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*MAIN CONTROLS Panel*
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* [Overview|#Main Overview]
* [Section A|#Main Sec A]
* [Section B|#Main Sec B]
* [Section C|#Main Sec C]
* [Section D|#Main Sec D]
* [Section E|#Main Sec E]
* [Section F|#Main Sec F]
* [Menus|#Main Menus]
** [File Menu|#Main File Menu]
** [Settings Menu|#Settings Menu]
** [View Menu|#Main View Menu]
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h3. Overview
The *MAIN CONTROLS* panel is the main ScanImage window. It is the panel from which image acquisitions are initiated (Section C). Closing the *MAIN CONTROLS* panel causes ScanImage as a whole to exit (after confirming intent). The panel is broken into two halves. The left half (Sections A-C) is always visible, while the right half (Sections D-F) can be shown or hidden. During certain types of acquisitions, the right half is hidden automatically to prevent certain commands from being processed during an ongoing acquisition.
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h3. Section A
* {blue:Configuration}: _(Read-Only)_ Displays the name of the currently loaded [_Configuration_|SI3.6_Config] (CFG file). If none is loaded, this field is blank.
* {blue:Repeats Done}: _(Read-Only)_ When in {blue:LOOP} acquisition mode, this indicates the number of repeat iterations that have been completed.
* {blue:Slices Done}: _(Read-Only)_ For {blue:GRAB}/{blue:LOOP}acquisitions, this keeps track of the number of slices that have been acquired (in the current repeat iteration, if using {blue:LOOP}), counting up to the {blue:# Slices} value set in the {report-info:data:StandardControls|render=wiki|source=SI3.7 Data} window.
* {blue:Frames Done}: _(Read-Only)_ For {blue:GRAB}/{blue:LOOP}acquisitions, this keeps track of the number of frames that have been acquired (in the current repeat iteration, if using {blue:LOOP}), counting up to the {blue:# Frames} value set in the {report-info:data:StandardControls|render=wiki|source=SI3.7 Data} window.
* {blue:Basename}: For {blue:GRAB}/{blue:LOOP} acquisitions, this sets the _stem_ of the filename to be saved for the next or ongoing acquisition. The {blue:Acquisition #} is appended to the specified {blue:Basename} to create the full filename, e.g. _beadTest3.tif_ in the example shown.
* {blue:Acquisition #}: For {blue:GRAB}/{blue:LOOP} acquisitions, this sets the number to append to the specified {blue:Basename} to create the full filename. This value is automatically incremented at the end of each acquisition (repeat iteration, if using {blue:LOOP}). The value can be manually edited, to affect the number that will be appended for the next acquisition.
* {blue:Timer}: This displays a value in seconds, that depends on the current state and acquisition mode:
** During {blue:FOCUS} and {blue:GRAB}acquisitions, this displays a _count-up_ value, in seconds, measuring the time elapsed for the ongoing acquisition.
** For {blue:GRAB}/{blue:LOOP}acquisitions with _External Triggering_ ({blue:EXT}) enabled, a _count-up_ value is displayed while waiting for the external trigger to arrive before beginning the acquisition (or next _Repeat_, if using {blue:LOOP}).
** During LOOP acquisitions, the behavior of {blue:Timer} is described in [LOOP Mode|SI3.6_AcqModes]
* {blue:SNAP}: This initiates a [_Snapshot_|Acquisition Modes (FOCUS, GRAB, and LOOP) (r3.6)#SnapshotMode] acquisition, which is a specially configured {blue: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 {blue:GRAB}/{blue:LOOP} acquisitions without adjusting the current ScanImage [_Configuration|SI3.6_Config] nor risking overexposure with a {blue:FOCUS} acquisition.
* {blue:LS}: _(CFG Value)_ This checkbox activates a _Line Scan_ acquisition, forcing the amplitude of the scan in the slow scan dimension to be zero.
* {blue:<</>>}: This control toggles the display of the right half of the *MAIN CONTROLS* window.
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h3. Section B
This section consists of three components, from left to right:
* {blue:AutoSave}: This checkbox determines whether _Auto Save_ functionality is enabled for {blue:GRAB}/{blue:LOOP} mode, causing image data to be automatically saved to disk _during_ the acquisition
(i) A running buffer of the most recently acquired frames is maintained in the {vi-statevar:state.acq.acquiredData} variable. The size of the running data buffer is specified by the {blue:Max Buffered Frames} values in the {report-info:data:UserSettings|render=wiki|source=SI3.7 Data}. A separate value is used depending on whether {blue:AutoSave} is selected or not.
* {blue:Status String}: _(Read-Only)_ This string displays status information regarding the state of ScanImage.
(i) When the _Status String_ specifies an error has occurred, it is recommended to look at the Matlab Command window to obtain additional information.
* {blue:EXT}: _(CFG Value)_ This toggle-button enables/disables _External Triggering_ for {blue:GRAB}/ {blue:LOOP} modes. It has no effect on FOCUS mode acquisition. If no _external trigger_ is configured in the INI file, this button is disabled.
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h3. Section C
This section allows the user to begin a ScanImage image acquisition, using one of the 3 available acquisition modes -- [FOCUS, GRAB, and LOOP|AcqModes (r3.6)].
Upon selecting one of the buttons, acquisition begins (or is armed to wait for an _External Trigger_), and the corresponding button changes to read {blue:ABORT}, while the others are hidden. Pressing {blue:ABORT} stops acquisition immediately.
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h3. Section D
There are three groups of controls in this section -- {blue:Rotate}, {blue:Shift}, and {blue:Zoom} -- which affect the scan command generated by ScanImage during acquisition.
(/) These controls can be adjusted while live imaging in FOCUS mode.
(/) The {blue:Rotate}, {blue:Shift}, and {blue:Zoom} values all comprise part of the current ScanImage [_Configuration_|SI3.6_Config] -- i.e. their values are captured whenever a CFG file is saved.
In addition, this section contains:
* {blue:Reset} controls in this section allow the {blue:Rotate}, {blue:Shift}, and {blue:Zoom} values to be rapidly restored to preset reference values.
* {Align} controls on a docked sub-window, containing controls to facilitate beam and scan alignment.
h5. Rotate Controls
* {blue:Rotate}: _(CFG Value)_ Specifies angle, in degrees, by which the scan field-of-view is rotated.
(i) At this time, scan rotation is not supported when [_Bidirectional Scanning_|SI3.6_ScanConfigBasics] is activated. The _Rotate_ control is disabled in this circumstance.
* {blue:0}: Resets the rotation value to 0 degrees.
* {blue:LS}: Activates a [_Graphical Interaction Tool_|Image Controls (r3.6)#GraphInteractionTools] allowing the user to select a line on the target image display window. The angle of the line updates the {blue:Rotate} value accordingly; the center of the line updates the {blue:Shift Fast/Slow} values accordingly.
(i) As the control's name suggests, this control facilitates the configuration of scans for _Line Scanning_ operation. Note however, that the updated {blue:Rotate} and {blue:Shift Fast/Slow} values apply regardless of whether _Line Scanning_ is active or not.
(i) Note that the length of the selected line has no effect.
h5. Shift Controls
* {blue:Shift Fast/Slow}: _(CFG Value)_ Specifies an offset, in optical degrees, to apply to the scan command signals in the _Fast_ and _Slow_ dimensions, shifting the field-of-view.
* {blue:Blue Arrows}: The arrows allow the {blue:Shift} 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.
* {blue:0}: Resets the shift values to 0 degrees
* {blue:CT}: Activates a [_Graphical Interaction Tool_|Image Controls (r3.6)#GraphInteractionTools] allowing the user to select a point on the target image display window. The location of this point updates the {blue:Shift Fast/Slow} values accordingly.
h5. Zoom Controls
* {blue:Zoom Indicator}: _(CFG Value)_ 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.
** ScanImage simply divides the {blue:Scan Amplitude Fast/Slow} values (specified in the {report-info:data:Configuration|render=wiki|source=SI3.7 Data} window) by the currently configured zoom factor, to determine the current scan amplitude.
** The {blue:Zoom Indicator} digits appear with a yellow background when the current zoom factor is below the {color:blue}*Constant @ Zoom >=*{color} value specified in the {report-info:data:Configuration|render=wiki|source=SI3.7 Data} window.
* {blue:Full}: Resets the currently configured {factor (and the _Zoom Indicator_) to 1, or to the {blue:Min Zoom} value specified in the {report-info:data:Configuration|render=wiki|source=SI3.7 Data} window.
h5. Reset Controls
* {blue:RESET}: By default, resets the {blue:Rotate}, {blue:Shift}, and {blue:Zoom} values to the values stored in the currently specified [_Configuration_|SI3.6_Config] (CFG file). In other words, the unsaved CFG changes made by adjusting {blue:Rotate}, {blue:Shift}, and {blue:Zoom}are undone.
(/) If a set of {blue:Rotate}, {blue:Shift}, and {blue:Zoom} values are cached using {blue:Set Reset}, then {blue:RESET} restores those cached values instead.
* {blue:Set Reset}: Caches the current {blue:Rotate}, {blue:Shift}, and {blue:Zoom} values so that subsequently pressing {blue:RESET} will restore these values.
(i) Note that this does not save the current {blue:Rotate}, {blue:Shift}, and {blue:Zoom} values to the current [_Configuration_|SI3.6_Config] (CFG file).
h5. Align Controls
* {blue:Align >>/<<} Toggles the display of the {report-info:data:Align|render=wiki|source=SI3.7 Data} sub-panel, docked to the *MAIN CONTROLS* panel.
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h3. Section E
This section consist of controls to define/manage/load _Regions of Interest_ (ROIs) within the scan's field-of-view. A _Region of Interest_ consists of four items of information:
# {blue:Shift Fast/Slow} value pair
# {blue:Zoom} value
# {blue:Rotation}
# Motor position (if motor is active)
Together these specify a square (or rhombus, if {blue:Rotation} is nonzero) subregion within the most recently scanned field-of-view that can be scanned (at higher rates or pixel density, if desired).
The selected _Region(s) of Interest_ are graphically depicted in the [_ROI Display_|SI3.6_ImageDisplay] window, with the current ROI displayed in blue.
{set-data:SnapAfterRegion|hidden=true}(i) If _Snapshot on Region Selection/Change_ is selected in the {report-info:data:UserSettings|render=wiki|source=SI3.7 Data} window, a _Snapshot_ acquisition of 1 frame is executed upon selecting the region.{set-data}
* {blue:ROI}: Activates a [_Graphical Interaction Tool_|Image Controls (r3.6)#GraphInteractionTools] allowing the user to select a square region on the target image display window. The currently configured {blue:Zoom} and {blue:Shift Fast/Slow} values are updated to reflect the size and center of the selected region.
(i) At this time, ScanImage does not support rectangular regions-of-interest, although the box drawn with the _ROI_ tool can be rectangular. The rectangular region is converted to a square region upon capturing the {blue:Zoom} and {blue:Shift Fast/Slow}values.
\\{report-info:data:SnapAfterRegion|render=wiki}
* {blue:UNDO}: Restores the {blue:Zoom}, {blue:Shift Fast/Slow}, and {blue:Rotation} values prevailing prior to the previous _Region of Interest_ selection with the {blue:ROI} tool.
* {blue:ADD}: Captures the current {blue:Zoom}, {blue:Shift Fast/Slow}, and {blue:Rotation} values as well as the current motor position (if motor is active) and stores values as a numbered ROI in the _ROI Selection Menu_.
* {blue:DROP}: Removes the currently selected numbered ROI in the _ROI Selection Menu_ from the list. Updates the currently selected numbered ROI value to a valid value (if any are left).
* {blue:ROI Selection Menu}: Selection of numbered ROI value in dropdown menu updates currently configured {blue:Shift Fast/Slow}, {blue:Zoom}, and {blue:Rotate} values to match those stored with numbered ROI. If motor is active, the X/Y/Z stage position(s) are also updated accordingly.
(i) The left/right arrows to right of _ROI Selection Menu_ can also be used to select the next lower/higher numbered ROI value.
\\{report-info:data:SnapAfterRegion|render=wiki}
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h3. Section F
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)|SI3.6_Config], which can be loaded, or started, by pressing the single numbered button.
See {report-info:data:FastConfigurations|render=wiki|source=SI3.7 Data} for more information about set up and use of _Fast Configurations_.
(/) When the current ScanImage [configuration|SI3.6_Config] corresponds to one of the current _Fast Configurations_, that button appears depressed.
(/) When the {blue:AutoStart} option is enabled for a particular _Fast Configuration_ in the {report-info:data:FastConfigurations|render=wiki} 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.
* {blue:CFG>>/<<}: This toggle button shows/hides the {report-info:data:Configuration|render=wiki} window, which is used to set the majority of values specifying the ScanImage [_Configuration_|SI3.6_Config].
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h3. Menus
{anchor:File Menu}
h5. File Menu
{anchor:Settings Menu}
h5. Settings Menu
{anchor:View Menu}
h5. View Menu
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