The Navigator window is used to keep track of stage positions and low magnification maps and can assist with locating positions on the grid after it has been rotated or repositioned in the holder. Each stage position and associated information is referred to as an item. The window has five kinds of controls; the table below has links to the controls with the most lengthy explanations:
| Properties of Current Item | At the top, properties of the currently selected item. |
| Acquisition Controls | Between item properties and the horizontal line, controls to set the properties when acquiring data at the current item. |
| Acquire | Mark items at which to acquire an image or map or run a script. |
| Tilt series | Mark items at which to acquire tilt series. |
| New file at item | Select to start a new file when acquiring the item. |
| New file at group | Select to start a new file when this item's group is reached |
| File Properties | Adjust properties or type of file being opened |
| Image State | Store the current imaging state to be used for acquisition. |
| Controls of General Behavior | Below the horizontal line, on the right, some controls governing overall behavior. |
| Current Registration | Adjust the registration number for a repositioned grid. |
| Collapse Groups | Summarize groups of consecutive points with a single line in the list box. |
| Show Acquire Area | Display a box in the image representing area to be acquired. |
| Edit Mode | Toggle an editing mode to select, add, and move points with the mouse. |
| Edit Focus | Toggle a mode for adjusting stored Low Dose Focus position with the mouse. |
| Action Buttons | Below the line, on the left, pushbuttons for the most commonly used actions. |
| New Map | Store the current image as a new map item. |
| Anchor Map | Make a lower-magnification map for realigning to the current item. |
| Realign to Item | Reposition at the current item by correlating with maps. |
| Item List Box | In the lower right, a box containing a list of items and their properties. |
The Navigator window can be resized to show more or less of the list box.
Label
The label is a short identifier that will be drawn on the image. The Navigator will assign labels as sequential numbers but you are free to edit them to say something more meaningful. When groups are collapsed and a single item is selected in a group, the label of that item will be shown.
Registration Point
Use this check box to mark a point as a registration point, which can be used to transform locations when the grid is repositioned in the holder. The first time that you set up a registration, you can use the spin buttons to select a unique point number (this should happen automatically). When you are adding corresponding points in a new registration, use the spin buttons to make each point number match the number of the corresponding point in the previous registration. The hot key R (without Shift or Ctrl) can be used to toggle this check box.
Corner Point
Use this check box to mark a point as a corner of an area for which you want to construct a montage. The hot key C (without Shift or Ctrl) can be used to toggle this check box.
Color
You can change the color of an item with this selector. By default, single points are red, drawn polygons are green, maps are blue, and supermontage polygons are yellow. You can also select "NoRealign" here either to prevent a map from being used for the first stage of the Realign to Item routine, or to prevent a higher magnification map from being aligned to in a second stage when realigning to that map. The item will be drawn in dark blue in this case. When a point or map is marked for acquisition and still has its default color, it is shown in a brighter red or blue, respectively (not quite magenta or not quite cyan). A point that is the current item or that is one of multiple selected items is shown in orange-yellow. In both of these cases, the item still has the basic color shown in this box.
Draw
Use this check box to control whether an item is drawn on images that it falls within. When groups are collapsed and a group is selected in the table, this box is still available as long as all items summarized on that table line have the same drawing state, and it can be used to toggle the drawing on or off for all of those items.
Rotate when load
Turn on this check box to have a newly loaded map automatically rotated into the same orientation as images at the current magnification. Rotation can take many seconds for very large maps.
For anchor state
Use this check box to mark a map item as a template for acquiring further medium-magnification maps that will be suitable for realigning to. Only one map item can be marked as such a template, so if there is already a map marked for this, it will be unselected when you check the box for a new item. See Anchor Map below for details.
Item #
To the left of the Note text box appears the number of the current item in the table, numbered from 1. When the current table line is a summary of a group of points, their range of item numbers is shown.
Note
This text box allows you enter an arbitrarily long note about the current item.
The controls in this section allow items to be marked for particular kinds of acquisition, including tilt series and montaging, both of which involve numerous parameters that can be changed from one item to another. As of SerialEM 3.9, 6/16/21, all of the tilt series and montaging parameters, names of files to be opened for individual items, and options associated with those files are saved to the Navigator file and will be restored when a file is reloaded. However, imaging states are not saved, nor is information about files to be opened at groups.
Use this check box to mark an item as a position to be acquired automatically. After marking such items, you can use the Acquire at Items command to open the Navigator Acquire dialog box and then acquire images at the sequence of locations and make each into a map, or perform other actions at each location. There are three hot keys that can be used to toggle this option on or off, provided that the main program window has the keyboard focus. The A key will just toggle the item currently selected in the list box. Ctrl-Shift-A will toggle all of the items. Shift-A can be used to toggle a selected range of items, but it has to be pressed twice to do so. First select the item at one end of the range with the mouse (or arrow keys) and press Shift-A. Then make the item at the other end of the range be the current item, and press Shift-A again. The Acquire state will be toggled for items between the first and second selection, except for items marked for tilt series.
Use this checkbox to set up a tilt series to be acquired at the current item's location. The first time that you select a tilt series, a series of dialogs will open:
If you cancel any of these dialogs, or the filename you select is already in use, the item will not be marked for a tilt series.
When you select a tilt series for an item and there is an item before it in the table already marked for a tilt series, no dialogs will open: all of the properties will be inherited from the preceding item, and a new filename will be generated by increasing a number, or adding one if there is no number in the previous name. However, you can change any of these properties by pressing the File Properties, TS Parameters, or Filename buttons, including whether the file is single-frame or montage.
When you use TS Parameters and leave the Tilt Series Setup dialog by pressing OK, the selected item will be given a new set of parameters if it is inheriting them from previous items. The new parameters will be inherited by any following items that shared these parameters and that have not been given their own parameters in this way. Similarly, when you use File Properties and leave the File Properties dialog with OK, the selected item will get its own parameters if they are being inherited from previous ones, and any following ones sharing these parameters will inherit the changes. Thus, the rule for both of these kinds of properties is that if you have never gone through the dialog for an item, the item will inherit the properties from the nearest previous item where you have gone through the dialog. The log window will show messages about these effects of changing parameters.
An imaging state will not be set for a tilt series unless you press the Imaging State button; when no state is set, the tilt series starts with whatever pre-existing state exists. Press the button to save the current state, which includes the current camera and Record image size and exposure parameters and whether the program is in Low Dose mode or not. When not in low dose, the state includes the beam intensity, spot size, and energy filter settings if any. When in low dose, the Record area parameters are saved as a whole, which encompasses those same parameters plus the magnification.
Tilt series can be set up for a range of items by selecting an item at one end of the range, pressing 'Shift T', selecting the item at the other end of the range, and pressing 'Shift T' again. If the range contains multiple maps at the same stage position, any map at the same position as one taken at higher magnification will be ignored. Thus, you can have Anchor maps and high-mag maps interleaved in the range, and Anchor maps will be ignored. If all items in the range not being ignored and not marked as 'Acquire' are already set for tilt series, this operation will turn off the tilt series designations for all of them. Otherwise, tilt series will be set up for each item not being ignored and not already marked as 'Acquire' or 'Tilt series'.
This checkbox allows you to open a new file for the current item if it is marked as 'Acquire'. These dialogs will open the first time that you check this, and in some other cases:
If you cancel any of these dialogs, or the filename you select is already in use, the item will not be set for a new file.
Usually, if there is a file scheduled to open for a preceding item marked 'Acquire', no dialogs will open: properties will be inherited from the preceding item, and a new filename will be generated by increasing a number, or adding one if there is no number in the previous name. These properties include the list of montage pieces needed to fit to a polygon; thus, if the preceding item has a montage fit to a polygon and the current item is a point, the new file will be a montage fitting the shape of that polygon but taken at the new location. You can then change the automatically inherited properties with the File Properties or Filename buttons, including whether the file is single-frame or montage. Dialogs will open, however, when the preceding item has a montage fit to a polygon, the current item is a polygon, and you did not select the option in the initial small dialog to fit without opening the montage dialog.
New files can be set up at a range of items marked as 'Acquire', or at a subset of items, by selecting an item at one end of the range, pressing 'Shift N', selecting the item at the other end of the range, and pressing 'Shift N' again. If all eligible items in the range are already set for new files, this operation will turn off the new file designations for all of them. However, if only some or no items are set for files, an entry box will appear that allows three choices:
Use this checkbox to set up a new file to be opened when the first item in a group is about to be acquired. This option operates similarly to 'New file at item', except that the option to fit a montage is not enabled. It does not matter which item in the group is the current item, or whether the current line is a summarized group, when you select this option.
You will not be able to define a new file for a group if any item in the group is marked as 'Tilt Series' or is set to have a new file opened at it. Similarly, once a new file is scheduled for a group, the 'Tilt series' and 'New file at item' options are not available for any items in the group.
Use this button to check or adjust the properties of a file that is scheduled to be opened for image or tilt series acquisition. The small dialog will open to allow you select montaging and fitting to a polygon if appropriate, then the Montage Setup dialog box , if you selected a montage, then the File Properties dialog box . If you cancel the latter box, changes made in the montaging properties will be retained. These dialogs open from this button even when you have selected options to skip them.
Use this button to store the current imaging state (microscope settings and imaging parameters) as a state to be set when the current item is about to be acquired. The button is enabled only for items where a file is set to be opened. If a montage is to be opened in Low Dose mode, the stored state will be for the Low Dose area to be used to acquire images, thus it can be Record, View, or Search. When in Low Dose mode, the state also includes the axis position of the Focus area, including rotation of the axis if any, and the amount that a subarea is displaced from the center in the Focus camera parameters. One or both of these settings can thus be varied between tilt series to focus on favorable locations, but if there is no other reason to save the state, it is preferable to use the Focus Pos button instead. The Imaging State button is enabled whenever there is a file set to be opened for the current item or group of items (including for a tilt series). The state is set when the Navigator first moves to the item position. Once you have a state set, the acquisition code in the item table (in the Acq column) will have an S at the end. To assess and modify the stored state for the current item, press Scheduled in the Imaging State dialog box , modify the state as desired, and press this Imaging State button to store the modified state.
(Set) TS Params
Use this button to check or adjust the parameters for the tilt series set to be acquired at the current item. The Tilt Series Setup dialog box will open, and new settings will be stored unless you Cancel out of the dialog.
(Set) Focus Pos
Use this button to store a specific location of the Low Dose Focus area for the item to be acquired. Just as for an imaging state, the position along the inter-area axis, rotation of the axis from the tilt axis if any, and offset of the subarea from the center of the camera field are stored and set when the item is about to be acquired. Unlike the imaging state, this information is stored as part of the Navigator item itself and saved in the Navigator file, so it is not lost when the program is restarted. It is thus preferable to save it this way instead of in a state, which is not stored to file. If you do save a state as well, the state will be set first, then the parameters saved with this button, overriding the values in the state.
If the Focus position is saved for one item, it will stay the same for later items being acquired, until the next one that has its own Focus position.
Stored Focus positions are listed for every item by List Files/Series/States. To set a stored position, select the item in the table and press Scheduled in the Imaging State dialog box. You can see the position by reloading a View map at that position, or taking a new View image there, and selecting Focus as the area to be defined in the Low Dose control panel. At that point you can also modify the position by clicking in such a View image, and store it by pressing this button again. Set the Edit Focus description below for an alternative way to see and adjust the Focus positions for items, which should be more convenient when working with maps.
If you turn off 'Acquire' or 'Tilt series' for an item, the stored position will be removed and not restored if you turn the check box back on, so toggling the acquisition is a way to delete a stored position. When items are acquired, their stored positions are not removed.
(Set) Filename
Use this button to change the name of the file that is set to be opened for this item or group. The existing filename is shown just to the right of this button.
The current registration starts at 1 and should be increased every time the grid is repositioned in the holder or the holder is replaced in the microscope. Use the spin button to change the current registration. An image is associated with the current registration when it is acquired. When items are created by marking on images, they are assigned the registration of the image, which is not necessarily the current registration.
(Draw:) All Reg.
Ordinarily the only items that will be drawn on an image are ones with the same registration as the image. Use this check box to turn on drawing of items from other registrations.
(Draw:) None
Use this check box to turn off drawing of all items.
(Draw:) Labels
Use this check box 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.
Items that are added together by various means are marked as belonging to a group with a unique ID number. Use this check box to have each group summarized by a single line in the table, showing the number of items in the group, the last 4 digits of the ID, the labels of the first and last points in the group, and whether some or all items in the group are marked for acquisition (Acq) or tilt series (TS). Several operations can be performed on all of the items summarized in a line: updating the Z coordinate, changing acquire status, and deleting. If you drag another item into the middle of a group, the items before and after that nonmember will be summarized on separate lines. In such a case, the operations just mentioned will be performed only on the items summarized on the selected line, not on the whole group.
When a summarized group is the current line, the 'Acquire' checkbox reflects whether the first item in the group is marked as 'Acquire'. Toggling the checkbox or typing 'A' will toggle the 'Acquire' status of the first item and set all the other items summarized on that line to the same status, except for items marked for tilt series.
Indexes
Use this check box to add a column to the table with the index of each item, numbered from 1.
Use this check box to turn on drawing of a yellow box representing the current acquisition area, centered on the marker point in the current image, which is placed by clicking with the left mouse button. The box will also be displayed around the endpoint of a drawn line; thus, you can hold down the Shift key and press and hold the left mouse button, and move the box around with the mouse. The acquisition area is defined by the size of a montage when montaging is on, otherwise by the size of a Record image at the current magnification or at the magnification of the Record area when in Low Dose mode.
Use this check box to turn on a mode in which the mouse can be used for editing points in a way similar to modeling mode in 3dmod. Ordinarily, Ctrl-left button click can be used to select the nearest point or polygon as the current item, which is drawn with thicker lines in the display. Shift-middle button double click near the rectangle around a map will load that map. In Edit mode:
Turn on this check box to be able to visualize and adjust the position of the Low Dose Focus area for individual Navigator items by clicking in View images. The View image can be a single frame image, a montage overview, or a piece from a montage map loaded for a selected point. When the current item is marked for acquisition (A or TS), a box representing the Record area is drawn with the item at its center, and a box and circle for the Focus area are drawn at the appropriate distance from the item, similar to what is shown when defining the Focus area with the button in the Low Dose control panel but with dashed instead of solid lines. The marker point will generally be placed at the center of the Focus area. Clicking with the left mouse button to set the marker will move the Focus area. (However, Ctrl-left click can still be used to select the nearest point.) If the axis between Low Dose areas is not free to rotate, only the position on the tilt axis will change. If axis rotation is enabled for this item's Focus position, the angle will be changed as well.
The Focus position initially shown for an item will be based on the position stored for that item, if any; or on the position stored for the last preceding acquisition item having a defined Focus position, if any. If no positions have been store for the current or preceding items , the position shown will be that of Focus area currently defined in the Low Dose panel. When you change the position for an item, a new position will be stored for that item or the existing position will be updated. Although these stored positions include a possible subarea offset in the Focus camera parameters, clicking will change only the image shift to the Focus area.
With Edit Focus on, turning on Show Acquire will display the Record and Focus areas on all points marked for acquisition. This display takes precedence over showing multiple Record areas on all points when the option for that is on. Toggle Edit Focus off and on to visualize those areas relative to the Focus area.
There are some restrictions. Low dose mode must be on. Edit Focus and Edit mode are mutually exclusive and turn each other off when selected. Turning on 'Define area' in the Low Dose panel disables the editing of Focus areas here, but it is enabled again when the 'Define area' returns to 'None'. There is no way to enable axis rotation here if it is not already enabled, or to forbid it if it is enabled. To do so, you would have to turn on 'Define area' and enable or disable rotation in the Low Dose panel, then use the Focus Pos button described above to store the parameters currently defined in that panel. At that point, you can use the mouse to set a position with or without the axis constraint, respectively. Similarly, to change the camera subarea, you would need to use the Focus Pos button after changing the camera parameters.
It is possible to set and edit focus positions in View maps loaded into an off-line ('dummy') instance of SerialEM. It is necessary to turn on Low Dose mode there. The same camera should be selected, using either the 'InitialCurrentCamera' or 'AssumeCameraForDummy' properties in the property file or the 'SelectCamera' script command. The Low Dose magnification settings need not match between the offline and real settings, but the boxes draw for the areas will not be the right size unless Focus and Record magnifications match. If you are doing tilt series, you should set items as Tilt Series to enable saving and editing focus. It is no longer necessary to set them as Acquire in the offline instance, because the tilt series parameters are now stored in the Navigator file. If you set such items as Acquire instead, you must turn off the Acquire before saving from the offline instance, because the focus positions will be lost if you turn off Acquire in the real session in order to turn on Tilt Series.
Add Stage Pos
Use this button to add the current stage position as a point item. Note that the stage position will be adjusted by any image shift, so it may not match the current X/Y coordinates of the stage.
Add Points
Use this button to start adding one or more points by clicking in an image with the left or middle mouse button. Each point will become a separate item. Push the button again to stop adding points. While you are adding points, you can press backspace to delete the points backwards one by one, and you can use the right mouse button to adjust the position of the last added point. Points can be marked on an FFT; such points will display only on an FFT.
Add Polygon
Use this button to start drawing a polygon by clicking points in an image with the left or middle mouse button. The polygon can then be used to define an area to be montaged. Push the button again when you are done adding points; the last point will then appear connected to the first. While you are adding points, you can press backspace to delete the points backwards one by one, and you can use the right mouse button to adjust the position of the last added point. Polygons can be drawn on a FFT.
Add At Marker
The marker is the green cross that is deposited on an image by clicking with the left mouse button. Use this button to add a point at the marker position in the currently active image.
Move Item
Use this button to reposition the current item by clicking a new center position for it in an image with the left or right mouse button. Push the button again to stop moving the item. If the item is a map, you will be asked to confirm the change.
Update Z
Use this button to change the Z value of the current item to the current Z position of the stage. If the current line in the table is a summarized group, all group members summarized there will be changed.
Go To XY
Use this button to move the stage to the position of the current item in X and Y, leaving Z unchanged. Image shift will be reset to zero when you move the stage.
Go To XYZ
Use this button to move the stage to the position of the current item in X, Y, and Z.
Go To Marker
The marker is the green cross that is deposited on an image by clicking with the left mouse button. Use this button to move the stage to the location corresponding to the marker position in the currently active image. This button will also work when the marker point is placed in the purple border outside the image or in the gray region when an image has been shifted with the right mouse button.
Load Map
Use this button to load in the image for a map, if the current item is a map. The image will be left in the buffer used for read-in images (typically E). If the map is a montage, the overview will be copied from B to this buffer. Maps can be loaded regardless of whether another file is open for saving images. If the current item is a point that was drawn on a montaged map, this button is relabeled Load Piece and it will load a frame containing this point. If the point is relatively near an edge or corner, the program will synthesize a frame from 2 or 4 overlapping pieces.
Use this button to define the current image as a map. A map consists of an image that has been saved to a known file. There must be an open file to create a map. If the current open file has single frames, the image in buffer A must either have been saved to the file or be capable of being saved to it. If the file is a montage, the image in Buffer B must be an overview from a montage capture. It is possible to use an image or montage overview read in from a file to make a map. For a single image, not all information is kept track of when the image is saved and read back in, but it may work well enough if no conditions have changed since the image has taken. For a montage, all information needed for making a map is stored in the .mdoc file (as of SerialEM 4.6.0, Dec. 19, 2016) and this will be used instead of any current settings. Thus, there should not be any problem making a map from a read-in montage, even if the file has been closed and reopened.
If the image in Buffer A has not yet been saved to a file, then the first time this occurs for a particular file, you will be asked whether you want images automatically saved to this file whenever you select this command. If you answer yes, then the image in question will be saved, and future images will also be saved provided that this file is the current file. If you answer no, then each time you try to make a map without saving an image, you will be asked if you want to save it to the file.
The binning of the montage overview used to define the map does not affect anything in the later use of the map. By default, montage maps are read back in unbinned if possible, and you will typically want to read a map back in before using it.
This button conveniently makes an intermediate-magnification map for realigning to later, such as when starting a tilt series. The button is enabled when 'For anchor state' has been checked for a map that will provide a template for further anchor maps. It performs the following operations:
When the current image is not saved, is at a higher magnification, and it can be saved into the current file, it will be saved and made a map. If it cannot be saved into the current file but there is one other open file that it can be saved into, the program will save it into that file. If there is no such file, it will issue a warning. If there is more than one other open file that it could be saved into, it will ask if you want to stop and select the appropriate file for saving.
Use this button to delete an item from the list, a group of items summarized on the selected line, or multiple selected items. You will be asked to confirm deletion of a map because it would be hard to recreate. For a group of items, or if you have selected multiple points in Edit mode with Ctrl-left mouse button, you will be informed of how many items are to be deleted and asked to confirm the deletion. A group is created whenever a set of items are added in single operation: i.e., when adding a series of points by clicking on an image, when defining a supermontage, or when adding a grid of points. If you do select multiple points when groups are collapsed, the selected points will be deleted rather than the ones summarized on the selected line.
Another way to delete a contiguous set of items is by using Shift D twice. Click to select one end of the range and press Shift D. Then select the other end of the range and press Shift D again. If there are collapsed groups in the range, all items summarized on those group lines will be included. If there is only one kind of item in the range, you will be asked to confirm the deletion unless there are fewer than 4 points. Otherwise, a choice box will open, telling you how many items of each kind are in the range, and giving you the choice of deleting all items or just one kind of item, namely just the points if any are included, or just the polygons if there are no point items. Once you have confirmed deletion of maps, they will all be deleted without a confirmation message for each one.
This button will start a routine to return accurately to the position of the current item by cross-correlation with an appropriate map. See the Realign to Item command for details.
The list box shows all of the items and their properties. It can be scrolled to bring text into view, or the whole window can be made bigger if desired. The following actions can be done in the box:
Although the box does not allow selection of multiple items by the usual Shift or Ctrl clicking, a range of items can be selected for several operations by pressing Shift and a key twice, once at each end of the range. These include:
As of SerialEM 4.1, 28-Dec-22, this range selection works with groups collapsed; all eligible items in a collapsed group line will be included in an operation. If you start an operation by mistake, you can end it with the Escape key as long as the main program has the focus.
The table can be scrolled with the mouse wheel when the mouse is over the Navigator window and not over the image display window, even though the main program window has the focus. The table can also be scrolled when the dialog window has focus; however, none of the hot keys for the Navigator will work then, so it best to keep the focus on the main program window.
The properties shown for each item are the label, the color, the X, Y and Z coordinates, and the type of item (point, polygon, or map, 'Imp' for imported map, 'Anc' for item to use for anchor map state). Next is the registration number with which the item is associated. If the item is a registration point, the point number is shown as well, with an entry '#R#', where the first # is the registration number with which the point is associated, and the second # is the unique point number for this point. Next is a cryptic summary of the acquisition status of the item:
C: corner point
A: Acquire item
AF: Acquire item at which a file is set to be opened
AG: Acquire item and member of a group, where a new file is to be opened on the
first point of the group
AL: Acquire item at which a reusable montage file is set to be opened and left open
AO: Acquire item at which a montage file will be opened only if needed and left open
TS: Tilt series to be acquired
AFS, AGS, ALS, TSS: A stored state will be set when the file is opened, or earlier
for a tilt series
AP, AFP, AGP, ALP, AOP, TSP: A stored Low Dose Focus area position and subarea offset will
be set before the item is acquired or tilt series is started
AFSP, AGSP, ALSP, TSSP: A stored state will be set then a stored Focus position will be set,
overriding the Focus position in the state
Finally, the note will appear at the end of the line.