Settings menu commands

The Settings menu offers the following commands:

About Settings Files

Settings files are used to store just about every parameter that can be set by you in SerialEM. The main exceptions are program states such as Montaging, Low Dose mode, and Tilt Series mode, which need to be activated by you each time you run the program. By default, SerialEM will remember all of your parameters from one session to the next in a file called SerialEMsettings.txt in the directory where SerialEM was started. One can use the options in this menu to save settings into other files and retrieve settings from such files. The menu displays a list of recently used settings files so that you can switch between settings rapidly if necessary.  It is also possible to set up a desktop shortcut that makes SerialEM start with a different settings file from the default; see Shortcuts, Command Line Arguments, and Administrator mode.

After parameters are read from a file, that file is left open, which has three implications: 1) Settings can be saved to that file via the entry in this menu; 2) Settings can be restored from the file to the value that they had when they were last saved there; and 3) When you quit the program, settings will be saved into that file. To prevent settings from being saved into a file when you quit the program, just Close the file or use Discard on Exit.

If your settings become too far from usable, you can restore them to default values by reading from a file called the System Default Settings file.

Scripts are not stored in settings files, as of SerialEM 3.8. Instead, they are stored in a separate file referred to as a script package file, and the settings file just has an entry with the name of the script package.  When you read a settings file, that script file will also be read and become the current script package file, which will be rewritten when the settings are saved.  If you read in a new settings file that loads a different script package, the scripts in the package file will replace the respective ones in the program, but any other scripts that you have defined will be lost (another change in behavior on 12/23/19). 

Storing scripts separately makes it possible for multiple settings files to share the same script package, thus preventing diverging versions of the scripts in different files.  This will happen as a matter of course when you save a new settings file specialized for some conditions.  If you already have multiple settings files from before this change and you want them to share the same script package, first decide which one's package should be the one that is shared.  It is recommended that you open that settings file first and use Save Package As in the Scripts menu to save it to a name that indicates its status as the master package.  Then open other settings files and use Load New Package in the Scripts menu to load that package.

Open command (Settings menu)

Use this command to open a file in which settings were stored previously. Ordinarily, your default settings file is open whenever you are running SerialEM. Thus, opening a new file will usually involve closing that file. If this is the case, you will be asked whether you want to save your current settings into the currently open file before closing it and opening a different one.

You will enter the File Open dialog box to select the file, which is a text file.

Below the Open menu entry is a list of the most recently used settings files. Select one of these files to open it. In this case, the settings will automatically be saved to the current file first, without requiring your confirmation. To prevent this, you could close the current settings file first.

Read Again command (Settings menu)

Use this command to read parameter values from the currently open settings file. You would do this if you do not want to keep any parameter changes that you have made and want to restore your settings to the state saved in this file.

Save command (Settings menu)

Use this command to save settings to a file. If there is a settings file open, then the program state will be saved to this file. If not, you will enter the Save As dialog box to specify a new file to save values into. A file that has been saved into is left open; in other words, it will be saved to again when the program exits, unless you close it first.

Save As command (Settings menu)

Use this command to save settings to a file different from the one that is currently open. You will enter the Save As dialog box to specify a file to save values into. Any previously open settings file will be closed, and the new one will be left open. This means that it will be saved to again when the program exits, unless you close it first.  The new settings file will use the same script package file as the old one unless you save the script package to a different name.

Close command (Settings menu)

Use this command to close a settings file. This means that it will not be saved to when the program exits, which you might want to do if you are going to experiment with parameters that you will not want to save. You will be asked whether you want to save your current settings to the file before closing it.

Discard on Exit command (Settings menu)

This command works like closing the file except that the program will not ask if you want to save settings first, and it will not ask if you want to save settings on exit or when loading new settings.  It is useful when settings have reached a state that you do not want saved.  It will prevent autosaving as well.  The selection will be toggled off again by reading or writing settings, and it does not persist from one run of the program to the next.

Read Defaults command (Settings menu)

Use this command to read the System Defaults settings file. If there is a settings file currently open, you will be asked whether you want to save your settings to that file before overlaying them with the system defaults.

Autosave command (Settings menu)

Use this command to control whether settings will be saved to a file periodically (every 5 minutes, except during a tilt series). Autosaving is useful if you are doing things that present a risk of crashing the program. If no settings file is open when Autosave is on, then nothing will be saved.

Reverse Wheel Zoom Direction command (Settings - Specialized & Misc. Options submenu)

Use this command to toggle whether moving the mouse wheel away from you zooms the image down (the default) or up (the behavior when the option is selected).

Turn Off Beam After Long Inactivity command (Settings - Specialized & Misc. Options submenu)

With this option, you can enable the program to close valves or turn off the filament if it is left idle for longer than a specified length of time.  After selecting the option, enter the number of minutes of inactivity after which the program should turn off the beam, or 0 to disable this feature.  Inactivity means no operations like running scripts, taking images, or other higher-level operations have occurred; simply accessing a menu item or pressing a button does not count as activity.  The option appears checked in the menu when a positive time has been entered.  On a JEOL with the property 'AllowStopEmissionIfIdle' set, a second entry box will come up allowing you to set the number of minutes after which the emission should be turned.  The menu item will be checked if either of these entries are non-zero.

Set Threshold for Right-dbl-click 2nd shot (Settings - Specialized & Misc. Options submenu)

Use this option to set the threshold fraction of the image field lost before a second image is taken after you double-click in an image with the right mouse button, causing the program to do a stage move to reach that position, take an image, and align it to image clicked in.  If hte fraction of image area no longer visiable after the shift exceeds the fraction set here, a second image is taken so that you can see the full area.

Disable Dark Trim in Align command (Settings - Specialized & Misc. Options submenu)

Even when 'Trim dark borders in Autoalign' is not selected in the Image Alignment & Focus control panel, this trimming happens automatically in three cases: when in Low Dose mode, when doing a task at a lower magnification and not in Low Dose mode, and in the first two rounds of Realign to Item or alignments after resetting image shift in Align to Template.  This option allows the automatic trimming to be disabled in selected cases.  Three dialog boxes will come up.  The first controls the trimming in Low Dose mode; enter 1 if you want to disable it just when doing a tilt series, or 2 if you want to disable it always.  The second entry controls the trimming when doing tasks; again, enter 1 if you want to disable it just when doing a tilt series, or 2 if you want to disable it always.  The third entry allows you to disable the trimming when running Realign to Item or Align to Template - this is the same option that can be set in the Navigator Align Setup dialog.  Note that the 'AlignTo' script command also has an optional entry to prevent trimming.  The decision to trim is made as follows:

• Trimming is not done if 'AlignTo' is run with that option set to prevent trimming
• Otherwise, if doing Realign to Item or Align to Template, trimming is determined by the option set here for those operations
• Or, if in low mag for another task and not in Low Dose, trimming is determined by the option set here for tasks
• Or if in Low Dose mode, not doing a Realign or  Template Align, trimming is determined by the option set here for Low Dose
• If not in Low Dose mode or doing Realign or Template Align or a task, trimming is controlled by the choice in the control panel

Adjust Focus on Probe Mode Change command (Tasks - Special Option submenu)

When changing between microprobe and nanoprobe TEM modes on Thermo/FEI scopes, the scope will restore the defocus last seen in a mode when returning to that mode.  With this option turned on, the program will try to maintain a constant difference between the focus levels in the two modes. It does this by tracking how much defocus changes during the time spent in one mode and imposing that focus change on the scope's restored focus value when switching to the other mode.  This means that you can use autofocus in one mode and have the required focus change applied when returning to the other mode. 

The option needs to be turned off in order to impose a needed focus difference between the modes.  As of SerialEM 3.7, focus differences are always applied in Low Dose mode only when this option is on.

If you want to "Reset Defocus" while this option is on and have that change in focus readout ignored, use the entry in the Focus menu instead of a button in the microscope interface.

Normalize All on Mag Change command (Settings - Specialized & Misc. Options submenu)

This option controls when all lenses are normalized after changing magnification on a Thermo/FEI or Hitachi scope.  Normally, the program will always normalize the projector lenses, and normalize condenser and objective lenses in addition when changing between LM and nonLM magnifications.  With this option, you can enter a 1 to normalize all lenses after all mag changes within LM, or a 2 to normalize all lenses after all mag changes.

Normalize Via View for Autofocus command (Settings - Specialized & Misc. Options submenu)

When this option is selected, the program will switch to the View area in Low Dose before going to the Focus area for autofocusing, unless it is currently in Focus and arrived there from View.  When 'Keep Focus and Trial identical' is selected in the Low Dose Control Panel, Trial and Focus are considered equivalent for the purpose of deciding whether this normalization needs to be done.

This option controls whether the beam is kept blanked except when acquiring images when the screen is up in Low Dose mode.   This blanking protects the specimen from being exposed when there is no camera inserted that would cause shuttering to keep the beam blanked. When there is a camera inserted, it also protects the specimen when the screen is lowered during the interval between the camera opening its shutter and SerialEM discovering that the screen is down.  Select this option to prevent the blanking if it is problematic for some reason.

Keep Focus & Trial at Same Position (Settings - Specialized & Misc. Options submenu)

Keep the Focus and Trial areas in Low Dose mode at the same position even when the Keep Focus and Trial identical option in the Low Dose control panel is not selected. 

Skip Beam Shift in TS command (Settings - Specialized & Misc. Options submenu)

When using a phase plate on a JEOL microscope, the beam shift that accompanies every image shift operation will change the centering of the phase plate.  Turn on this entry to suppress the beam shift for the alignment operations involving image shift during a tilt series.

Piezo for LD Axis Shift command (Settings - Specialized & Misc. Options submenu)

If there is a piezo plugin loaded that can provide stage movement along the tilt axis, and the properties file contains both an entry 'UsePiezoForLDAxis' specifying this piezo and an entry 'PiezoScale' defining the range and scaling of this piezo, this option can be turned on to use this piezo movement as a substitute for on-axis image shift between Record/View and Trial/Focus areas in Low Dose mode.  The option can be toggled only when Low Dose mode is off.  When Low Dose is turned on with this option enabled, the piezo is moved to the end of its range appropriate for the Record area.  Several restrictions are also enforced: Focus and Trial are constrained to the same properties; 'Balance Shifts' is turned off; rotation of the interarea axis away from the tilt axis is turned off.  The 'Position on tilt axis' entry can be negative or positive as needed, but the stage will be moved to the other end of its range when the sign is changed.

Allow Continuous in TS command (Settings - Specialized & Misc. Options submenu)

Ordinarily, the program will acquire images in single-frame mode for almost all automated operations, even when using a camera parameter set that has continuous mode set.  If this option is selected, images acquired directly by the Tilt Series Controller will be allowed to be taken in continuous mode if that mode is set in the camera parameters.  Such continuous acquisitions must be stopped manually by the user before the tilt series can go on.  This exception does not apply to images taken when autofocusing or doing other tasks; all tasks enforce single-frame mode.  Thus, it applies to Trial and Record, as well as to View and Preview images taken in Low Dose mode.

Set Email Address command (Settings menu)

Use this command to set the address(es) to which emails from SerialEM will be sent. You can enter more than one address, separated by commas or spaces. The address entered here will be used for any emails sent from SerialEM; i.e., ones sent by the Navigator or a script as well as ones after a tilt series stops.

Set a property command (Settings menu)

Use this command to set the value of one program property.  The command can be used with nearly all of the general (non-camera-specific) properties that contain just a single numeric entry and can be set by name in SerialEMproperties.txt.  First enter the full name of the property as listed in the properties file or the help file (but matching to this entry is case-insensitive, so case does not matter).  If this does not match one of the properties that can be set, an error message is given.  Otherwise, another dialog box opens for entering the property value.  The existing value of the property is shown in the box.

Basic Mode command (Settings menu)

Use this command to toggle a mode in which selected menu items and dialog elements are not displayed or are disabled.  This basic mode must be defined in a file with a list of the desired elements, either a file SEMbasicModeItems.txt in the system directory with the properties file, or a file specified with the property 'BasicModeDisableHideFile'.  See Hiding and Disabling Menu and Dialog Items for details.

Read Basic Mode File command (Settings menu)

Use this command to read in a different file defining which items are hidden or disabled in Basic Mode.  This filename will be stored in the settings file and reloaded when the program is restarted with those settings, or when those settings are read in.