series when images are acquired that are too dim.  The termination will occur at the point when a message box would usually appear: in Low Dose mode, after one Record that is too dim; otherwise, after three trials to obtain an adequate image.

After failure to tilt to expected angle

When the stage fails to tilt to the expected angle, the options are to terminate the tilt series or to continue with it. Termination is the default on a Thermo/FEI scope because this condition usually arises from a pole touch; continuing is the default on the JEOL because the less precise tilting there can generate this failure when the tolerance property is not set high enough.

When Record image loses too much area in Low Dose mode

This decision point is reached in Low Dose mode when you have 'Repeat Record if percentage of field lost is more than' checked and the given limit is exceeded. The options are to take the Record again, continue with the existing Record image, or terminate the series.

When Record image is too dim in Low Dose mode

The program has an expectation of how many counts should be in Record images, and when there are too few counts, the behavior in regular mode is to retake the image, while in Low Dose mode the decision is left to the user. The options here are to take the Record again, continue with the existing Record image, or terminate the series. If the option to retake the image is selected, it will try to take it three time then terminate the series if the images are still too dim. If the option to continue is selected, this should not result in a runaway series of dark images, because it will still terminate the series if subsequent tracking or focusing images are too dim after three tries.

Autosave log and start new log for each tilt series

If this option is selected, then the program will start a new log file for each tilt series run from the Navigator, and will automatically keep the log file up to date during the series. The log file name will be based on the name of the output file of the series. If the file already exists, the program will make a numbered variation on this name rather than replace an existing file. New logs will be started automatically even if the Autosave Log option is not selected in the Tilt Series menu.

Consider batch series successful or end first part of bidirectional or dose-symmetric series at high angles

This option can be selected to keep either dim images or a failure of autofocus from being treated as an error in some cases when the tilt angle is high enough.  The angle is sufficiently high when it is either greater than the absolute angle in the 'above' text box (default 55 degrees) or within the number of degrees of the ending angle in the 'within' text box (default 5 degrees).  This policy applies during a batch series when a dim image or autofocus failure occurs near the ending tilt angle of the series.  It applies during any bidirectional or dose-symmetric tilt series, batch or manual, when a dim image or autofocus failure occurs near the 'Tilt to' angle that is the high angle for the first part of the series.  In the latter case, the program terminates the first part of a bidirectional series and goes on to the second part automatically, or continues a dose-symmetric series to the end on the other side of 0 degrees.

Do similar at high tilt if intensity/exposure set for mean exceeds X times its minimum value

With this option checked, if intensity or exposure time is being varied to achieve a target number of counts, the program will keep track of the cumulative changes in whichever parameter is being varied and test whether it has increased by more than the given factor from the lowest value that it has had in the tilt series.  If it does, and the angle fits the criteria described for the previous option, the program will do one of three things: 1) end the first part of any bidirectional tilt series and go on to the second part; 2) terminate a batch tilt series and consider it successful; 3) stop with an error message when not running a batch series.  The latter stop will happen only once, not again if you go on.

This feature will not work if intensity changes are combined with scheduled changes in exposure time.  Also, if the tilt series is unidirectional, it provides protection only on the ending side of the series, since it does not start keeping track of changes until the first Record is saved.

Close column or gun valves after message box is open X minutes

Use this option to control whether the valves are closed (or filament turned off, in some cases) when a message box has been open for the length of time specified in the edit box. This setting will apply not just during batch tilt series, but any time that certain message boxes are opened, including all message boxes that could occur during a tilt series. If the valves do get closed, you will be notified about this when you close the message box.