Navigator Acquire Dialog
This dialog opens when the 'Navigator-Acquire at Points' menu item is selected and lets you control what actions are taken at a series of Navigator items marked as 'Acquire' or 'Tilt Series'. For items marked as 'Acquire', the primary actions available are to take and save an image, take an image and save it as a map, or run a script at each point. If there are only items marked as 'Acquire', the Tilt Series option is unavailable; if there are only items marked as 'Tilt Series', the other actions are unavailable. If there are both kinds of items marked, the dialog will open with the Tilt series option selected but the other options available; however, the selected action will be taken only on the appropriate kind of item ('Acquire' or 'Tilt Series') and items of the other kind will be skipped.
Control of the tilt series or script acquisition after it is started is complex because it involves two levels of activity: the Navigator acquisition and the operation being run. Buttons in the Camera and Script control panel will be modified and enabled to allow control at both of these levels. The effect of these buttons is described for each action in the Primary Task section below.
Prior to the primary action are a series of optional steps that can be run after moving the stage to each item's position. They are shown in the order in which they would be run:
Rough eucentricity - The rough eucentricity task should be selected if it is necessary that the specimen be eucentric and if the Z height might be off by more than 10 microns. It is run first because it does not retain alignment to a specimen position.
Autocenter beam - This task will condense the beam and take a picture to determine how to recenter it. Beam autocentering must already be set up for the current magnification in the Beam Autocentering Setup dialog box .
Realign to item - This task will realign to a selected specimen feature, but requires that the item be located within a sufficiently large medium-magnification map, as described in Realign to Item . If rough eucentricity is not being run during the acquire sequence, then the realign operation will be done at the Z height of the item being aligned to, since changing Z after aligning would lose the alignment. However, if rough eucentricity is being run, then the Z height found during that operation is retained for the realign operation. Thus, a new map acquired at this position will have the right Z height. There will be some error in realigning to the map because of the Z height difference. This error will be recorded for the new map and taken into account when realigning to this pair of maps in the future.
Cook specimen - This task will stabilize the specimen by pre-exposing it for a certain amount of time or to achieve a certain dose. The parameters for this operation must already be set up in the Specimen Cooking Setup dialog box .
Fine eucentricity - This task can be selected if eucentricity needs to be found with the highest accuracy, but the Z height should be within 10 microns of eucentric before running this task. If 'Realign to item' was also selected, the task is run in a way that maintains alignment to the specimen position (the Refine & Realign command).
Autofocus - Select this option to run the autofocus routine prior to the main action. If 'Only at start of group' is checked, then autofocus is run only when the first item in a group is encountered, or when an item is not a member of a group. If the
Run script - This task is available as a preliminary action for all kinds of primary tasks. When the primary task is tilt series acquisition, the script should be used for quick actions such as opening secondary files; if extended tasks are performed, the script is responsible for maintaining alignment to the specimen position. Even if the script is stopped or fails to complete successfully, the program will go on to the primary task, unless the script runs the command 'SkipAcquiringNavItem'. If you stop the script with 'End Loop' or 'STOP' in the Camera and Script control panel, you can then resume it with 'ResumeS', or you can end the script and go on to the primary task with 'End Script'. The program keeps track of the script choice separately for tilt series and other primary tasks.
Acquire map image - The image file must already be opened before starting the operation, unless a new file is set to be opened when the first item is acquired. As each area is acquired, it will be added as a map item with a label based on the label of the point being acquired (e.g., 12-A for point 12). The original point will no longer be marked for acquisition and it will no longer be drawn, to reduce clutter. Once the acquisition is finished, you could delete the original points.
Just acquire and save image - Again, the image file must be open before starting unless a file is set to be opened on the first item. This option is useful if you do not need to make maps of your acquired images. For both this option and the previous one, buttons in the Camera and Script control panel allow you to stop the acquisition immediately ('STOP'), end it after the current item is complete ('End Nav'), or pause the acquisition after the current item is complete to allow some intervention ('PauseN'). Once acquisition is paused, it can be resumed on the next item with 'ResumeN' or ended immediately with 'End Nav'.
Run script - Select the script to run by its number or name. When the script completes, the Navigator will go on to the next item. If it stops with an error that cannot be resumed from, the Navigator acquisition will also stop, unless the script includes the command 'NoMessageBoxOnError', in which case the Navigator will go on to the next item. If there is an error that can be resumed from, or if you stop the script with 'End Loop' or 'STOP' and it is then resumable, then the Navigator will not go on to the next item and the status bar will show 'STOPPED NAV SCRIPT'. At this point you can do several things: 1) Resume the script with 'ResumeS'; 2) abandon this script and go on to the next item by using 'End Script'; 3) terminate the acquisition after this item is completed or abandoned by pressing 'End Nav' or by selecting 'End Acquire' in the Navigator menu; or 4) end the acquisition immediately by pressing 'End All', which avoids having to remember to press 'End Nav' before 'End Script'. The Camera and Script control panel will also include a button 'PauseN' for pausing acquisition after the current item is completed. Once paused, acquisition can be resumed with the 'ResumeN' button or ended immediately with 'End Nav'.
Acquire tilt series - All parameters and file properties should already be set up when you go to start the series. Once a tilt series is started, the regular tilt series control buttons in the Camera and Script control panel function just as they do for tilt series started manually to allow stopping, resuming, and stepping through the series. However, there is also an 'End Nav' button to stop Navigator acquisition after the current series is completed. When the tilt series is stopped, an 'End TS' button can be used to end the tilt series and go on to the next. Press 'EndNav' before 'End TS' to terminate all acquisition.
Run script after - This task can be run after all kinds of primary tasks. If you stop the script with 'End Loop' or 'STOP' in the Camera and Script control panel, you can then resume it with 'ResumeS', or you can end the script and go on to the next item with 'End Script'. The program keeps track of the script choice separately for tilt series and other primary tasks.
Do subset from index
Select this option to acquire from a subset of items. Enter the item index at which to start and end in the two text boxes. If there are no items within the subset marked for acquisition and compatible with the selected primary task, it will switch the primary task between tilt series and a non-tilt series selection. When a subset is done, only the information stored for items in that subset is accessed during that run. Specifically, files set to be opened and states to be set on items before the subset will not be available. Thus, if file-opening through the Navigator is needed, it must be done on the first item of the subset. If tilt series are being done and a state needs to be set, it should be done on the first item as well.
The subset selection is reset after every run. However, if you close this dialog with Postpone, the subset setting is saved. It will reappear when you reopen the dialog and will apply if the acquisition is started from a script command.
Skip initial stage move
Select this option to suppress the initial stage move to the area, which is redundant when Realign to Item is going to be run. Several conditions must be satisfied in order for the move to be skipped; if they are not, the option is disabled and it has no effect if is already selected. When the primary task is other than to run a script, it is disabled when Realign to item is not selected, and also when Rough eucentricity is selected, because it would make no sense to do rough eucentricity before the stage move. If Autocenter beam is selected, the stage move will not be skipped on the first item, to ensure that there is a usable area being viewed.
If the primary task is to run a script, this option is available even when Realign to item is not selected. In such a case, the program just assumes that the script will run Realign to Item or otherwise move the stage, and it will issue warnings that it is relying on this. However, it will not skip the move (and this option will be disabled) if Cook specimen, Fine eucentricity, or Autofocus is selected without Realign to item, because those operations can only be done after moving to the item.
Skip Z moves in initial move and Realign
Select this option to leave the Z height unchanged in the initial stage move to the item, and in Realign to Item if it is run. Otherwise, the Z height will be set to the Z value of the item in the initial move, and to the Z value of the first map used for aligning in ReAlign to Item unless Rough eucentricity was selected as an initial action. This option would be useful if the Z heights of the items are not correct, yet Z height is approximately the same from one point to another.
Restore scope state after aligning to item
This option is enabled when you select 'Realign to item' as an initial task and are running a script. If it is checked, then the current magnification and beam settings will be restored after running 'Realign to item'. Usually, this is appropriate, which is why it happens by default when making maps or taking images. However, if you are realigning to a high-magnification map embedded in a medium magnification map, then you could turn off this option if the beam and magnification were already carefully adjusted before acquiring the high-magnification map. That way, you would not have to readjust these settings before starting the acquisition, and you would be protected against the scope being in an undesirable state before starting a particular realign operation.
Close column/gun valves at end
If this option is available, you can set it to have the column or gun valve closed at the end of the set of acquisitions. On a JEOL without a FEG, this option can be used to turn the filament off instead.
Send email at end
If this option is enabled, you can select it to have an email sent to the address entered with Set Email Address in the Tilt Series menu when the acquisition finishes. An email will be sent if the acquisition stops with an error, but not if you stop it yourself. For this option to be enabled, an SMTP server and address to mail from must be specified in the SerialEM properties file. The program keeps track of this option setting separately for tilt series and other kinds of primary tasks.
GO - Postpone - Cancel
GO starts the acquisition with the selected parameters. Postpone closes the dialog but saves the parameters, which is useful if acquisition is started subsequently with the StartNavAcquireAtEnd script command. Cancel closes the dialog and discards any changes in parameters.