Tilt Series menu commands

The Tilt Series menu offers the following commands:

Setup/Start command (Tilt Series menu)

Use this command to open the Tilt Series Setup dialog box to set the parameters for a new tilt series and start the series, or to adjust the parameters of one that is running. If a tilt series is already running, you will have the option of resuming the series at the next step in its sequence, or of leaving the dialog box and resuming the tilt series at another point through the Tilt Series Resume dialog box .

Terminate command (Tilt Series menu)

Use this command to terminate a tilt series and restore all program controls to their normal state. The Tilt Series Controller will no longer control the various buffer and saving options in the program. You will have the option of leaving your image file open or closing it. For a tilt series run in batch mode from the Navigator, the tilt series will be terminated, the file will be closed, and the Navigator will go on to the next tilt series.

If you use this command in the first half of a bidirectional tilt series, the program will ask whether you want to terminate the whole series or just end that half of the series and go on to the second half.  The behavior is more complex for a dose-symmetric series.  If the series is still going through the programmed sequence of tilts, it will ask whether you want to terminate the series or just end one side and finish the other.  In the latter case, it will then ask whether you want to end the positive or negative side.  At this point it tries to find the next tilt to do on the other side, and if there are none left, it gives you a final choice: end the series or cancel the termination so that you can extend the tilt range on the desired side.  If you cancel, then you would open the Tilt Series Setup dialog box and set a higher angle on the side you want to continue with. After that, reselect this menu command to end the other side of the series.

Extra Output command (Tilt Series menu)

Use this command to open the Tilt Series Extra Output dialog box to control output of images to additional windows or image files. You can have a separate window that holds a buffer stack with binned down copies of the final Record or montage overviews during a tilt series. You can save each type of image shot by the Tilt Series Controller (autofocus, tracking, and preview in low dose mode) to a separate output file. You can also use this dialog to do a series of Record images at different focus settings or at different filter settings.

Batch Policies command (Tilt Series menu)

Use this command to open the Tilt Series Batch Policy dialog box to control how errors are handled during a tilt series started automatically from the Navigator. The most important choice is between having the series stop with a message box after an error to allow the usual kinds of interventions, versus having the series automatically terminated. If the latter is selected, other choices essentially answer the various message boxes that give the user a choice after an error.

Reset Pole Angle command (Tilt Series menu)

When the program finds that the stage has not tilted as much as expected, it stops and asks if you want to stop the tilt series. If you answer yes, it sets this angle as an internal 'pole touch' angle beyond which it will not tilt. If you answer yes incorrectly, you will not be able to go on until you use this command to reset the 'pole touch' angle and remove this limitation.

Run Script in TS command (Tilt Series menu)

Use this command to run a chosen script before a selected step in the tilt series loop.  The available steps are the tracking shot before autofocus, autofocus, the tracking shot after autofocus, and the Record or Montage.  The script will be run on every loop of the tilt series, regardless of whether the chosen step is performed at that tilt angle or ever.  This command is disabled until a script number is set with the following command.

Unlike when running scripts from the Navigator, there are no layers of control in this situation; if the script is stopped, this will stop the tilt series, and there will be no way to resume the script from the stopping point. The tilt series will also stop if there is an error in the script. It should be possible to make the script run again by selecting to go back to an earlier step when resuming the tilt series.  The script can be edited, and the selections of which script and which step can be changed, whenever the tilt series is stopped.

There are no protections against running a script that interferes with the Tilt Series Controller's operations and controls in some way, such as by manipulating open files or copying buffers.  Malfunctions or crashes would be expected in such cases.

Set Script To Run command (Tilt Series menu)

Use this command to specify the  script to be run during the series, then a number for the step in the series of actions at which to run the script. First, a dialog will open with a drop-down box where you can choose the script.  Then an entry box for the step number will open and will list the available steps, numbered from one.  The chosen script is stored in settings by its number, not its name, and may no longer be the right one after rearranging the scripts.

Call TS Plugins command (Tilt Series menu)

It is possible for SerialEM plugins to provide functions that can be called at defined points in the tilt series.  If this entry is checked, those functions will be called.  It is grayed out if there are no plugins loaded with such functions.

Fixed # of K2/3 Frames command (Tilt Series menu)

If this entry is checked, then if intensity is being changed during a tilt series with a K2/K3 camera, the program will adjust the frame time to keep the number of frames constant.  Aside from keeping the signal-to-noise ratio of the frames comparable, this may also result in finer changes in exposure time, which would otherwise be constrained to be a multiple of a fixed frame time.  However, there may be increased drift within the early frames for the longer frame times.  This adjustment will not be made if you have scheduled changes in frame time explicitly with the Tilt Series Scheduled Changes dialog.

Set Bidir Return Delay command (Tilt Series menu)

Use this command to add a delay between returning to the starting point of a bidirectional tilt series and taking an image.  Enter the delay in seconds.

Send Email at End command (Tilt Series menu) menu)

If this entry is checked, SerialEM will send an email when a tilt series reaches its end or stops in need of attention, except when the stop is immediately after an action that you have taken. To send email, an SMTP server and an address to send from must be defined in the SerialEM properties file, and you must enter an email address with the Set Email Address command in the Settings menu.

Stop command (Tilt Series menu)

Use this command to stop a tilt series at the next logical step. The Tilt Series Controller will still be in control of the program. If you open the Tilt Series Resume dialog box you will be able to see exactly where the series stopped, because the dialog box contains a statement of the next action to be performed.

End Loop command (Tilt Series menu)

Use this command to stop a tilt series after all actions have been completed at the current tilt angle. The Tilt Series Controller will still be in control of the program.

Back Up command (Tilt Series menu)

Use this command to open the Tilt Series Back Up dialog box in order to back up to a previous tilt angle and redo operations from that point. You can use this procedure more than once, if necessary, before selecting the point from which you want to resume. When you back up, the Tilt Series Controller will try to set up an appropriate reference image for the new tilt angle.

Resume command (Tilt Series menu)

Use this command to open the Tilt Series Resume dialog box . This dialog box will give you a chance to change the next action to be performed. You can choose to redo some actions at the current tilt angle, or, to a limited extent, you can skip some actions that you have performed manually.

One Loop command (Tilt Series menu)

Use this command to perform one loop of a tilt series. The Tilt Series Controller will resume from the point at which it was stopped and will go on until all operations are complete at a tilt angle.

One Step command (Tilt Series menu)

Use this command to advance one step of the tilt series. There will be a message in the log saying which step is executed.

Save X/Y/Z File command (Tilt Series menu)

Use this command to save a text file with a list of tilt angles and X, Y, and Z positions in the order in which they occurred during the series.  The file may be saved after the tilt series is finished, or a partial file can be saved any time that the series is stopped.  The data are available for saving until the next tilt series is started.

With IMOD 4.7, a simple plot of the data can be generated with
     onegenplot -col 1,2,3,4 filename.txt
with other options available to embellish the plot if desired.  With IMOD 4.8.40 or later, a properly labeled plot with different colors can be produced with
     tomodataplots -typ 14 filename.txt
where the option '-con 1' can be used to add connecting lines between the points.

Autosave X/Y/Z File command (Tilt Series menu)

Use this command to toggle automatic saving of a text file with a list of tilt angles and X, Y, and Z positions at the end of each tilt series.  If the output file name is 'imagefile.mrc', this file will have the name 'imagefile_xyz.txt'

Verbose command (Tilt Series menu)

Use this command to toggle output of tracking and prediction information and other status messages to the Log window during a tilt series. If this item is not checked, then only the summary information about each image saved will be printed.

Autosave Log command (Tilt Series menu)

Use this command to toggle automatic saving of the Log Window to a file after every tilt. If the Log Window has not yet been saved to a file, a log file will be started with a name derived from the name of the tilt series output file.

Debug Mode command (Tilt Series menu)

Use this command to toggle output to the Log Window of numerous state variables in the Tilt Series Controller. The output will occur before each action.