| {alias:SI3.6_Configuration}
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!Configuration_demarcated.png!
*CONFIGURATION Panel*
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-----
* [Overview|#Overview]
* [Section A|#Sec A]
* [Section B: Basic Scan Parameters|#Sec B]
* [Section C: Live Adjustable Scan Parameters|#Sec C]
* [Section D: Scan Parameter Array|#Sec D]
* [Section E: Pockels Control Parameters|#Sec E]
* [Section F: DAQ Sample Rates|#Sec F]
* [Section G: Slow Dimension Scan Settings|#Sec G]
* [Section H: Dependent Parameter Display |#Sec H]
* [Section I: Miscellaneous Parameters|#Sec I]
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h3. Section A
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{tip:title=_Current_ vs _Active_ Configuration}It is important to distinguish between the _current_ ScanImage [_Configuration_|SI3.6_Config] and the _active_ [_Configuration_|SI3.6_Config] (*CFG*) file. The former represents the current _state_ of all ScanImage controls (both on the *CONFIGURATION* panel and otherwise) which comprise the ScanImage [_Configuration_|SI3.6_Config], while the latter represents the most recently loaded ScanImage [_Configuration_|SI3.6_Config] (*CFG*) file (whose settings may no longer all be in effect){tip}
* {blue:Configuration}: (_Read-Only_) Displays the name of the _active_ [_Configuration_|SI3.6_Config] (*CFG*) file -- i.e., the most recently loaded *CFG* file, if any.
* {blue:Load...}: Launches dialog to select a ScanImage [_Configuration_|SI3.6_Config] (*CFG*) file to load. Identical to selecting *File >> Load Configuration...* from the {report-info:data:MainControls|render=wiki|source=SI3.6 Data} panel menubar.
* {blue:Save as...}: Launches dialog to save the _current_ ScanImage [_Configuration_|SI3.6_Config] to a specified *CFG* file. Identical to selecting *File >> Save Configuration As...* from the {report-info:data:MainControls|render=wiki|source=SI3.6 Data} panel menubar.
* {blue:Apply}: Changes made to controls throughout the *CONFIGURATION* panel do not immediately update the _current_ ScanImage [_Configuration_|SI3.6_Config], i.e. the current ScanImage [_state_|SI3.6_StateVar]. When a change is made, the {blue:Apply} button becomes active and changes are applied only when pressed.
(/) Note that the controls in the [{blue:Live Scan Params} section|#Sec C] DO take immediate effect IF the changes occur during [*FOCUS* mode|SI3.6_AcqModes] operation
* {blue:Save}: Saves the _current_ ScanImage [_Configuration_|SI3.6_Config] to the *active* _Configuration_ (*CFG*) file. Identical to selecting *File >> Save Configuration...* from the {report-info:data:MainControls|render=wiki|source=SI3.6 Data} panel menubar.
(i) This control only appears active if a change to one of the controls in the *CONFIGURATION* panel has occurred (and been _applied_) since the *active* _Configuration_ (*CFG*) file was last loaded.
(/) If a change to the _current_ ScanImage [_Configuration_|SI3.6_Config] is made _outside_ of the *CONFIGURATION* panel, then *File >> Save Configuration...* should be selected from the {report-info:data:MainControls|render=wiki|source=SI3.6 Data} panel menubar in order to save the changes (if desired).
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h3. Section B: Basic Scan Parameters
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The controls in this section pertain to the concepts described in [Scan Configuration Basics|SI3.6_ScanConfigBasics].
* {blue:Pixels/Line}: Specifies the number of [_input sample bins_|SI3.6_InputDigitization] to use during the _Acquisition Period_ of each scanned line. This value becomes the number of horizontal pixels in the [displayed image|SI3.6_ImageDisplay] and the [stored image|SI3.6_ImageFile].
* {blue:Lines/Frame}: Specifies the number of lines to scan with the fast (*X*) dimension scanner during each _Frame_ of acquisition, while simultaneously adjusting the slow (*Y*) dimension position (except during a _Line Scan_). This value becomes the number of vertical pixels in the [displayed image|SI3.6_ImageDisplay] and the [stored image|SI3.6_ImageFile].
* {blue:Nominal Ms/Line}: Specifies the time (in ms) to spend during each line scanned by the fast (*X*) dimension scanner, including both the _Acquisition Period_ as well as non-acquiring time for _flyback_ and/or _turnaround_.
(!) The {blue:True Ms/Line} value can differ somewhat from the {blue:Nominal Ms/Line} value, based on the {blue:Fill Fraction} setting (as described in [Fast (X) Dimension Optimization|SI3.6_FastScanDetails])
(/) The *_Acquisition Period_ = 0.8192 \** {blue:Nominal Ms/Line} (as described in [Fast (X) Dimension Optimization|SI3.6_FastScanDetails])
(/) At this time, ScanImage supports values down to *0.5 ms/line* with {blue:BiDi} enabled and *1ms/line* otherwise
* {blue:BiDi}: Enables, when selected, [_Bidirectional_ scanning|SI3.6_ScanConfigBasics]. When not selected, [_Sawtooth_ scanning|SI3.6_ScanConfigBasics] is used.
* {blue:X (Fast) Dimension Chan}: ScanImage generates [*X* and *Y* command signals|SI3.6_ScanConfigBasics] on the 2 output channels of the board specified by *mirrorOutputBoardIndex* in the [*INI* File|SI_IniFile]. This value specifies on which channel the *X* command signal is generated; the *Y* command signal is generated on the other.
(/) At this time, all the [DAQ boards|SI3.6_DAQBoards] supported by ScanImage for generating mirror output signals only have 2 output channels.
* {blue:Scan Amplitude X/Y}: Specifies in optical degrees the half-angle that the physical scanner associated with each dimension should cover during the _Acquisition Period_.
(/) The conversion between optical degrees and command signal units (e.g. volts) is specified by the *opticalDegreesConversion* value in the [*INI* File|SI_IniFile].
(/) ScanImage allows scanning of non-square aspect ratio regions, via the appropriate adjustment of the {blue:Scan Amplitude X/Y} values
(i) The command signal generated for the _Fast_ (*X*) dimension has a larger half-amplitude than {blue:Scan Amplitude X}, as described in [Fast (X) Dimension Optimization|SI3.6_FastScanDetails].
(i) When _Line Scanning_ is active (via {blue:LS} in the {report-info:data:MainControls|render=wiki|source=SI3.6 Data} panel), the {blue:Scan Amplitude Y} value used internally by ScanImage becomes *0*, but the value stored/displayed by the [_Configuration_|SI3.6_Config] remains as previously set.
{info:title=Adjust Infrequently}In general, the {blue:Scan Amplitude X/Y} values are not intended to be varied frequently -- they are typically set to the maximum half-amplitude the physical scanner supports in all [*CFG* files|SI3.6_Config] maintained by a user. Adjusting the scan range is usually accomplished by the {blue:Zoom} value instead. However, using the {blue:Scan Amplitude X/Y} values to adjust the scan range allows scans of: 1) areas which would require a fractional {blue:Zoom} (e.g. 1.5x) and 2) non-square aspect-ratio areas.{info}
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h3. Section C: Live Adjustable Scan Parameters
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The parameters in this section relate to the _Fast_ (*X*) Dimension command signal. The full meanings/effects of the parameters in this section, as well as procedures to set their values optimally, are described in [Fast (X) Dimension Optimization|SI3.6_FastScanDetails].
Unlike other parameters on the *CONFIGURATION* panel, changes to these parameters are immediately applied during a live acquisition (only in [*FOCUS* mode|SI3.6_AcqModes]), allowing their effect on the acquired image to be readily visualized. When these parameters are varied while not live imaging, then {blue:Apply} must be pressed for the changes to update the _current_ ScanImage [_Configuration_|SI3.6_Config].
The parameters set in this section apply to the currently configured {blue:Zoom} value (in the {report-info:data:MainControls|render=wiki|source=SI3.6 Data} panel). When changes are applied, the {blue:Scan Param Array} values are updated accordingly.
* {blue:Acquisition (Acq) Delay}: Adjusts the _Acquisition Delay_ value required by ScanImage during [processing the input data|SI3.6_InputDigitization]. To produce the optimal/correct image from the scanned data, this value must match the actual delay between the _Acquisition Period_ of the _Fast_ (*X*) command signal and the corresponding period in the physical scanner's position response.
(/) Adjusting this value while _Sawtooth_ scanning will shift the displayed image; adjusting it while _Bidirectional_ scanning will adjust the alignment of every-other-line in the image.
{tip:title=Fast Acq Delay Adjustment}To rapidly visualize the results of adjusting the {blue:Acquisition Delay} during live [*FOCUS* mode|SI3.6_AcqModes] imaging, the options {blue:Blank Flyback} and {blue:Staircase Cmd} should be temporarily disabled (if they were enabled), to prevent the Pockels and _Slow_ (*Y*) scan command signals from needing to be recomputed as the value is adjusted. \\ \\This is particularly useful when [optimizing _Bidirectional_ scans|SI3.6_FastScanDetails#BidiOptimization]{tip}
* {blue:Fine}: Selecting this enables adjustment of the {blue:Acquisition Delay} in fine increments
(/) The fine increment for the {blue:Acquisition Delay} is the sampling period determined by the {blue:Input Sample Rate} value
* {blue:Scan Delay}: Value represents time (in microseconds) by which to extend the linear ramp at the beginning of each _Acquisition Period_ in the _Fast_ (*X*) command signal.
(/) This value is _read-only_ when _Bidirectional_ ({blue:BiDi}) scanning is enabled, as the ramp extension is determined (implied) by the {blue:Fill Fraction} value.
* {blue:True Ms/Line}: (_Read-only_) Value displays the duration of each period of the _Fast_ (*X*) command signal, each of which corresponds to the scan of a single _Line_. This value may differ somewhat from the user-specified {blue:Nominal Ms/Line}) value, according to the currently specified {blue:Fill Fraction}.
* {blue:Fill Fraction}: Value represents the fraction of the {blue:True Ms/Line} occupied by the _Acquisition Period_ -- the portion of each period of the _Fast_ (*X*) command signal during which the [input signal data is processed|SI3.6_InputDigitization]. Adjusting this value actually sets the {blue:True Ms/Line} value (because the _Acquisition Period_ is fixed for a given {blue:Nominal Ms/Line}).
(/) The value of *0.8192* corresponds to case where the {blue:Nominal Ms/Line} matches the {blue:True Ms/Line} value
(/) (Reducing/increasing) the {blue:Fill Fraction} (below/above) *0.8192* (increases/decreases) the {blue:Nominal Ms/Line} value
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h3. Section D: Scan Parameter Array
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As described in [Fast (X) Dimension Optimization|SI3.6_FastScanDetails], optimal settings for the _Fast_ (*X*) command signal can be amplitude-dependent and therefore vary with the {blue:Zoom} value. To address this, ScanImage allows distinct sets of the {blue:Live Scan Params} discussed in the last section to be stored for different {blue:Zoom} levels as part of the ScanImage [_Configuration_|SI3.6_Config]. These sets of variables correspond to the entries in the _Scan Parameter Array_ -- which is 'indexed' by the {blue:Zoom} level.
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(/) The _Scan Parameter Array_ allows the {blue:Zoom} to be adjusted during ScanImage operation without requiring a separate set of [_Configuration_|SI3.6_Config] values for each {blue:Zoom} level
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* {blue:Min Zoom}: This value stores the minimum zoom level to allow for the current ScanImage [_Configuration_|SI3.6_Config]. This value constrains the {blue:Zoom} value set in the {report-info:data:MainControls|render=wiki|source=SI3.6 Data} panel.
(/) This is useful when preparing a ScanImage [*CFG* File|SI3.6_Config] which employs a fast (small) {blue:Nominal Ms/Line} value that may stretch the [physical scanner limits|SI3.6_PhysicalScanner] (e.g. current drive, servo control, or thermal limits)
* {color:blue}*Constant @ Zoom >=*{color}: This value determines the _length_ of the _Scan Parameter Array_. {blue:Zoom} levels above this level use the same {blue:Live Scan Params} values as those configured at this {blue:Zoom} level.
* {blue:@ Zoom}: This determines the zoom level to set and/or display in the _Fill Fraction_, _Acq Delay_, and _Scan Delay_ text controls within the {blue:Scan Param Array} section.
(/) This value can range from 1 to {color:blue}*Constant @ Zoom >=*{color} (values can be stored for zoom levels below the {blue:Min Zoom} value, although they have no effect).
(/) Scrolling through the {blue:@ Zoom} values allows one to scroll through the _Fill Fraction_, _Acq Delay_, and _Scan Delay_ values stored for each {blue:Zoom} level
* {blue:Fill Frac/Acq Delay/Scan Delay}: These correspond to the parameters described in the {blue:Live Scan Params} section, specifying the parameters to use at each {blue:Zoom} level.
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(/) Adjusting the _Scan Parameter Array_ values (and applying the changes) for the currently configured {blue:Zoom} level (as set in the {report-info:data:MainControls|render=wiki|source=SI3.6 Data} panel) causes the corresponding {blue:Live Scan Params} values to be automatically updated.
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h3. Section E: Pockels Control Parameters
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Further background on these parameters can be found in [Pockels Flyback Blanking|SI3.6_FlybackBlanking].
* {blue:Blank Flyback}: Enabling this option implies --
** The Pockels Cell command signal(s) generated by ScanImage for the (active) _Beams_ are 'blanked' outside of the _Acquisition Period_ of the [*X* command signal|SI3.6_FastScanDetails]
** If {blue:Flyback on Final Line} is selected, the Pockels Cell command signal(s) generated by ScanImage for the (active) _Beams_ are 'blanked' during the the final line of each _Frame_ to allow for _flyback_ of the _Slow_ (*Y*) dimension scan
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(/) 'Blanking' the beam implies setting to the minimum power level measured during that _Beam's_ most recent [Pockels calibration|SI3.6_PockelsCalibration]
(/) The Pockels Cell command signal(s) is/are shifted in time by the currently configured {blue:Acquisition Delay} value, in order to match the _Acquisition Period_ of the physical scanner's position 'response'.
(/) It is useful to disable {blue:Blank Flyback} during live adjustment of the {blue:Acquisition Delay}, as this avoids requiring the Pockels Cell command signal(s) to be recomputed for each {blue:Acquisition Delay} value, causing a small interruption in the ongoing acquisition.
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* {blue:Fill Frac Adjust}: Specifies a time (in microseconds) by which the _Acquisition Period_ value used to determine the Pockels Cell command signal(s) is extended (increased) relative to the actual value for the _Fast_ (*X*) command signal.
(/) This parameter specifies extra 'cushion' to use in the Pockels command signal(s), ensuring the signal is not 'blanked' during the actual _Acquisition Period_.
(/) This cushion 1) accounts for light modulator response time and 2) provides tolerance for errors in the {blue:Acquisition Delay}.
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h3. Section F: DAQ Sample Rates
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This section determines the sample rates used by the _Analog Input_ and _Analog Output_ channels used by ScanImage.
* {blue:Input Sample Rate}: Specifies the sample rate (in MHz) of the _Analog Input_ channels used by ScanImage to digitize the [PMT (or other photodetector) input signals|SI3.6_InputDigitization]
* {blue:Output Sample Rate}: Specifies the sample rate (in kHz) of the _Analog Output_ channels used by ScanImage to generate the _Fast_ (*X*) and _Slow_ (*Y*) scanner command signals, as well as the Pockels (or other light modulator) command signal(s) generated for each _Beam_
(/) Increasing this value can improve the positioning accuracy of scan regions selected for the [Power Box|SI3.6_PowerBox] feature and with the {blue:ROI} tool (in the {report-info:data:MainControls|render=wiki|source=SI3.6 Data} panel).
(i) At this time, the _Analog Output_ sample rate for the channels used for the scanner and Pockels cell command signals are required to be equal
* {blue:Auto}: This option (available for both the {blue:Input Sample Rate} and {blue:Output Sample Rate} controls) causes the sample rate to be automatically determined by the current {blue:Nominal Ms/Line} value
(/) For the {blue:Input Sample Rate}, selecting {blue:Auto} causes the {blue:Bin Factor} to remain constant for common values of {blue:Nominal Ms/Line} -- this allows the ScanImage [image displays|SI3.6_ImageDisplay] to appear consistent as the scan speed is varied, with fixed {blue:White/Black} levels (set in the {report-info:data:ImageControls|render=wiki|source=SI3.6 Data}
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h3. Section G: Slow Dimension Scan Settings
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The full meaning/effects of the parameters in this section are described in [Slow (Y) Scan Dimension Settings|SI3.6_SlowScanDetails].
* {blue:StaircaseCmd}: Specifies that the _Slow_ (*Y*) command signal should be a staircase -- i.e. should step to a discrete level for each line in the _Frame_ -- rather than a continuous ramp.
* {blue:Flyback on Final Line}: Specifies that beginning of _flyback_ for _Slow_ (*Y*) command signal will coincide with start of final line in the _Frame_; also, if {blue:Blank Flyback} is selected, then the Pockels (or other light modulator) command signal will be 'blanked' during this (entire) final line
(i) If this option is disabled, then the _Slow_ (*Y*) command signal _flyback_ begins at the end of the _Frame_ meaning, practically, that it occurs during the first line of the succeeding frame
(/) This option is valuable for fast scan speeds (low {blue:Nominal Ms/Line} values) as the _flyback_ may take nearly as long as a single line scan; hence the Pockels 'blanking' is appropriate
* {blue:Discard Flyback Line}: Specifies that the final line of acquired data during the _Frame_ is discarded and does not appear in the [image display figures|SI3.6_ImageDisplay] and is not recorded to the stored [image files|SI3.6_ImageFiles].
(i) This option is disabled and inactive if {blue:Flyback on Final Line} is disabled
(/) This option is often used with an odd value for {blue:Lines/Frame} specified, so that the stored/displayed number of lines is even (e.g. 257 can be specified to store/display a 256 line image)
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h3. Section H: Dependent Parameter Display
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This section displays _read-only_ parameters determined by the other values specified in the *CONFIGURATION* panel.
* {blue:Samps/Line}: Specifies the number of samples acquired on the _Analog Input_ channels used for the [PMT (or other photodetector) input signal|SI3.6_InputDigitization] during the _Acquisition Period_ occurr ing during each _Line Period_ ({blue:True Ms/Line}) of the _Fast_ (*X*) dimension scan. This value depends on:
** {blue:Nominal Ms/Line}
** {blue:Input Sample Rate}
* {blue:Bin Factor}: Specifies the number of _Analog Input_ samples from the [input signal(s)|SI3.6_InputDigitization] which are summed together to compute the value for each horizontal pixel that is computed by ScanImage to assemble an image for each _Frame_ of acquisition to display|SI3.6_ImageDisplay] and/or [store|SI3.6_ImageFiles]) . This value depends on:
** {blue:Samps/Line} ({blue:Nominal Ms/Line} and {blue:Input Sample Rate})
** {blue:Pixels/Line}
* {blue:Pixel Time}: Specifies the total time spent during the acquisition of {blue:bin Factor} samples for each horizontal pixel computed by ScanImage.
(/) This value is computed simply as: {blue:Pixel Time} *= {blue:Bin Factor} /* {blue:Input Sample Rate}
* {blue:Frame Rate}: Specifies the total time spent for each _Frame_ of acquisition.
(/) This value is computed simply as: {blue:Frame Rate} *= 1 */ (* {blue:Lines/Frame} *\** {blue:True Ms/Line} *)*
(/) The total time for a ScanImage acquisition is determined exactly by the number of frames acquired times the _Frame Period_ (*= 1 /* {blue:Frame Rate}*)*) -- i.e. there are no gaps between _Frames_
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h3. Section I: Miscellaneous Parameters
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* {blue:Shutter Delay}: Specifies the time (in ms) following the start ([_trigger_|SI3.6_Triggering]) of a [*GRAB* acquisition or *LOOP* _Repeat_|SI3.6_AcqModes], or an [_Image Stack Slice_|SI3.6_ImageStacks], that the optional _shutter_ signal generated by ScanImage should switch to _Open_ state.
(/) See [Shutter Control|SI3.6_Shutter] for more information.
* {blue:Disable Image Striping}: In many circumstances, ScanImage [processes the input data|SI3.6_ImageDigitization] in evenly-subdivided segments of each _Frame_ termed _Stripes_, allowing the update of [image display figures|SI3.6_ImageDisplay] to appear more 'real-time'. Selecting {blue:Disable Image Striping} prevents this from occurring, forcing ScanImage to display images one _Frame_ at a time.
{tip:title=Why Disable Image Striping?}There are two primary reasons to forcibly disable image striping:
# For fast scans (low {blue:Nominal Ms/Line}) and/or large {blue:Acquisition Delay} values, the _Acquisition Period_ of the physical scanner position response will be delayed sufficiently to overlap the *next* _Line Period_ of the _Fast_ (*X*) scan command signal. In such cases, ScanImage must ['wrap' the input data|SI3.6_ImageDigitization] obtained during each segment of acquired data. Forcing data to be acquired in _Frame_ segments avoids the 'wrap' artifact from occurring in the middle of the _Frame_
# When the {blue:Draw crosshairs on images} option is enabled (in the {report-info:data:UserSettings|render=wiki|source=SI3.6 Data} dialog), image striping must be disabled for the crosshair to display correctly in the ScanImage [image display figures|SI3.6_ImageDisplay].{tip}
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