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MAIN CONTROLS Panel
Overview
The Main Controls panel is the main ScanImage window. It is the panel from which image acquisitions are initiated (Section D). Closing the Main Controls panel causes ScanImage as a whole to exit (after confirming intent).
Section A
: (Read-Only) Displays the name of the currently loaded Configuration (CFG file). If none is loaded, this field is blank.- : Launches dialog to select a new CFG file to load
- : Saves current configuration to currently loaded CFG file. (Use File >> Save Configuration As... from menubar to save current configuration to a new CFG file).
- : (Read-Only) Displays the name of the currently loaded User Settings (CFG file). If none is loaded, this field is blank.
- : Launches dialog to select a new USR file to load
- : Saves current user settings to currently loaded USR file. (Use File >> Save User Settings As... from menubar to save current user settings a new USR file).
Section B
- : Specify # of Cycle Iterations to execute when operating in Cycle Mode, on the right. If cycle auto-reset is disabled, the iteration # to execute can also be set here, on the left.
- : Open or close the Cycle Controls panel
- (and : For GRAB/LOOP acquisitions, specify at right the number of slices to acquire (in the current Repeat, if using LOOP). Left control indicates the number of slices acquired during an ongoing acquisition.
- (and ): For GRAB/LOOP acquisitions, specify at right the number of frames to acquire (in the current Repeat, if using LOOP). Left control indicates the number of frames acquired during an ongoing acquisition.
- (and ): For LOOP acquisitions, specify at right the number of repeat iterations to acquire. Left control indicates the number of iterations completed during an ongoing LOOP acquisition.
Value of Inf can be specified for the , causing LOOP acquisition to continue indefinitely until is pressed
- : When operating in LOOP mode, this determines the total time following the trigger of each LOOP Repeat to wait before ScanImage generates trigger to begin the next Repeat. In other words, this specifies the trigger-to-trigger time between Repeats.
The specified time should be at least as long as the acquisition during each Repeat plus any post-acquisition processing.
When a Stack Acquisistion is employed, this value indicates the time for the entire stack, and specifically the time between the ScanImage triggers issued for the first slice of each Repeat
This setting only has effect when internal triggering is employed
- : This displays a value in seconds, that depends on the current state and acquisition mode:
- During FOCUS or GRAB acquisitions, this displays a count-up value, in seconds, measuring the time elapsed for the ongoing acquisition.
- For GRAB/LOOP acquisitions with external triggering () enabled, a count-up value is displayed while waiting for the external trigger to arrive before beginning the acquisition (or next Repeat, if using LOOP mode)
- During LOOPacquisitions, the behavior of is described in LOOP Mode
Section C
- : For GRAB/LOOP acquisitions, this sets the stem of the filename to be saved for the next or ongoing acquisition. The is appended to the specified to create the full filename, e.g. mosaicDemo008.tif in the example shown.
- : For GRAB/LOOP acquisitions, this sets the number to append to the specified to create the full filename. This value is automatically incremented at the end of each acquisition (or Repeat if using LOOP). The value can be manually edited, to specify the numeric value that will be appended for the next acquisition.
- : Launches dialog to select save directory. Files will be saved to the specified directory.
- : This checkbox determines whether disk logging functionality is enabled for GRAB/LOOP mode, causing image data to be automatically saved to disk during the acquisition
A running buffer of the most recently acquired frames is maintained in the 
variable. The size of the running data buffer is specified by the values in the User Settings panel. Distinct values are used depending on whether is selected or not.
Control is linked to checkbox on Configuration panel
- : Specifies the # of frames to average together before appending frame to current log file. Values > 1 imply a file-size reduction, i.e. raw per-frame data is lost. This functionality is separate from the display rolling average available from the Image Controls.
Section D
- : This initiates a Snapshot acquisition, which is a specially configured GRAB acquisition to acquire and display an average of the number of Frames specified in the adjoining text control.
This is useful for quickly visualizing the specimen/field-of-view in between configured GRAB/LOOP acquisitions without adjusting the current ScanImage _Configuration nor risking overexposure with a FOCUS acquisition.
- : (CFG Value) This toggle-button enables/disables external triggering during GRAB/LOOP modes. It has no effect on FOCUSmode acquisition. If no external start trigger or next trigger is configured in the Triggers panel, this button is disabled.
- : (Read-Only) This string displays status information regarding the state of ScanImage.
When the Status String specifies an error has occurred, it is recommended to look at the Matlab Command window to obtain additional information.
- //: These buttons start a ScanImage image acquisition, using one of the 3 available acquisition modes – FOCUS, GRAB, and LOOP. Upon selecting one of the buttons, acquisition begins (or is armed to wait for an external trigger), and the corresponding button changes to read , while the others are hidden. Pressing stops acquisition immediately.
Section E
There are four groups of controls in this section – , , , – which affect the scan command generated by ScanImage during acquisition. The set of these 4 values are referred to as the ROI Scan Parameters in ScanImage parlance.
These controls can be adjusted while live imaging in FOCUS mode.
The , , , and values all comprise part of the current ScanImage Configuration – i.e. their values are captured whenever a CFG file is saved.
Rotate Controls
- : Specifies angle, in degrees, by which the scan field-of-view is rotated.
At this time, scan rotation is not supported when bidirectional Scanning activated (in the Configuration panel). The Rotate control is disabled in this circumstance.
- : Resets the rotation value to 0 degrees.
Shift Controls
- : Specifies an offset, in optical degrees, to apply to the scan command signals in the Fast and Slow dimensions, shifting the field-of-view.
- : The arrows allow the values to be adjusted without entering a new value. The value is adjusted (incremented or decremented) by the amount specified (in optical degrees) in the two nearby text edit controls – one each for horizontal and vertical adjustments.
- : Resets the shift values to 0 degrees
- : Activates an image interaction tool allowing the user to select a point on the target image display window. The location of this point updates the values accordingly.
Zoom Controls
- : The 4 numbers represent the currently configured zoom factor and allow independent adjustment of the 1s, 10s, and 100s digit of that value. In additional, fractional zoom values can be specified with one decimal digit.
The zoom factor divides the scan angular range by the same factor in the fast & slow dimensions. See Scan Command Amplitude Determination.
The digits appear with a yellow background when the current zoom factor is below the Constant @ Zoom >= value specified in the Configuration panel.
- : Resets the currently configured factor to 1, or to the value specified in the Configuration panel.
Scan Angle Multiplier Controls
- Values from 0 to 1 specifying respective multipliers of the values in the INI File. See Scan Command Amplitude Determination.
When values are unequal (and values are equal), the scanned area has a rectangular aspect ratio (non-square)
= 0 implies a line scan
= 0 implies a point scan
Align Controls
- : Show/hide the Align sub-panel, used for beam and scan angle alignment
Section F
Controls in the section affect or pertain to the ROI Scan Parameters (, , , and ) in Section E.
- : Resets ROI Scan Parameters to their default values
- : Sets ROI Scan Parameters to the Base ROI scan parameter values. By default these are equal to the ROOT values (see above), but can be set to user-defined values via
- : Sets the Base ROI scan parameter values to match the current ROI Scan Parameter values
The current Base ROI scan parameter values can be seen in the ROI Controls
- : Sets ROI Scan Parameters to match that of the last-added or last-set line-scan ROI (ROI Scan Parameters with =0) at the current motor position. If there is no cached line-scan ROI, then user is prompted to select/add a line-scan ROI – equivalent to selecting in Section G.
- Sets ROI Scan Parameters to match the parent ROI of the last-added or last-set line-scan ROI at the current motor position. If there is no cached line-scan ROI, this control has no effect.
The parent of the last line-scan ROI is necessarily an area ROI, square or rectangle
- : Checkbox that toggles between 0 (LS ON) and the Base ROI value (LS OFF). If is set to any value other than 0 or the Base ROI value, control is disabled.
Section G
Graphical ROI Addition Tools
The 6 buttons at left generally activate an image interaction tool to specify one or more region of interests (ROI), adding it or them to the current ROI list managed in the ROI Controls, for the current motor position. The following ROI types are supported:
- : A square ROI (Scan Angle Multiplier Fast = Scan Angle Multiplier Slow, non-zero)
- : A rectangle ROI (Scan Angle Multiplier Fast/Slow both non-zero)
- : A line ROI (Scan Angle Multiplier Slow = 0)
- : A point ROI (Scan Angle Multiplier Fast/Slow = 0)
- : A set of points (finish selection by hitting Enter)
- : A point ROI is added corresponding to the center of the last-acquired ROI scan parameters (no image interaction tool is launched)
Other ROI Controls
- : The currently set ROI Scan Parameters (set in Section F) are added to current ROI list managed in the ROI Controls, for the current motor position.
- : If selected, the ROI Scan Parameters are updated to match the added ROI when one of the graphical ROI Addition Tools is used
- : If selected, a Snapshot acquisition is taken at the newly added ROI when one of the graphical ROI Addition Tools is used. Control is disabled if is disabled.
Section H
This section contains 6 toggle buttons corresponding to the 6 Fast Configurations which can be defined in ScanImage. These correspond to ScanImage configurations (CFG Files), which can be loaded, or started, by pressing the single numbered button.
See Fast Configurations for more information about set up and use of Fast Configurations.
When the current ScanImage configuration corresponds to one of the current Fast Configurations, that button appears depressed.
When the option is enabled for a particular Fast Configuration in the Fast Configurations dialog, the corresponding button appears green in the Main Controls panel
The tooltip for each Fast Configuration button contains the name of the CFG file saved as that particular Fast Configuration, so it is easy to identify the 6 Fast Configuration names.
