Navigator Window menu commands

The Navigator window has its own menu to keep the main Navigator menu from being unwieldy and to provide more organized access to the commands included here.

Save command (Navigator window - File menu)

Use this command to save Navigator items to a file. The file is a simple tab-delimited text file with the properties of each item. If there is no current Navigator file, you will enter the Save As dialog box to specify the file, which will have the default extension .nav. When you select this command again, the entries will be saved to this file.

Save As command (Navigator window - File menu)

Use this command to save Navigator items to a file different from the current file. You will enter the Save As dialog box to specify the file. The new file will become the current file for saving into.

Load command (Navigator window - File menu)

Use this command to read in a Navigator file. The file will become the current file for saving into.  See the Read & Open command for details on the Navigator file reading.

Merge File command (Navigator window - File menu)

Use this command to read in the items from another Navigator file and merge them in with the items currently present in the table.  Duplicate items in the file being merged will be eliminated, with no change in the properties of the existing items.  If an item has a label that matches that of an existing item, it will be changed by adding '-1' to it (or '-2' if the label with '-1' on it exists, etc.).

The file being merged in need not be in the same directory as the current Navigator file.  Map files in the merged file will be located as described in the previous command, except that files not at their defined paths will be sought at locations relative to the file being merged in, not the current Navigator file.

Close command (Navigator window - File menu)

Use this command to close the Navigator window. If the contents of the window have changed since it was last saved, you will be asked if you want to save them to a file.

Set Point Label Threshold command (Navigator window - Options menu)

Use this command to set a threshold for skipping the drawing of most labels on points when they belong to groups bigger than the threshold.  Enter the maximum group size for which all labels should appear, or 0 to draw labels regardless of group size.  The labels of the first and last points in the group will be drawn in groups bigger than the threshold. Also, the labels of up to five points around the currently selected point will still be drawn even if the selected point is in a group larger than the threshold.  Labels will also be drawn for points whose distance from the previous point is greater than 40 microns.

Use Item Labels in Filenames command (Navigator window - Options menu)

Toggle this menu item on to incorporate the item label in the filename created when a new file is to be started for an item.  If there are no filenames defined for previous items when you select New file at item or Tilt series, the filename will be initialized to the item's label plus the appropriate file type extension, and that name will appear in the file chooser window that comes up for defining the filename. You can add more text or replace the label as you desire for this file.  If you add text that might be the same as any label (i.e., having numbers), be sure to add it before the label.  If there is a previous filename that is the basis for a new name and it still contains the label of its respective item, then the current item's label will be substituted for the previous one.  The last occurrence of the label will be replaced if it occurs more than once.  To stop having names based on the label, either turn off this option or remove the label from the next name that you define.  To start having names based on the label when there is a preceding filename without its label, press Set Filename and insert the current item's label into the name (but again, after any other numbers in the name).

This option should be particularly useful for generating names that correspond between the two axes of dual-axis tilt series.

Autosave Nav File command (Navigator window - Options menu)

Toggle this menu item on to have the Navigator items saved to a file periodically if they have changed. If there is no currently open file, the program will save to a file named AUTOSAVEmmddhhmm.nav, where 'mmddhhmm' are two-digit values for month, day, hour, and minute. This file will be removed when you save to a file or when the program exits (if you elect not to save at that time). However, if the program crashes, you should find the file in the directory in which your SerialEM shortcut starts the program.

Write as XML File command (Navigator window - Options menu)

This command toggles an option to save the Navigator file as an XML file instead of in autodoc format.  Either one can be read back in by SerialEM.  The autodoc writing is significantly faster because it is optimized to write each line directly to file, whereas to write an the XML file the program builds an autodoc data structure, builds an XML structure from that, then writes out the XML.  This will matter only for very large numbers of points, over 10,000.

Convert Maps to Bytes command (Navigator window - Options menu)

This command toggles an option to keep maps in memory as bytes. The option does not affect how maps are stored in the image file (typically as integers). Byte conversion will reduce memory usage by 2/3, so that the memory required is just one byte per pixel. The intensity scaling determined by the Black and White levels in the Image Display control panel will be associated with an image when a new map is created. This scaling is then applied to convert the image to bytes, both when the map is defined and when the map is reloaded from file. This scaling could make it impossible to see some light or dark image details. There are two ways to prevent such scaling problems. First, adjust the Black and White levels to avoid truncating image intensities before designating an image as a map. Second, use this menu entry to turn off the conversion option, load the map, adjust the Black and White levels as desired, and turn the option back on.  This option is not saved in the settings file between sessions; it can be turned off by default with the general property 'ConvertMapsToBytesDefault 0'.

Load Maps Unbinned command (Navigator window - Options menu)

This command toggles an option to have montage maps always loaded unbinned, i.e., with overview binning of 1. This is almost always what one wants, but if you are short on memory and do not need to see a map at full resolution, you can turn off the option and set a higher overview binning in the Montage Control panel . However, if the map file is open, you must make it the current open file before setting the binning in the control panel.

Indexes command (Navigator window - View menu)

Use this command to add a column to the table with the index of each item, numbered from 1.

Labels command (Navigator window - View menu)

Use this command to turn on or off the drawing of labels.  With it off, no labels will appear.  With it on, labels will appear except for closely-spaced points in groups larger than a threshold size that can be set with the Set Point Label Threshold command.

All Registrations command (Navigator window - View menu)

Ordinarily the only items that will be drawn on an image are ones with the same registration as the image. Use this command to turn on drawing of items from other registrations.

Draw Nothing command (Navigator window - View menu)

Use this command to turn off drawing of all items.

Import Map command (Navigator window - Map/Polygon menu)

Use this command to define an image obtained elsewhere, such as on a light microscope, as a map. First, a dialog will open to allow you to select the file. You can select TIFF and DigitalMicrograph files (dm3 or dm4 type) as well as MRC files, and you can use color images. Then the Navigator Import dialog box will open to allow you to specify the section number, a stage position, a registration number, and a transformation between stage and image coordinates. If you import a TIFF file, the stage position and the stage to image transformation may be automatically selected if there are tags in the file defined in the SerialEMproperties.txt file. The dialog will also allow you to make a color overlay of the selected file and the currently selected Navigator item, if the latter is an imported map of the same size. Imported maps are originally forced to have a registration number separate from those of non-imported items, so points marked on imported maps will not appear on other images, and vice-versa. However, once you transform the imported map into the same registration as the other images, then points marked on the imported map will appear on other images and can be used to move the stage to a desired location.

When points are marked on a map, the program stores the ID of the map that they were drawn on.  This "drawn on" ID is used to help decide what map to use for the Realign to Item routine, but an imported map cannot be used in that routine.  When the imported map is transformed into registration with another map, the "drawn on" ID of any non-registration points marked on the imported map will be switched to the ID of the map that was registered to, and any points added after the transformation will also be given that "drawn on" ID.  Thus, that map will be preferred for realigning to.  In order for this to occur, all the registration points must be picked on just the two maps, one imported one and one native one being aligned to.

Rotate Map command (Navigator window - Map/Polygon menu)

Use this command to rotate the map in the active buffer into the correct orientation for the current magnification and registration, or to rotate an imported map by a desired angle and optionally flip it. Specifically, the rotation may include two components: the relative rotation between the magnification at which the map was acquired and the current magnification; and whatever rotation and mirroring around the X axis resulted from any transformations that have been applied to the map item. Points will still display correctly on the rotated map, and new positions can be marked on it. A map can be rotated more than once, or it can be reloaded and rotated to a new orientation.

If a map is imported and has not yet been transformed into registration with native EM maps, then the program will ask you the angle by which to rotate the map (counterclockwise is positive), then ask whether to flip the image around the X axis after rotation.

Adjust for Backlash command (Navigator window - Map/Polygon menu)

With this command, the program will measure the stage backlash at the location of the current item and then adjust the item's stage position and record the backlash direction used.  When stage backlash is substantial, this can improve the accuracy of returning to that location.  The measurement involves dropping magnification if necessary, or going to the View area in Low Dose mode, taking an image, then moving away and back by the backlash amount, taking a new image, and aligning it.  The stage position of the item will be adjusted by the alignment shift.  The backlash used is the same as the backlash for a montage at the starting magnification.  The command is available only for an item with a directly measured stage position (i.e., a map, or point created with Add Stage Pos), and only if the stage is still at the original position.

Note that whenever a map has a backlash recorded for it, the program will correct for backlash in the corresponding way when moving to a point marked on the map.  Montages made with stage movement automatically have a backlash recorded, but other maps may require this backlash adjustment, unless they were taken at a location where the stage was in a known state with respect to backlash.

Backlash Settings command (Navigator window - Map/Polygon menu)

Use this command to open a dialog box for settings that control whether the backlash adjustment routine described just above will be run when a new single-frame map is added.  The dialog has a text box for specifying the minimum size of map for which the program should even consider running the routine.  There is no maximum size setting, but the routine will not be run for a map taken in low magnification. There are three choices:

1. Do not run the adjustment routine automatically or ask whether it should be run.
2. Ask whether the adjustment routine should be run when making a new map larger than the minimum size.
3. Run the adjustment routine automatically when making a new map larger than the minimum size.

When you use the Anchor Map function, the program will automatically adjust for backlash, if necessary, unless you have chosen option 1.  The higher magnification item that you are anchoring will also have its position adjusted, provided that the stage is still at the same location.

Set Map Acquire State command (Navigator window - Map/Polygon menu)

Use this command to return to the conditions under which the currently selected map item was acquired, to facilitate acquiring another map in the same state. The microscope state includes magnification, intensity, spot size, and energy filter settings. The camera acquisition state includes the binning, exposure time, and drift settling of the Record parameter set. Low dose will be turned off if it is on. If the file containing the selected map is still open in SerialEM, it will be made the current file. If the file is not open, it will be reopened so that a new map can be saved into it. This command performs the same operation as the Set Map Acquire State button in the Imaging State dialog box.

Restore State command (Navigator window - Map/Polygon menu)

This command will restore the microscope and camera acquisition state that was present before the last time that 'Set Map Acquire State' was run, or before the imaging state was set from the Imaging State dialog box. If a file was opened when 'set Map Acquire State' was run, that file will be closed again. If the file that was current at that time is still open, it will be made the current file again. Low dose mode will be restored to its state prior to the state changes. This command does the same thing as the Restore Prior State button in the Imaging State dialog box.

Add Circle Polygon command (Navigator window - Map/Polygon menu)

Use this command to add a polygon that is a circle. First mark the desired center point by clicking in an image. Then select this command and enter the desired radius in microns.

Polygon from Corners command (Navigator window - Map/Polygon menu)

Use this command to make a polygon from the current set of points marked as corners.  After the polygon is made, you will be asked whether you want to delete all of the corner points. If you answer No, they will be retained but no longer be marked as corners.  With this command, you can use corner points to define one polygon after another, and then set up each polygon for automatic acquisition into a different montage file.

Shift to Marker command (Navigator window - Transformations menu)

This command provides a potentially simple method of shifting items without having to make registration points. One way to use it is to add a single point at a recognizable feature on an existing map. Then take a new image, click on the feature with the left mouse button, and select this command. The Shift to Marker dialog will open with information about the shift and some choices for applying to a subset of items and for saving the shift for reuse. If you press OK, all items at the registration of the image that was clicked on (typically the current registration) will be shifted by the same amount. (See the dialog help for explanations of the options there.) Another way to use this command is to run the Realign to Item command on a map or an item located in a map. When the procedure is done, take an image, click in the center of it, and select this command. Items will be shifted by the error in stage position found in the procedure. Finally, the command can be used to shift registration points to fit imported items. Suppose you import a map, work out registration points, transform the map, and then import another map that is shifted in position. Then select one of the registration points, click on the corresponding point on the new imported map, and select this command. The registration points will be shifted but the map will not, so the points should appear at the right place in this map. This map can then be transformed into registration with EM maps.

This menu item is enabled either when the conditions are satisfied for doing the Shift to Marker operation, or when there are saved shifts. In the latter case, the dialog will open to allow shifts to be inspected or removed, but none of the other controls will be available.

Apply Saved Shift command (Navigator window - Transformations menu)

Use this command to shift a set of items at a particular magnification for which a shift was saved in the Shift to Marker dialog. Specifically, if a shift was saved for a magnification, maps taken at that magnification that have not been shifted with the Shift to Marker procedure can be shifted, as well as any points or polygons marked on them. First, you will be asked to confirm or specify the magnification of the stored shift to use. If there has been more than one shift saved for that magnification, you will next need to specify which one to used, identified by the magnification of the image on which the marker point was placed. Finally, you be asked to confirm the specific amount of shift to apply. See the Shift to Marker dialog help for some scenarios in which this is useful.

Undo Last Shift command (Navigator window - Transformations menu)

Use this command to undo the shift imposed by the 'Shift to Marker' or 'Apply Saved Shift' commands. It is disabled if the 'Transform Points' command is used.

Transform Items command (Navigator window - Transformations menu)

Use this command to transform items from one or more other registrations to the current registration. The program will find a transformation whose complexity depends on the number of registration points available. Just a shift will be found with 1 point, a rotation and shift with 2 points, rotation, scaling, and shift with 3 or 4 points, or a full linear transformation including stretching and possible image inversion with 5 points. All items except the registration points will then be transformed and associated with the current registration. The program will give a message about how well the points fit the transformation equation. If the fit is very poor, you can undo the transformation with the command described next, fix the problem, and redo this command.

If stretch in the stage coordinate system has been calibrated with the Stage Stretch command , then transformations based on 2 - 4 points will incorporate this stretch, and the report on the transformation in the log will include the text '(corrected for stage stretch)'. When transforming after a large specimen rotation, such transformations may not be very accurate in the absence of such a calibration, but the calibration allows reliable transformations with only two or three points.

Undo Transformation command (Navigator window - Transformations menu)

Use this command to undo the last transformation done with the Transform Points command . Each item will be returned to its former registration, even if items were transformed from more than one registration. This is the only way to undo a transformation of imported items.

Change Registration command (Navigator window - Transformations menu)

Use this command to change the registration of an existing item without changing the current registration. This is different from changing the registration point number, and in fact the command cannot be applied to registration points. If you need to change the registration of a registration point, turn off its the 'Registration point' button before changing the registration.

Align with Rotation command (Navigator window - Transformations menu)

This command opens the Align with Rotation dialog box , which allows you to align a current image with a map taken prior to rotating the specimen. You can also use this alignment to transform items into the new registration, although this transformation is of limited accuracy at long distances from the point being aligned. In order to open this dialog, the map must be in the buffer that images are read into (i.e., just load the map), and there must be either an image in buffer A, or a montage overview in buffer B and montage center in A, at a different registration from that of the map. Thus, after rotating the specimen, increase the current registration in the Navigator, then take an image at the same magnification as the map.

Realign to Item command (Navigator window - Realign menu)

This command can be used to return accurately to the position of an item by correlating with available map images. The item must be located within, or must itself be, a map whose extent is large enough to allow the position to be found reliably. Specifically, the map must be at least 3 microns in extent (or more, if the property file specifies a larger limit). Maps taken in LM mode will not be used for these correlations unless they are from a relatively high magnification in LM where images can be taken with the objective aperture in.  The limit for how low a magnification it will use is controlled by the property RealignItemMaxLMField. There are basically four different situations in which this procedure can be used:

1. The item is not a map, just a point or polygon. It must be located within a big enough map, but it can be very near the edge of the map. In this case, the program will first move the stage to the center of the map, or to the center of one frame of the map if it is a montage, then take an image and align it to determine the error in stage position. It will then move the stage to the position of the item, take a new image, and align it to work out the error from that small stage movement. If this procedure has been run on a nearby area recently enough, the program is able to use the results of previously aligning to the map center and go directly to the second round of alignment at the item position.
2. The item is a map that is not located in a larger map, so it must itself be large enough for reliable localization. The program proceeds as just described, except that it ends up aligned to the center of the map.
3. The item is a map located within a significantly larger map. In this case, the larger map must be the minimum required size, but the item being aligned to can be small. The program proceeds as above to find the item position by correlating with the larger map. Then it does a third round of alignment by raising the magnification to that of the item itself, takes a new picture, and aligns it with the map item using image shift. This image shift should be relatively small provided that the position was found accurately at the lower magnification, and that the calibration of image shift offsets between magnifications is still accurate.
4. The item is a position on a map at a lower magnification than that at which images are to be acquired, and the operation is run in a way that allows it to do a third round of alignment between an image at the higher magnification an appropriately scaled and rotated portion of the map centered on that point.  This method is only available when running through the Navigator Acquire at Items procedure or from a script command, not through the menu or the button in the Navigator window.  If the position can be marked accurately enough on the map, it has three advantages:
   • There is no need to store a map at the higher magnification as in situation 3.
   • The scaled-up reference image can be bigger than the camera frame, which allows shifts larger than half the field of view to be found reliably, provided that the image is not dominated by periodic structures.  This is also an advantage over the virtual maps of Schorb et al., Nature Methods 16: 471-477 (2019).
   • If the higher magnification image has a large enough field of view (10 microns by default) and the routine is able to skip the first round of alignment, it will skip the second round as well, go directly to the item position, and just do the third round.  This is particularly useful for aligning at an intermediate magnification to an LM map, as it avoids going in and out of LM.
   This method requires a camera parameter set or Low Dose area to be designated for the image to be aligned.  In Low Dose mode, the area must be at a higher magnification than the map.  Outside of Low Dose, the routine must start at a higher magnification than the map.  The third round will simply be skipped if these conditions are not met.  Parameters for this method are set in the Navigator Align Setup dialog.

When a map is defined, the program stores the brightness, spot size, and exposure settings used to take the map images, as well as the state of the energy filter if appropriate, and these settings are used in this routine to take the images for correlation. The beam size and centering must be robust enough to work at the different magnifications. In other words, if the beam shifts between the different magnifications, it must be spread enough at one of the magnifications so that it still covers the field without being centered.

The previous state of the microscope is restored after the procedure when it is run with this command from the menu or the corresponding button in the Navigator window. When it is run from a script, the state may or may not be restored depending on what is specified in the script command.  However, when the routine is called while in Low Dose mode, the state is always restored by going back to the previous Low Dose area after taking images in the same conditions as the map.

When in Low Dose mode and realigning to a map taken in Low Dose, the routine will attempt to remain in Low Dose if the current parameters of the area with which the map was taken match the parameters used for taking the map.  The match is not considered good enough if there is a change in the camera, the magnification, or the probe mode (on Thermo/FEI) or alpha (on JEOL); or if the defocus offset (for a View or Search map) has changed by more than a limit set by the RealignItemFocusChangeLimit property, which is not set by default.  If the match is not good enough, the program will internally leave Low Dose mode by going to the Record area first, which can waste many seconds.   If the match is good enough, the routine will substitute the map parameters into the Low Dose area and take images with those parameters, unless an option is set in the Tasks-Specials Options submenu to realign with the current area parameters.

In most cases, the routine will adjust for misalignments between magnifications even if you have not selected the 'Adjust image shift between mags' option in the Alignment & Focus control panel. Specifically, in situations 1) and 2) above, if the microscope state is being restored after the routine runs, then the feature being aligned to should appear centered at the restored magnification. In situation 3, the feature will be centered at the magnification of the map item being aligned to.

Setup Align/Realign (Navigator window - Realign menu)  

Use this command to open the Navigator Align Setup dialog and set parameters and set up a template for the Align to Template command.  Some options for resetting image shift after such an alignment can also be set; these parameters are also used when Navigator Acquire at Items runs the Realign to Item routine.

Force Center Align (Navigator window - Realign menu)  

This command makes the Realign to Item routine forget previous information about a recent alignment to the center of the map and do the first round of alignment to the map center.  By default, Realign to Item will skip that first round if the same map was aligned to recently and the alignment error was low enough.  If the first round fails, it may be necessary to use this command to prevent the skipping on the next attempt.

Erase Periodic Peaks in LD (Navigator window - Realign window - Realign menu)  

This command toggles whether alignment correlations for Realign to Item in Low Dose mode are done after trying to identify and erase periodic peaks in the FFTs used for the correlations.  Erasing of peaks seems to work well for gold grids and is essential when working with ones having hexagonally spaced holes, which are much closer together.  It does not work reliably for regular carbon grids, which may not have enough remaining non-periodic signal.  This option alone determines whether erasing is done in Low Dose mode; the general option in the Image Alignment & Focus control panel determines whether erasing is done outside of Low Dose mode.

Use Current LD Params in Realign command (Navigator window - Realign menu)

This command toggles an option to use the current Low Dose parameters for Realign to Item instead of the Low Dose parameters set when the map was acquired.  The option applies only when staying in Low Dose mode for the Realign operation, which occurs as long as the current camera, magnification, and probe mode (on a Thermo/FEI scope) or alpha (on a JEOL) match the map condition.  By default, the Realign operation imposes the map conditions when realigning to a map.  This option is available because there are situations where it is advantageous to take the map under different conditions.  For example, more dose might be desired for the map to allow either better visualization of features or more reliable montage piece alignment, while less dose can be used for correlating with those maps.

Try Scaling in Realign (Navigator window - Realign menu)

This command toggles an option to try to adjust for specimen shrinkage when doing Realign to Item .  On the first round of the realignment, where an image is aligned to the center of a map frame, the program will search for the image scaling that makes it align best to the map frame.  This scaling is then used to adjust the target position (which is not at the center) for the shrinkage that occurs.  The scaling will not be done if the program is in Low Dose mode prior to the Realign operation.

Search + and - Scaling in Realign command (Navigator window - Realign menu)

This command toggles an option to try scalings both below and above 1 when searching for the best scaling in Realign to Item.  This might be useful when aligning to a synthesized map or one made on a different microscope with somewhat lower magnification.