Imaging State Dialog
This dialog allows you to store and return to a set of microscope settings and Record parameters. It distinguishes between two kinds of states:
Imaging states: An imaging state consists of the state of the microscope together with the parameters used to acquire a Record image. Specifically, the state includes the magnification, spot size, intensity, probe mode for an FEI scope, and energy filter settings if any (slit in/out, slit width, energy loss, whether to do zero loss). The state also includes whether Low Dose mode is on; in fact, if it is, then the stored state consists of all of the settings of the Record area. The acquisition parameters 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. Since maps are not acquired in low dose mode, the imaging state must be in regular mode.
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' if it is a Low Dose state, camera number, magnification, spot size, intensity as a percent C2/C3 value, exposure time, binning, and frame size in 1000's (e.g., 2048 x 1536 shows up as 2.0x1.5). Clicking a line in the table selects the current line in the table, and double clicking actually sets the state.
Add Current State
This buttons adds the current microscope and Record parameters as a new imaging state in the table.
Add Nav Item State
This button adds the imaging state used to acquire the current Navigator item as a new line in the table. This is not a map acquire state, so the file where the map was saved is irrelevant. This button can be used to convert the 'Stock states' that could be saved in a Navigator file in previous versions of SerialEM. Open the stock state file in the Navigator, select each item in turn in the Navigator and press this button to add its state to the table.
This button deletes the current line of the table.
This button updates the state in the current line of the table with the current microscope and Record parameters.
You can enter a name for the current state in the table with this text box.
This button will change the microscope and Record 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 the Low Dose Record area will be replaced by the parameters of the stored state. 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.
(Set) Map Acquire
This button is enabled if the Navigator is open and the current item there is a map. It will change the microscope and Record 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.
This button is enabled if the current Navigator item is marked for acquisition and there is a stored imaging state scheduled to be set when that item is ready to be acquired. Press this button to revisit and check the stored state. If you need to change some properties of the scheduled state, you can make the change then press the Imaging State button in the Navigator to update the state that will be set.
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 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.