Dewar and Vacuum Management Dialog

This dialog allows management of the various events that can occur periodically on the microscope and interfere with stable imaging during acquisition: the running of vacuum pumps and the filling of nitrogen dewars.  (In order for the latter options to show up on non-Krios Thermo/FEI scopes, a property entry is needed; see below). In some cases, the program can only check whether an event has started and then wait for it to finish; in others it can initiate an event periodically.  It is used to set parameters only; the selected operations are performed when the scope management routine is run either from the 'DewarsAndPumps' script command or by an action during Navigator acquisition.  That routine can be run frequently (i.e., on every acquisition item) because the actual times between operations are all governed by the intervals set here.  The operations are run through the same mechanism as when run by the 'LongOperation' script command, so timing is based on the same times when each operation was last run that are kept track of when running through script and stored in the short-term calibrations file between program sessions.

Vacuum Management

The top section of the dialog currently appears only for Thermo/FEI scopes.

Check for PVP running and wait until done

Select this option to have the program check whether the PVP is running and pause acquisition until it has stopped.

Run buffer cycle every N minutes

Select this option to run the regular buffer cycle periodically, and fill in the text box with the number of minutes between runs (an integer).

Run autoloader buffer cycle every N minutes

Select this option to run the autoloader buffer cycle periodically, and fill in the text box with the number of minutes between runs (an integer).  Whether this option appears is governed by the first bit (1) of the property 'DewarVacCapabilities', which is on by default for a Krios but must be explicitly provided for other scopes with autoloaders.

Nitrogen Management

The bottom section of the dialog appears if there is any way to control or monitor an automatic nitrogen filling system.  For Thermo/FEI scopes, this is determined by the second bit (2) of the 'DewarVacCapabilities' property, which again is on by default for Krios.  For JEOL scopes, it is determined by the 'JeolHasNitrogenClass' property, and both the transfer tank and the stage tank are treated together.  For either type of scope, the section will also appear if the 'HasSimpleOrigin' property is set, and commands to the Simple Origin filling system will be used.

Refill nitrogen every N hours

Select this option to refill dewars periodically and fill in the text box with the interval between filling in hours (a floating point entry is allowed).  When the management routine is run with this option selected, the program will first check whether filling has already started.

Check for ongoing filling and wait until done

Select this option to check for whether filling has started and wait until it is done. Even if filling is specified to be done at an interval, it would be advisable to check this option too if there is some chance that it might occur spontaneously.

Pause if time to next refill is below N minutes

This line and the next one appear if SerialEM can determine the time until the system plans to start a filling - with Thermo/FEI and Simple Origin but not with JEOL.  When the program checks for ongoing filling, it also checks the time interval until the next filling.  If that interval is below the time entered on this line (a floating point value), the program will pause and wait for it to start.

Start the refill if time to next refill is below N minutes

If this option is selected, the program will start the filling immediately when the interval to the next filling is longer than the time on the previous line but below the time entered here (also a floating point value).  This option is provided particularly for tilt series, where it allows you to minimize wasted time while avoiding pauses or disturbances during the acquisition.  When using it, a small entry like 0.5 would be appropriate for the entry above, and the time here would be set longer than the expected acquisition time.

Time to wait after filling is done

Enter the interval in minutes to wait after the filling done (a floating point value).  This wait will occur both when filling is discovered to be ongoing and when it is started by the program.

Repeat checks just before primary action in Acquire at Items

This option appears at the bottom of the dialog regardless of whether there is one section or two.  It allows the Navigator to run the management routine twice during the acquisition cycle.  It can be run first, to minimize the chance that a long operation occurs between the initial preparations (e.g., alignment and focusing) and the actual acquisition. Then the Navigator will run it again, just prior to acquisition, doing just the checks for ongoing operations.  The same thing can be accomplished when running from script by running 'ScopeManagement -1' early on and 'ScopeManagement 1' just before acquiring.