Navigator Acquire Dialog

Introduction
Primary Action
Primary Action-Related Options
Options for Other Tasks
General Options
Tasks Before and After Primary Action
General Controls for Selected Task
Other Task List Controls
Bottom Action Buttons

Introduction

Actions and Tasks - This dialog opens when the 'Navigator-Acquire at Items' menu item is selected and lets you control what operations are done at a series of Navigator items marked as 'Acquire' or 'Tilt Series'. These operations are of two kinds: the "Primary Action" performed to acquire images, and "other tasks", optional steps to prepare for that acquisition.  For items marked as 'Acquire', the primary actions available are to take and save an image, optionally making it a Navigator map; acquire with the Multiple Records procedure; 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.

A unique non-modal dialog - This dialog is non-modal, like various others that can stay open indefinitely, but unlike them, most operations are disabled because the program is considered to be busy doing a task when this dialog is open.  This restriction is primarily to avoid changes in the Navigator data while the program is poised to start acquisition.  Selected operations like taking images, loading a map, and opening, closing, and switching files are allowed; more may be allowed upon request.

Operation control after starting - 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 Action section below.

Acquisition parameter sets - Because the acquisition of maps for target selection typically requires fewer operations and simpler parameter settings than actual data collection, the dialog allows you to maintain two sets of parameters.  You can switch between them at any time with the Mapping and Final Data buttons at the top.  The dialog works with a local copy of both sets, so Cancel will discard changes in both sets of parameters. All parameters are saved in your settings file.  If you want to access more sets of parameters easily, without having to keep them in separate settings files, you can use the Save Parameters to File button at the bottom to save just the parameters in the currently selected set to a file, or Read in Parameters to load saved parameters into the currently selected set.

Ordering of tasks - This dialog allows the order of the associated tasks to be changed as desired, with some restrictions, including the ability to run tasks after the primary action.  The order that they are listed in the column on the right, from top to bottom, is the order in which they will be run.

Intelligent stage movement - The program moves the stage only when necessary.  The primary action has to be done at the location of the item being acquired, but some other tasks can be done elsewhere, such as on the carbon film or in an area allowed to have higher doses.  If you set up one or more tasks to be done at another location, the program will move to that location for those tasks and will move to the current item's location for most other tasks and for the primary action.  The exceptions are Manage Dewars/Vacuum, Flash FEG, and Update Dark Reference, which will be done wherever the stage is currently, and Realign to Item, which does one or more stage moves itself.  It is most efficient if tasks done elsewhere are all done at the same location and are grouped together, before tasks that need to be done at the current item.

Simplify the dialog - The dialog has three features that allow you to simplify it and focus on selected settings.  Unselected options on the left can be hidden; tasks not selected for running can be hidden; and the group box with controls for when and where a selected task will run can be closed up by 'unselecting' the selected task.  These features should be especially useful for mapping where parameter choices may be much simpler.

 

Primary Action

Acquire and save image or montage - When this option is selected, turn on the Make Navigator map checkbox to make a map from each image or montage.

Acquire multiple Records - The parameters set in the Multiple Record Setup dialog are applied in this acquisition routine and take precedence over some similar parameters here, which are disabled.  Specifically, the choice of whether to save images in that dialog governs saving, not the option to skip saving here, and the setting there for adjusting beam tllt and astigmatism for image shift determines whether that is done.  If saving is being done, the file must be opened already or a file must be set to open on the first item.

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 - 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'.

Primary Action-Related Options

Cycle defocus target from X to Y um in N steps

Select this option to change the defocus target systematically for each item, cycling repeatedly from the value in the from box to the to box in the number of steps selected with the spinner.  The number of different targets is the number of the steps plus one; e.g., if it is set to cycle from -2 to -1 micron in 5 steps, it will set the target to -2.0, -1.8, -1.6, -1.4, -1.2, and -1.0.  Underfocus is negative as usual.  This target applies to all autofocusing done, either with the Autofocus task in the task list, when running tilt series, when waiting for drift with autofocus runs, or when running a script.  Hence the option is enabled in all those cases.  Whenever the program changes the target, it will also change the defocus by the same amount.  Thus, you can do autofocus on only a subset of items and the focus will be set correctly for the items in between the directly focused ones.

Adjust beam tilt & astig for image shift

This option is enabled when you are saving images or maps, if you have calibrated the beam tilt needed for coma-free alignment as a function of image shift with Coma vs. Image Shift in the Calibration - Focus & Tuning submenu. The program wiil adjust beam tilt, and astigmatism if that is calibrated too, for any image shift present just before taking the Record image.  If you are taking multiple Records, the option is disabled because the corresponding setting in the Multiple Record Setup dialog applies instead, and that routine adjusts for the starting image shift.

Do early return with sum of N frames

This option appears if there is a K2 or K3 camera and allows the program to resume some operations as soon as possible after starting a frame-saving acquisition.  The SerialEMCCD plugin will return control to SerialEM before the saving is finished, and return either an image with the given number of frames if a positive number is entered in the text box, no image if 0 is entered, or a sum of all the frames if -1 is entered.

Acquire non-montage images in Low Dose with

This set of radio buttons lets you take single images in Low Dose mode with either the View or Search area, instead of just the Record area, just as you can when montaging.  They are enabled and have an effect only when the primary action is to acquire images, and when not montaging.

Skip saving to file

This option is enabled when just acquiring images and allows you to skip saving to a file, which might be desired when saving frames.

 

Options for Other Tasks

Do hybrid Realign to Item/Align to Template

This option is enabled when you have set the Align to Template task to run on every item and also set Realign to Item to run on at least some of the items.  When the Realign to Item routine is run, it will test whether it can skip the first round of alignment to the center of the map or of a map frame and rely on a recent alignment to that position.  If not, it will proceed with its full operation.  If it can skip the first round, it will compute the position of the item based on the stored results of the first round, move to that location, and end without taking or aligning any images.  This should largely compensate for accumulated errors in positioning and make the position be close enough so that alignment to the template can work reliably.  This approach will not work if the spacing between target features is too small and the stage movement is sloppy even with backlash or has periodic variability in its positioning (i.e., older Tecnai compustages).  However, for typical center-to-center spacing between holes in a carbon film, the hybrid approach may well worlk with such stages.

Relax stage after final movement

Select this option to move the stage by a small amount opposite to the direction of the last movement, provided that the stage is in a known backlash state.  This operation has been found to reduce stage drift in some microscopes but could be counterproductive elsewhere.  You should use it only if it has been verified that drift does indeed settle faster, using the 'TestRelaxingStage' script command.

Skip Z moves in initial move and Realign

Select this option to leave the Z height unchanged in the stage move to the item's location, 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 one of the three eucentricity routines was run prior to the these stage moves.  This option would be useful if the Z heights of the items are not correct and eucentricity is run on only a subset of points, provided that Z height is approximately the same from one point to another between runs of a eucentricity routine.

Skip stage move to item if possible

This option is disabled and its setting has no effect except when a script is run before or as the primary action.  Select this option to suppress a stage move to the area prior to the primary action, if one still seems necessary (i.e., if no task was done that required being at the area already).  In the cases where the option is enabled, the program is willing to rely on one script or the other having moved to the area, either with an explicit stage move or with Realign to Item. 

 

General Options

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.

No message box when errors occur

Selecting this option has two effects: message boxes that would block unattended operation are converted to messages in the log, and the underlying failures are either ignored or cause the program to skip the current item and move on to the next.  Without the option set, a message box will pop up and the acquisition will be stopped.

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.

Retract cameras at end

If there are any retractable cameras, this option can be selected to retract them at the end of the set of acquisitions.

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 Settings 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.

Hide unselected options

This option allows you to simplify the left side of the dialog by hiding all options that are not checked.  However, if you uncheck an option when hiding is turned on, it will stay visible to make it easier for you to turn it back on.  Toggle this option off and back on to hide any newly unselected options.

Tasks Before and After Primary Action

This section has a series of lines corresponding to optional steps that can be run on some or all items. Their order from top to bottom corresponds to the order in which they will be run, with a line 'Primary Action Runs Here' showing where that occurs in the sequence.  Each line has 4 elements:

The checkbox at the left selects whether the task is run.

The button with the task name selects the task as the one whose parameters are shown in the 'General controls for task' group box below.  It is possible to close up this group box by pressing the selected button again, so that no button is selected. 

A text string to the right of the button summarizes when the task is set to be run.

A Setup button is also present for most tasks.  For some, this button will open the same setup dialog that can be opened from a menu entry in the Tasks or Navigator menu.  For others, it will either invoke a parameter setting sequence available from another menu item, or bring up a small dialog with a parameter choice.

The tasks will now be described in their default order:

Manage Dewars/Vacuum (or Manage Nitrogen on JEOL) - This task can be used to pause acquisition when a disturbing event occurs on the microscope, or to initiate such an event periodically.  The events are the running of vacuum pumps on Thermo/FEI scopes, and the filling of nitrogen dewar(s) filling on various scopes.  The Setup button opens the Dewar and Vacuum Management dialog.  (In order for the nitrogen filling options to appear in that dialog on non-Krios Thermo/FEI scopes, the property entry 'DewarVacCapabilities' is needed).  The timing for running operations is all controlled by the management procedure itself, so this task should be run on every item.

Flash FEG - This task can be used to flash a cold FEG.  For Thermo/FEI scopes, the scripting interface can tell whether flashing is advised, and it is reasonable to flash only when advised.  Thus, the task can be run frequently, even on every item.  There is a Setup button to pop up a dialog for you to choose whether to do high-temperature flashes if those are advised, or only low-temperature flashes when they are advised.  For JEOL scopes, there is no Setup button, and the task will flash the FEG unconditionally when it is run, so it is important to specify an appropriate interval at which it should be flashed.  (In order for this task to appear, there must be a Selectris filter or a property entry 'AdvancedScriptingVersion 4' or higher for Thermo/FEI scopes, or the property entry 'HasNitrogenClass 1' or higher for JEOL scopes.)

Coma-free Alignment - This task will run the coma-free alignment routine that uses CTF fitting.  The Setup button will run the Focus menu Set CTF Coma-free Params command then the Set CTF Acquire Params command; you can cancel out at any point in the long series of entry boxes.

Astigmatism - This task will run one of the two astigmatism routines.  The Setup button will first pop up a dialog for you to choose whether to use fitting to the CTF or analysis of beam-tilted image displacements (BTID).  For CTF fitting, it then runs the Focus menu Set CTF Acquire Params command.  For the BTID method, it with run the Focus menu Set BTID Astig Beam Tilt command.  Yes, all these coma and astigmatism parameters should be on a single dialog...

Condition Phase Plate - This task will run the phase plate conditioning routine after moving the phase plate to a new area.  The Setup button opens the Phase Plate Conditioning Setup dialog box, but the button to start the routine from that dialog is disabled.  If the Run at nearest item with label or note option in the General Controls section is set for this task, it will be run at the indicated item, regardless of the setting for where to run it in the Setup dialog.  However, if that option is not checked here, it will be run at the place indicated in the Setup dialog.

Update Dark Reference - This task will acquire a new dark reference for a DE camera based on the current Record parameters, or update the hardware dark reference for a K2/K3 camera.   Set the time interval for doing so in the General controls group box.  For a DE camera, there is a Setup button which will bring open the Direct Electron Server Reference Maker dialog in a restricted mode that has settings based on the current Record acquisition parameters.

Refine ZLP - This task runs the Refine ZLP routine started by the button in the Filter Control panel.

Rough Eucentricity - Either the Rough Eucentricity or the Eucentricity by Focus 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. Neither one retains alignment to a specimen position so they should be run prior to 'Realign to Item' or 'Align toTemplate'.  When you change the selected parameter set or close this dialog with GO or Postpone, the program will check whether operations are not in this order and ask you to confirm that you want to proceed if so.  The Rough Eucentricity task uses tilting to set Z to the eucentric point.

Eucentricity by Focus - This task will set the Z height to either the eucentric point or to another chosen height relative to eucentricity by setting a standard focus value then adjusting Z height so that measured defocus matches the value measured previously for that standard focus value.  This routine should be faster than Rough Eucentricity and may be more accurate, but it requires a calibration done in the Eucentricity by Focus Setup dialog, which the Setup button opens.

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 eucentricity has not been set yet during the acquire sequence, then the realign operation will be done at the Z height of the item being aligned to.  However, if eucentricity has been 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.  The Setup button opens the lower part of the Navigator Align Setup dialog, where there are options for resetting image shift after the alignment operation.  This task will restore microscope state afterwards when not in Low Dose mode, but not when in Low Dose mode.  There used to be an option to control whether state was restored when the primary action was a script, but it was eliminated because this default behavior seems appropriate.  If for some reason it is not, incorporate the Relaign To Item into the script instead.

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.  This operation maintains alignment to the specimen position.

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 either 'Realign to Item' or 'Align to Template' has also been run for this items, the task is run in a way that maintains alignment to the specimen position (the Refine & Realign command).

Align to Template - This task will align to a map containing a template image, such as a cropped image of one hole in the carbon film.  The Setup button opens the full Navigator Align Setup dialog, where the label of the template map and the maximum shift for the alignment can be set.  Image shift can also be reset after this alignment.  If both Realign to Item and this task are being run and image shift is being reset, it will be reset only after the Align to Template.  If you are primarily relying on Align to Template for positioning, consider selecting the option for the hybrid Realign to Item/Align to Template approach explained above.  If the routine does not find a shitf within the limit and the No message box on error option is selected, the Navigator will skip this item and go on to the next.

Autofocus - Select this option to run the autofocus routine prior to the main action.  The Setup button opens an popup box for you to enter the maximum change in focus to be allowed.  When that maximum is exceeded, or if the autofocus aborts due to inconsistent changes, the Navigator will skip this item and go on to the next.

Wait for Drift - This task will wait for drift to settle to a desired level, using parameters set in the Wait for Drift Setup dialog.  If the operation fails and the No message box on error option is selected, the Navigator will skip this item and go on to the next.

Run Script Before - This task is available for all kinds of primary actions.  When the primary action is tilt series acquisition, the script should be used for quick operations 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 action, 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 action with 'End Script'. The program keeps track of this script choice separately for tilt series and other primary actions.

Run Script After - This task can be run after all kinds of primary actions.  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 this script choice separately for tilt series and other primary actions.

General controls for selected task:

How often to run task - radio button group

These radio buttons provide several different ways to run a task periodically instead of at every item, the choice depends partly on how your points are divided into groups, e.g., one group versus multiple groups per grid square.

Every N items - Select this and set the number to 1 to run the task for every item, 2 for every other item, 10 for every tenth item, etc.

Only at start of group - Select this to run the task on the first item in a group.

Only at end of group - Select this to run the task on the last item in a group.

Every N minutes - Select this and specify a number of minutes (an integer) to run the task at intervals of that many minutes.

When moved > X um - Select this and specify a distance in microns to run the task whenever the distance since the last place where it was run exceeds the given distance.  This might be useful for a eucentricity task.

Position in sequence - button group

Move Up - Press this button to move the task up one step in the ordering.  It is possible to move a task from after to before the primary action with this button; this will turn off the Run after Primary Action checkbox.

Move Down - Press this button to move the task down one step in the ordering.  The button will be disabled when a task that is not allowed to run after the primary action reaches the last position before the primary action.  For other tasks, it can be used to move the task from before to after the action.

 

Run after Primary Action

Select this option to run the task after the primary action instead of before.  It is disabled for tasks where doing so makes no sense.  The line for the task will leap from one side of the Primary Action line to the other when this option is toggled.

Run at nearest item with label or note starting with

Select this option to run the task at a location different from that of the item for which it is being run.  The location is that of a different Navigator item.  Select whether to specify that other item by the note or label, and enter some text with which the note or label must start.  The text matching is case-sensitive. There can be many such items, in which case the program will find and go to the nearest one.  This capability is good for dose-intensive operations or ones that need to be done on the carbon film.  For maximum efficiency, all such tasks should be done prior to ones that need to be done at the target location, and they should be done at the same location. This option to run elsewhere is disabled for tasks where it makes no sense.

Other Task List Controls

Hide unused tasks

Select this option to hide the tasks that are not selected for running, to simplify the dialog and make it more evident what will be run.    When it is turned off, all tasks will be shown again.  When you turn off a task, it will not be hidden immediately so that it is easy to turn on again, but it will disappear if this option is toggled off and on again.

Restore Default Order

Press this button to set the order of the task list back to the default order defined in the program.

Bottom Action Buttons

Save Parameters to File

Press this button to save the currently selected set of parameters to a text file; set the name of the file in the chooser that opens.  The parameters saved consist of all those adjusted on the dialog itself plus a few others set by small popup dialogs that open only from one of the task Setup buttons.

Read in Parameters

Press this button to read saved parameters in to replace the currenly selected set of parameters.  If you load an undesired set of parameters, you can still use Cancel to return to the previous parameters.

GO - Postpone - Cancel

GO starts the acquisition with the selected parameters in the currently selected set.  This button will be labeled Resume if the Navigator was paused during acquisition.  Postpone closes the dialog but saves the parameters, which is useful if you need to open a file, or if acquisition is started subsequently with the StartNavAcquireAtEnd script command.  Cancel closes the dialog and discards any changes in parameters.