Imaging State Dialog

This dialog allows you to store and return to a set of microscope settings and imaging parameters. It distinguishes between three kinds of states:

Imaging states: An imaging state consists of the state of the microscope together with the parameters used to acquire an image.  Outside of Low Dose mode, such a state can store Record or Mont-map parameters; whereas in Low Dose mode, states can be stored separately for Record, View, Focus, Trial, and Search, as well as for Mont-map, where the Record microscope parameters and the Mont-map camera parameters are stored.  A state always includes the magnification, spot size, intensity, probe mode for a Thermo/FEI scope or alpha for a JEOL, and energy filter settings if any (slit in/out, slit width, energy loss, whether to do zero loss). The stored state for a Low Dose area consists of all of the settings of the respective area; a Search or View area state also includes the added beam shift and beam tilt values, and the Search or View shift and defocus offsets.  The latter makes it convenient to save states for different defocus offsets, which would typically require different shift offsets.

The acquisition parameters stored with a state include the camera, binning, exposure time, frame size, drift settling, and type of shuttering and processing, as well as whether subframes are being stored from a direct detector.  For a direct detector camera, parameters also include the processing mode if relevant (linear, counting, super-resolution), the frame time, whether alignment is being done, the type of alignment (in the camera software, in SerialEM or the SEMCCD plugin, or in IMOD), and the index of the frame alignment parameter set.  Also, the processing mode will be saved for all other camera parameter sets for a non-Low Dose state, since such a state specifies illumination for all camera modes and it might be necessary to switch to or from linear mode.

Map Acquire states: A map acquire state consists of all the parameters needed to acquire more maps of the same kind as a given Navigator map. This state includes both an imaging state and the file where maps are to be saved, which can be a montage.  The state for a map taken in Low Dose mode will be either Record, View, or Search.

Scheduled states: These states can be stored with the Imaging State button in the Navigator dialog for an acquisition item where a file is set to be opened (including for a tilt series).  Outside of Low Dose mode, the state saved is Record as usual.  In Low Dose mode, it is Record if a single-frame file is to be opened, but can be Record, View, or Search if a montage is to be opened, depending on how the montage is set to be acquired.

The table: The dialog shows a table of imaging states that are saved with your settings. The essential properties of the state are summarized in the table:
    LD: 'R', 'V', 'F, 'T', or 'S' for a Low Dose state, ' - ' otherwise
    Cam: The camera number, based on their order in any dialogs and numbered from 1
    Mag: The magnification
    Spot: The spot size, plus 'uP' or 'nP' for probe mode on Thermo/FEI scopes or 'a#' for alpha on a JEOL
    Int: Intensity: Percent C2 or C3 or illuminated area
    Def: Either the defocus offset for a View or Search state, or the target defocus if saved for a non-Low Dose state
    Exp: Exposure time in seconds
    Bin: Binning
    Frame: The frame size in 1000's (e.g., 2048 x 1536 shows up as 2.0x1.5) , followed by 'M' for a Mont-map state
    Name: The name entered in the text box
Clicking a line in the table selects the current line in the table, and double clicking actually sets the state if possible.

The Prior state: The 'Prior' line summarizes the state that was left upon the first setting of a state, and that will be returned to if Restore State is pressed or if state is restored by other means.  When multiple states of the same kind are set in succession, the states do not form a stack that can be undone in succession, nor does a previously set state become the Prior state.

Controls

Add Current State

This button adds the current microscope and imaging parameters as a new imaging state in the table.

#

This checkbox toggles between showing the names with index numbers before them and names without numbers.

Name

You can enter a name for the current state in the table with this text box.

Add Mont-Map State

This button adds the Mont-map camera parameters and either the current microscope parameters (outside of Low Dose) or the Low Dose Record area parameters as a new imaging state.

Save Target Defocus

This button allows you to save the value of the target defocus for autofocusing in a non-Low Dose state.  Saving target defocus is optional because it is a recent addition and saving it by default would not be desired in some scenarios.  When a state with target defocus stored is entered or left, the microscope defocus is changed by the change in target defocus, so the target can also be used as a defocus offset.

Go to Selected State

This button will change the microscope and acquisition settings to the imaging state on the current line of the table. It is equivalent to double clicking on a line of the table. If the selected state is a Low-Dose state, then the parameters of one Low Dose area will be replaced by the parameters of the stored state, but the program may not go to that area if it is in another one. The pre-existing state is summarized on a line starting with 'Prior' in the same format as the table. 

• After setting one imaging state, you can still use this button to set a different state, without first returning to the pre-existing imaging state.  The previously set state does not replace the original pre-existing state.
• Outside of Low Dose mode, setting a different state will completely replace the previously set state.
• In Low Dose mode, the state can be set for each of the five areas independently, so you can set the state for Record or Mont-map, View, Focus, Trial (if different), and Search in succession without restoring or replacing any of those.  However, if you go to another state for the same area, it will replace the previously set state for that area.  The situation with Record and Mont-map is a bit different; if you set the state for one then the other, the microscope parameters of the Record area will be replaced when the second state is set.
• If the option to keep Focus and Trial identical is checked in the Low Dose panel, then setting one of these states will change the microscope parameters for the other, but not its camera parameters.
• The area position relative to Record and the offset of a camera subarea from center are saved for both Focus and Trial states.
• When Focus or Trial is set and the scope is currently in that area (or the other area, if they are kept at the same position), the program will switch to Record area before changing the parameters of the state being set.
•  If one or more states are set in Low Dose and then the mode is turned off, the prior state of Low Dose parameters is restored to avoid inconsistent changes and loss of some parameters.
• When Low Dose mode is toggled, what happens to the prior state is governed by internal factors and depends on the circumstances:
• When entering Low Dose by setting a state, a prior state is kept or set.
• When entering Low Dose by toggling the mode in the Low Dose panel or with a script command, a prior state is cleared.
• When leaving Low Dose by setting a state, a previous prior state is cleared but a new one is set with the last Low Dose state.
• When leaving Low Dose otherwise, the prior state is cleared.
• Each currently set state is marked in the table with a † after the frame size.

Update It

If an imaging state has been set from the currently selected line of the table, this button is enabled and allows you to update that state with the current microscope and imaging parameters.

Delete It

This button deletes the current line of the table.

Go to Map Acquire State

This button is enabled if the Navigator is open and the current item there is a map. It will change the microscope and imaging parameters to the state used to acquire that map, and make the file where that map is stored be the current file (opening it if necessary). Once you have set a map acquire state, you can only return from it, not set a different map acquire or imaging state.  When the map was taken in Low Dose mode, switching to its state may or may not stay in Low Dose mode, depending on whether the given Low Dose area parameters have changed too much from their values when the map was acquired.

Go to Scheduled State

This button is enabled if the current Navigator item is marked for acquisition and there is a stored imaging state or Low Dose Focus area position scheduled to be set when that item is ready to be acquired. Press this button to revisit and check the stored state or Focus position. If you need to change some properties of a scheduled state, you can make the change then press the Imaging State button in the Navigator to update the state that will be set.

Add Map Acquire State to Table

This button adds the imaging state used to acquire the current Navigator item as a new line in the table. This is not a full map acquire state, so the file where the map was saved is irrelevant. This button is of limited usefulness in Low Dose mode because the area-specific information is not preserved and the result is a non-Low Dose state that sets Record parameters only.

Restore Prior State

The button restores all settings to what they were before a state was set by any of the above means. If the imaging state was set two or more times in succession, the system is returned to the condition it was in before state was set the first time, not to the state just before the last one. If you set the imaging state for more than one Low Dose area, they will all be restored to their prior states.  If you are leaving a map acquire state, the file that was current prior to entering that state will be made current again, and the file associated with that map state will be closed again if it was opened

Forget Prior State

Use this button to make the current state the one that will be returned to after going to new states and restoring from them. In other words, the program will forget that you changed state. You are then free to select a new map acquire state without returning from the current state.