Navigator menu commands

The Navigator menu has commands for opening the Navigator window, operating on Navigator files, and performing less common Navigator operations.

Open command (Navigator menu)

Use this command to open the Navigator window.

Read & Open command (Navigator menu)

Use this command to read in a Navigator file as well as open the window if it is not already open. The file will become the current file for saving into.

When a Navigator file is read, each map file will be located if possible.  The program will look first at the path specified in the Navigator file.  If this fails, it will next look in the same directory as the Navigator file.  Next it will test whether the path starts with './'. '.\', '../', or '..\', and if so, then the program will look for the map file at this path relative to the location of the Navigator file. (SerialEM saves an absolute path for the map file, but other software might use relative paths.)  Finally, it will use the information in the Navigator file about where it was last saved to see if there was a relative path from the Navigator file to the map file previously, and if so, it will look at this relative path from the current location of the file.

If any map file cannot be found, the program will issue a message listing such files.   If each such map  file is moved into the directory of the current Navigator file, its maps will be found when needed.

Run Script in Multi-shot (Navigator - Options submenu)

This command toggles an option to run a script in place of the Record acquisition in the Multiple Records routine.  The Multiple Records cannot itself be run from script, it must be run from Navigator Acquire at Items.  There are probably other restrictions of what the script can do, which will be revealed by malfunctions and crashes.  If you want a Record to occur, you must include the 'Record' command in the script.

Set Script to Run (Navigator - Options submenu)

Use this command to select the script to run instead of taking a Record in the Multiple Records routine.  When you select this command, a dialog will open with a drop-down list in which you can select the script by its name or number.  It is best to have a (short) name assigned to the script so that if scripts are rearranged, or a different set is loaded, the program will not run the wrong script.

Setup Full Montage command (Navigator menu)

Use this command to set up a montage to capture the whole grid area. A set of points will be composed that contain the grid area. The following description applies to how the area within these points is treated and to next two commands that involve fitting a montage to an area.  Outside of Low Dose, be sure to go to the desired magnification before activating this command.  In Low Dose mode, the program will use the pre-existing settings of the 'Use View in Low Dose Mode' and 'Use Search in Low Dose mode' options to determine how to fit the area.  If it finds that the fit requires too many pieces, it will switch to a mode with a larger field of view.  More likely, it will open anyway with the wrong area selected and you will have to change this selection.

 You will be opening a new image file for the montage, so if there is already a file open the program will ask whether you want to close it. The program will compute the number of montage frames in X and Y required to capture the area, and decide whether the montage should be acquired with image shift or stage movements. If the area of the Record parameter set is substantially smaller than the camera field, you will be asked whether you want the frame size to be kept smaller than the current Record area. You might want this if the beam is too small to fill the whole camera field. Otherwise, the program will make the frames as large as possible. Unless there are too many frames, you will then go on to the Montage Setup dialog box, in which you will see the number of frames and their size and overlap. If the size of the montage is not reasonable (e.g., bigger than 20K by 20K pixels), outside of Low Dose you can change the magnification to adjust the number of frames and achieve the desired image size.  In Low Dose mode, you can only switch to using View or Search mode instead. You can also adjust the percentage overlap, which may also change the number of frames needed to fit the desired area. Once you have set up a reasonable montage, go on to the File Properties dialog box then the Save As dialog box.

After the montage is defined, the program will compose a list of pieces that are not needed to capture the intended area. These pieces will be excluded when the montage is acquired.

Set Grid Limits command (Navigator menu)

Use this command to enter lower and upper limits in X and Y for the full grid montage.  Specifically, these limits will be used to construct the polygon that is fit when setting up the full montage, but not to limit the stage positions visited to acquire a montage covering that polygon.  Actual stage movement can be limited only by the 'StageLimits' property in the SerialEMproperties.txt file, and this property, not the setting here, determines the coordinates of the dashed red rectangle that will be drawn on images that extend beyond the limits when the Navigator is open.

A dialog box will come up for each limit; enter the desired limit in microns or 0 to use the default limit that is shown, which is the property-based limit that can be modified with 'StageLimits'.  If you enter a number bigger than one of the defaults, you may get farther out to the corners of the usable area, but the stage will still not be moved beyond the property-based stage limits.  If you want access to the full range of motion on a JEOL scope, you need to enter or change the 'StageLimits' property to be '-1190 1190 -1190 1190' (or less extreme values if appropriate).

Setup Polygon Montage command (Navigator menu)

If the current Navigator item is a polygon, use this command to set up a montage to capture the area within the polygon. It works the same as the Setup Full Montage command .  Once the montage is set up to capture an area of a particular shape, it can be used to capture the same area at other locations without drawing a new polygon.

Setup Corner Montage command (Navigator menu)

Use this command to set up a montage to capture the area within the current set of corner points. It works the same as the Setup Full Montage command .

Acquire at Items command (Navigator menu)

Use this command to acquire images or maps or run a script or tilt series at a series of items marked for acquisition with the 'Acquire' or 'Tilt series' check box in the Navigator window. There must be an image file open before the command can be used to acquire images or maps, unless 'New file at item' has been set for the first item to be acquired. If montaging is to be used, this means that the montaging must be set up already. Be sure to have magnification, intensity, and exposure times set before starting the acquisition, unless an imaging state has been set for the first item. This command opens the Acquire at Items dialog box, which allows various options to be set.

End Acquire command (Navigator menu)

After starting an 'Acquire at Items', use this command to stop the Navigator from going on to the next item after finishing the current one.  If the acquisition is already paused after finishing an item, the command will stop acquisition immediately.

List Files/Series/States command (Navigator menu)

Use this command to get a list in the Log window of everything that has been scheduled to happen in the course of running an 'Acquire at Items' operation. Specifically, the list will show the files that will be opened and their properties, the imaging states to be set when files are opened, and the tilt series that are set up to run.  For a Low Dose state (marked as LD), the list will include (after 'F pos') the focus position along the axis between low-dose areas, the rotation of the axis if any, and the offset from center of a Focus subarea in binned pixels. In addition, the Focus position will be listed for any items that have it stored, regardless of whether a file is to be opened or a state set.

Multiple Grid Operations command (Navigator menu)

Use this command to open the Multiple Grid Operations dialog and control acquisition on multiple grids.  The Navigator will be opened if it is not open yet.  If the property 'ScopeHasAutoloader' is set to 0, this menu item appears as Multiple Operations on Grid and the dialog is modified to work appropriately when doing the same operations on a single grid.

Reopen Multi-grid Session command (Navigator menu)

Openthe Navigator window if it is not open yet, and read in a file saved by the Multiple Grid Operations dialog or multi-grid routine, open the dialog if it is not open yet, and load the contents into the grid table in that dialog.  Session files are named with the format 'multiGrid_date_#.adoc'.  The file chooser will open on the last session file saved, if any.  After a file is read in this way, the session information will be saved into a file with the same name.

Clear Multi-grid Session command (Navigator menu)

Use this command to clear out the grid table in the Multiple Grid Operations dialog and re-initialize the session.

Identify Grid on Stage command (Navigator menu)

Use this command to specify which grid is actually on the stage, in case the program has lost track of this information.

Load All Grid Maps command (Navigator menu)

Use this command to load all grid maps that have been acquired in a session with the Multiple Grid Operations dialog, or to load all apparent grid maps from the currently open Navigator file when there is either no multiple grid session or no grid maps available in a session.  The command is thus useful for a different style of working, where multiple grid maps are all in one file at different registrations.  In this case, the program looks for the lowest magnification at which maps were obtained, in LM only, and loads as many maps taken at that magnification as possible.  In either case, it will load the maps in buffers past the read buffer if possible, and thus ordinarily past the rolling buffers, but they may start in lower buffers if necessary to fit all the maps. If this does not fit your needs, the script command 'LoadAllGridMaps' allows you to specify the starting buffer to load into.  Once all these maps are loaded, it is tempting to add points to any one of them, but this would often result in points in the wrong Navigator file.  As long as the Multiple Grid Operations dialog is open, the program will prevent adding points to a map that is not in the table for the open Navigator file.  When you try to do so, it will print a warning up to 5 times in the log.

Autocontour Grid Squares command (Navigator menu)

Use this command to open the Autocontouring Grid Squares dialog, which can make contours around grid squares at an intensity threshold, allow you to set criteria for eliminating some contours, and convert selected contours into Navigator polygons.

Reverse Contour Colors command (Navigator menu)

Use this command to invert the order in which colors are assigned to groups of contours generated by the Autocontouring Grid Squares dialog in inverted order, from magenta and purple to orange and red, instead of from red through magenta.  This could be useful if you use only 5 or 6 groups and find the colors on the blue-magenta end more distinguishable.

Keep Colors for Polygons command (Navigator menu)

This command toggles whether the groups of contours generated by the Autocontouring Grid Squares dialog are assigned the same colors when they are converted to polygons, rather than given the default polygon color.

Find Holes in Regular Array command (Navigator menu)

Use this command to open the Hole Finder dialog, find circular holes in a support film, and make Navigator points from them. The Navigator must be open to open this dialog.

Add Grid of Points command (Navigator menu)

Use this command to add a set of points on a regular rectangular lattice. Four different kinds of grids can be defined: points in a rectangle; points on a defined rectangular lattice to fill a polygon or map; points along a line, and points at a defined spacing to fill a polygon or map. For the first two kinds, the position of the lattice is specified by a group of 5 points, three at corners of a rectangle and two more adjacent to one of the corners. Here, holes that should be marked with a point are shown with 'X' and the rest of the holes are shown with 'o'.

X      o      o      o      o

o      o      o      o      o

o      o      o      o      o

o      o      o      o      o

X      o      o      o      o

X      X      o      o      X

To make all of the points be in one group, press the 'Add points' button and mark all 5 points before pressing 'Stop Adding'. As long as one of the points is the current item, you can select this command. The program will then ask for the label of a polygon that you want to fill. If you leave the text box blank, it will create points for all positions in the rectangle indicated by the corners. If you enter a valid label for a polygon that contains the points (specifically, the centroid of the points), then it will add points to fill the polygon, extending the rectangle beyond the corners that you have marked if necessary.  If you are filling an elongated region, you can reduce errors from extrapolation by marking the corner with two adjacent points near the middle of the region instead of near one end.

For a large grid, it may be difficult to mark the two adjacent points accurately enough to end up with the right number of points between them and the endpoint.  You can overcome this with a group of 7 points, where the points along one axis would look like

X      X      o      o      X      o      o      o      o      o      o      o      o      o      o      o      o      o      o      o      X

and similarly along the other axis.  The additional point between the adjacent pair and the endpoint (X) allows it to get a more accurate initial estimate of the interval between points, so that when it divides the longer distance by this interval and rounds to the nearest integer, it comes out with the right number. Placing this point at the square root of the total number of points along the line should be optimal (e.g, at the fifth point if there are 25).  (The additional point needs to be far enough out to give a sufficiently accurate initial estimate but not so far that it mis-estimates the number of points along the line to that point.)  If you start with a 5-point group and the placement fails, you can add the two points to the same group by turning on Edit mode, selecting any point in the group with the left mouse button, and adding the two intermediate points with the middle mouse button.

Once you have added a grid with a 5- or 7-point pattern like this, you can add a grid in a new area with the same spacing and orientation by simply adding a single point in the new area.  It must be the only point in the group, so press 'Add points', add the point, and press 'Stop Adding'.  If you are not filling a polygon, the point should be at the same corner of the region to fill as the corner of the 5-point pattern with two adjacent points.  If you are filling a polygon, the program will test for whether either this point itself, or the center of the grid that would extend from that point as its corner, is in the polygon.  Thus, you can put the point near the middle of the polygon to reduce extrapolation errors.  (The test for the point itself being in the polygon was added in SerialEM 3.7.4).

To add a line of points, simply add a group of three points to indicate the extent and spacing of the line, such as:

X    X    o    o    o    o    o    o    X

As long as one of these points is the current item, the command will be available and will add a line of points between the endpoints.

Finally, to add equally spaced points within a polygon or map but not on a defined lattice, simply make the polygon or map be the current item and select this command. Then enter the desired spacing in microns.  Alternatively, keep one of the points in the group as the current item and start this command.  You will be asked to identify a polygon or map to fill with the grid, either by the item's label or by the negative of the item's index in the table. 

When adding points to fill a polygon or the rectangle of a map, the points will not be placed right up against the border of the polygon. Rather, a square box around each point is required to be fully within the polygon. The size of this box as a fraction of the spacing between points is controlled by the GridInPolygonBoxFraction property, whose default value is 0.75.

Grid points can be added in two different patterns. One is a zigzag path, in which points go in alternating directions between successive rows or columns. This was originally the only pattern in SerialEM and was designed to minimize stage movement when moving between points. The other pattern goes in the same direction in each row and column, and proceeds in an overall direction away from the location of the Focus area in Low Dose mode. This pattern ensures that focusing is done in areas that have already been acquired from.  However, this pattern is not used when added points are placed into separate groups.

Add Grid Like Last One command (Navigator menu)

After adding a grid of points with the previous command, you can use this command to add another grid of the same kind without having to answer any queries.  'Of the same kind' means that if the last grid was added on a group of points or a single point, the command can be used if a point is selected; whereas if the last grid was added with a polygon or map selected, a polygon or map must again be selected.   If you added a grid with a group of points or single point selected and chose to fill a polygon or map with the grid, then the program will search for the smallest polygon or map containing either the point itself or the center of the pattern extending from the current point as its corner and fill that area.  In other words, when you use a single point to reuse a previous 5 or 7 point pattern, you can put the point right in the middle (as of SerialEM 3.7.4) or you can put it in the corner of the grid square, even outside the polygon, as long as the position at the center of the previous pattern, starting at that point as its corner, is inside the polygon.

In sum, this command should work just the way you want: add a point at the corner of a new area to be filled and run the command, which you can do with the menu accelerator Alt-N-M-L.  The easiest way to add a single point is to place the marker there first, then press 'Add Marker'.

Divide Points into Groups command (Navigator menu)

When this option is selected, the set of points added with the Add Grid of Points command will be divided into multiple groups.  The middle point of the group will be the first point, and its distance to every other point in the group will be less than the maximum radius set with the Set Group Radius command.  With this arrangement, you can use the option in the Acquire at Items dialog to focus only on the first point in a group, and other points will be within a certain distance of the location where focus was last done.

When points are divided into groups, the program will display the result, tell you the number of groups and points per group, and ask if you want to keep this grouping.  If groups are too large or small, just press No and all the points will be removed.

Set Group Radius command (Navigator menu)

Use this command to set the maximum radius used for dividing points into groups as described above.  Sometimes groups will be smaller than they could be for a particular radius, because the total extent in each direction of the grid gets divided into groups as evenly as possible.

Set Multi-shot Parameters command (Navigator menu)

Use this command to open the Multiple Record Setup dialog and set parameters for using image shift to take multiple Record images in a circular pattern around the current position, on a regular array, or in a custom pattern of positions.

Set Hole Order for Regular Array command (Navigator menu)

Use this command to set the order in which holes in a regular array are acquired.  The choices are: 1) Jump from the center to the corner then do alternating rows in opposite direction, referred to as a zigzag path, so as to minimize the shifts between holes after the initial jump.  2) Jump to the corner and do all rows in the same direction, a raster pattern.  3) Start in the center and do concentric squares, following a spiral path to minimize all shifts between holes.  If the array is not square, the spiral path is followed in a the largest possible square, then the extra rows or columns are added in a zigzag path that still minimizes shifts.

Combine Points for Multi-shots command (Navigator menu)

Use this command to open the Multiple Hole Combiner dialog, which lets you convert a regular array of points marked for acquisition into a subset that are set up for multiple Record acquisition.

Show Shots when Show Acquire command (Navigator menu)

This command toggles whether selecting the 'Show Acquire area' checkbox in the Navigator window will also result in a pattern of circles being drawn based on the parameters set in the Multiple Record Setup dialog when that dialog is not open.  The circles will represent the area covered by the beam, assuming the beam size specified there.  The pattern will be drawn around the marker point if one is present; otherwise it will be drawn around the current item, if it is marked for acquisition, or around multiple selected items.  However, it will not be drawn if the current item is set to acquire an incomplete pattern (i.e., in which some positions are being skipped), so that it is clear which positions will be acquired for that item.  If Edit mode is not on, use Shift-Left-click to turn off the marker and see the pattern around the current point.  If Edit mode is on and there are multiple hole positions in a regular (non-custom) pattern, then Shift-double-Left-click near one of the positions will remove it from the pattern.

Show Whole Area for All Points (Navigator menu)

Use this command to have the envelope of all acquire areas from multiple Records drawn around all points marked for acquisition, when the 'Show Acquire area' checkbox is turned on in the Navigator window or the  Multiple Record Setup dialog is open.  If the multi-hole pattern around a point is incomplete and there are points missing inside the drawn boundary, then the program will draw either boxes representing the areas being acquired, or light blue triangles around the holes being skipped, whichever gives fewer points to draw.  For the current point, the program always shows boxes at all the holes being acquired, so that they have be deleted with mouse, and the envelope is omitted.

Setup Super Montage command (Navigator menu)

Use this command to add a set of rectangles at the positions of overlapping montages, laid out on a rectangular grid that is aligned to the camera axes. First, you must have montaging set up with the desired number of pieces and magnification. Specify a center position in the active image by clicking with the left mouse button. Then select this command. You will be asked to enter the number of montages in X and in Y then the number of pixels of overlap in X and Y. A set of polygons will be created, numbered by their positions in the super montage. To try again with different parameters, just use the Delete button in the Navigator to delete the whole group of items.

To get fairly accurate overlaps between montages, use the following procedure. First take a montage that encompasses the whole needed area, at a lower magnification if necessary. On a Thermo/FEI microscope, it is recommended that you use the option to realign with image shift (see Acquiring High-Quality Montages of Large Areas in Montaging and the last paragraph of Returning to a Position Reliably in Using the Navigator for details). Turn on 'Align pieces in Overview', and also have 'Sloppy montage' on as well if this is needed to get the pieces properly aligned. Make this montage be a map. Then go to the working magnification for the supermontage and set up the montage file. After you answer the queries about number of montages and overlaps, you will be asked if you want the positions to be laid out at regularly spaced image positions rather than stage positions. Do not select this option unless the pieces are indeed properly aligned in the area covered by the supermontage (there can be errors in alignment elsewhere). Also, only select this option if you are going to use the 'Realign to Item' routine at some point to get to individual montage positions. One approach would be to check 'Acquire' for each of the new montage position items and then run the Acquire at Items command with the option checked to 'Realign at item'. This will yield montages that can be blended and analyzed for overlap.

The Setup Super Montage command was originally called Aligned Super Montage, and there was also a Skewed Super Montage command to lay out montages on a grid that is aligned to the specimen axes. Such montages require more overlap to avoid gaps between montages, and the stitching programs in IMOD work well with the aligned supermontages, so the skew capability has no apparent merit.

Polygon Super Montage command (Navigator menu)

Use this command to add a set of rectangles at the positions of overlapping montages that will fill a polygon. First, you must have montaging set up with the desired number of pieces and magnification, and the current Navigator item must be a polygon. After you select this command, specify whether the positions should be marked for acquisition. The supermontage will include any montage that is needed to cover the area within the polygon, with a little allowance for errors in positioning. You can then use the 'Skip pieces outside Navigator item' option in the Montage Setup dialog box, to have each individual montage include only the frames inside the polygon. If you use an entry of 0 there to specify the current Navigator item, be sure to reselect the polygon item after defining the supermontage.