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{info:title=About this Documentation}ScanImage 3.7 is quite similar to 3.6. This documentation 1) describes _changes_ and _new features_ since ScanImage 3.6 and 2) contains updated _Getting Started_ and _Window Reference_ guides. Aside from these changes, Otherwise, the various _Key Concepts_ described in the [ScanImage 3r3.6.x Documentation] are, broadly speaking, still applies.{info}
{infoapplicable. The _Key Concepts_ section/pages thus simply link back to the 3.6 documentation.{info}
{note:title=Version Compatibility}Please note/follow the [Matlab and NI version compatability|ScanImage Matlab and NI Version Compatibility] information. Use_Other ofversions otherare versionsknown willor likely resultnot in trouble.to work!_ As discussed further below, it is possible to co-install ScanImage 3.7 with earlier ScanImage versions, by installing multiple Matlab versions on a machine. In such cases, DAQmx 8.8 should be used. {infonote}
{toc:maxLevel=3|indent=6pxcache}
h1. New Features in ScanImage 3.7
h3. Major New Features
{multi-excerpt-include:pageTitle=ScanImage r3.7 README|name=MajorEnhancements|nopanel=true}
h3. Other New Features
{multi-excerpt-include:pageTitle=ScanImage r3.7 README|name=OtherEnhancements|nopanel=true}
{anchor:UpgradeInfo}
h1. Upgrading from ScanImage 3.5 or 3.6 (Important Changes)
* 3.7 has a [new model INI file|http://openwiki.janelia.org/wiki/display/ephus/ScanImage+INI+File+Overview] , which is thoroughly self-documenting. You should make a new standard.INI file based on this model, following the comments.
(/) It is recommended to create a separate folder(s) for your *INI*/*CFG*/*USR* files under 3.7, to keep them separate from data files for any older version you may also maintain installed.
* The {blue:Scan Amplitude X/Y} values are replaced by {blue:Scan Angular Range Fast/Slow} values, in * +Getting Started Guide+
{pagetree:root=Getting Started Guide (r3.7)|startDepth=2}
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* +Window Reference Guide+
{pagetree:root=Window Reference Guide (r3.7)|startDepth=1}
* +Key Concepts (r3.6)+
{pagetree:root=Key Concepts (r3.6)|startDepth=1}
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h1. New Features in ScanImage 3.7
h3. Major New Features
{multi-excerpt-include:pageTitle=ScanImage r3.7 README|name=MajorEnhancements|nopanel=true}
h3. Other New Features
{multi-excerpt-include:pageTitle=ScanImage r3.7 README|name=OtherEnhancements|nopanel=true}
{anchor:UpgradeInfo}
h1. Upgrading from ScanImage 3.5 or 3.6 (Important Changes)
* 3.7 has a [new model INI file|http://openwiki.janelia.org/wiki/display/ephus/ScanImage+INI+File+Overview], with [several changes|ScanImage r3.7 standard_model.INI] from r3.6. You should make a new standard.INI file based on this model, following the comments.
(/) It is recommended to create a separate folder(s) for your *INI*/*CFG*/*USR* files under 3.7, to keep them separate from data files for any older version you may also maintain installed.
* The {blue:Scan Amplitude X/Y} values are replaced by {blue:Scan Angular Range Fast/Slow} values, in the {report-info:data:Configuration|render=wiki|source=SI3.7 Data} dialog. They now represent the *full*-angle (peak-peak) of the scan range, specified in optical degrees, rather than *half*-angle as in 3.6 (and *half*-voltage of command signal in earlier versions). Therefore new values will generally be _twice_ the {blue:Scan Amplitude X/Y} values in ScanImage 3.6.
(/) In general, the new default {blue:Scan Angular Range Fast/Slow} values of *15 optical degrees* should not often require modification by most users. If you see the field-of-view is different (smaller) than you're used to, look closely at the {blue:voltsPerOpticalDegree} value/notes in the *INI* file.
* If using two boards (i.e. second board for Pockels and/or new clock export signals), ScanImage 3.7 requires the [clock synchronization|http://openwiki.janelia.org/wiki/display/ephus/Wiring+Your+System+%28r3.6%29#WiringYourSystem%28r3.6%29-ClockSync] between boards be on *RTSI 7*, not *RTSI 6* as with ScanImage 3.6.
(/) If running both 3.6 & 3.7 (see below), you should connect both *RTSI 6* and *RTSI 7*(or connect all, with a ribbon cable).
(/) If running both 3.5 & 3.7 (see below), no change is required
* The *INI* file now contains a {blue:voltsPerOpticalDegree} value which should be set correctly to convert optical degree values specified in ScanImage to correctly scaled voltage commands. Please read the comments carefully!
(!) If the {blue:voltsPerOpticalDegree} value in 3.7 differs compared to your {blue:opticalDegreesConversion} setting in 3.6 , you will need to (further) adjust your {blue:Scan Angular Range Fast/Slow} values compared to previous {blue:Scan Amplitude X/Y} values.
* The {blue:Shift Fast/Slow} and {blue:Scan Amplitude Fast/Slow} values that previously were specified as *X* & *Y* are now referred to as *FAST* & *SLOW*. A new control in {report-info:data:Configuration|render=wiki|source=SI3.7 Data} dialog indicates mapping from *X*/*Y* to *FAST*/*SLOW* axes. Adjusting this allows you to rotate the image 90 degrees.
* The *INI* file now contains the separate mapping of *X*/*Y* to DA Channels 0 & 1 ({vi-statevar:state.init.X/YMirrorChannelID} values) which is fixed on initialization.
* It is recommended to copy your old *CFG* files to a separate folder for 3.7, and then load and re-save each of them individually. This will make your *CFG* files 3.7 compatible.
(!) Note the {blue:ScanAmplitude X/Y} values from 3.6 will not be applied in 3.7. The new {blue:Scan Angular Range Fast/Slow} values should be adjusted before saving each *CFG* file.
{anchor:CoInstallation}
{info:title=Running ScanImage 3.7 together with earlier versions}You *can* run 3.7 together on same machine that is running 3.6.x or 3.5.x
* Typically, your newer Matlab will set path to 3.7 and older Matlab will set path to older version
* If running both 3.5/3.6 & 3.7 on same machine, [DAQmx 8.8|http://joule.ni.com/nidu/cds/view/p/id/1085/lang/en] is required. This is earliest version of DAQmx supported by 3.7, while 3.5/3.6 doesn't run on 8.9 or higher.
* Note that X series boards are only supported from 9.0 forward.
* Note that maintaining multiple Matlab versions on same machine does _not_ require an additional license or count as an additional activation.{info}
h1. Major New Features
{anchor:PZAdjust}
h3. Power Adjustment During Stacks
When collecting image stacks in scattering tissue, the power level required at each slice in the stack generally increases with depth in order to maintain a fixed signal. ScanImage 3.7 can make this adjustment automatically, using a simple exponential length constant (_Lz_).
The {report-info:data:PowerControls|render=wiki|source=SI3.7 Data} panel allows this capability to be enabled:
h5. {toggle-cloak:id=PZAdjust} Show...
{cloak:id=PZAdjust}
{panel:title=Power Controls}{center}!Power Controls (r3.7)^PowerControls.bmp!{center}{multi-excerpt-include:name=PZAdjust|pageTitle=Power Controls (r3.7)|nopanel=true}{panel}
{cloak}
From the {report-info:data:MotorControls|render=wiki|source=SI3.7 Data} panel, ScanImage 3.7 also provides a facility to measure the *Lz* value suited for the given preparation:
h5. {toggle-cloak:id=OverrideLz} Show...
{cloak:id=OverrideLz}
{panel:title=Motor Controls}{center}!Motor Controls (r3.7)^MotorControls.bmp!{center}{multi-excerptexcerpt-include:name=OverrideLz|pageTitle=Motor Controls (r3.7)|nopanel=true}{panel}
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{anchor:ClockExport}
h3. Frame/Line/Pixel Clock Export
ScanImage 3.7 introduces a Frame/Line/Pixel clock export feature intended to allow external hardware to be synchronized with start (or end) of each Frame, Line, or Pixel during image acquisition.
The {report-info:data:ExportedClocks|render=wiki|source=SI3.7 Data} dialog controls the Frame/Line/Pixel clock feature:
h5. {toggle-cloak:id=ExportedClocks} Show...
{cloak:id=ExportedClocks}
{panel:title=Exported Clocks}{center}!Exported Clocks (r3.7)^ExportedClocks.bmp!{center}{multi-excerpt-include:name=uno|pageTitle=Exported Clocks (r3.7)|nopanel=true}{panel}
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h3. External triggering enhancements, including _Next Triggering_
ScanImage 3.7 has more options for external triggering. There are now two types of external triggers:
* _Start_ Triggers: Trigger signals which initiate *GRAB/LOOP* acquisitions, when *EXT* is enabled in the {report-info:data:MainControls|render=wiki|source=SI3.7 Data} window
* _Next_ Triggers: Trigger signals which stop or advance data file of ongoing *GRAB/LOOP* acquisition. They may also act as a _Start_ trigger and initiate acquisitions.
External trigger signals to ScanImage are input on one of the PFI (programmable function interface) lines specified in the [*INI*|SI_INIFile] file as {vi-statevar:externalStartTrigTerminals} and {vi-statevar:nextTrigTerminals}. These specify the list of _available_ trigger sources on a particular rig/setup.
The {report-info:data:Triggers|render=wiki|source=SI3.7 Data} dialog, accessed from *Settings >> Triggers...* on the {report-info:data:MainControls|render=wiki|source=SI3.7 Data} menu, allows selection of which trigger source to use:
h5. {toggle-cloak:id=Triggers} Show...
{cloak:id=Triggers}
{panel:title=Triggers}{center}!Triggers (r3.7)^Triggers.bmp!{center}{multi-excerpt-include:name=uno|pageTitle=Triggers (r3.7)|nopanel=true}{panel}
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h3. Enhanced User Functions capability
ScanImage 3.6 and earlier had some support for [_User Functions_|User Functions (r3.6) - Concept]. The original implementation had a few critical limitations, however:
* Only one event -- the end of a *GRAB* acquisition or *LOOP* repeat -- lead to user function execution
* User functions were required to be on the Matlab search path
* No ability to pass arguments to the user functions, i.e. to modulate their function
ScanImage 3.7 completely re-implements the _User Functions_ feature to overcome these limitations. The new implementation makes use of the concept of [_events_|http://www.mathworks.com/help/techdoc/matlab_oop/bqvggvt.html] recently added to the Matlab language.
The {report-info:data:UserFunctions|render=wiki|source=SI3.7 Data} dialog, accessed from *Settings >> User Functions...*, allows _User Functions_ to be specified:
h5. {toggle-cloak:id=UserFunctions} Show...
{cloak:id=UserFunctions}
{panel:title=User Functions}{center}!User Functions (r3.7)^UserFunctions.bmp!{center}{excerpt-include:User Functions (r3.7)|nopanel=true}{panel}
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{anchor:FastConfig}
h3. Enhanced Fast Configurations
ScanImage 3.7 enhances the interface and capabilities of _Fast Configurations_ -- [configurations|Configurations, CFG Files, & Fast Configurations (r3.6)] which are configured to be rapidly loaded, at the touch of one key or one button. ScanImage users are encouraged to create several configurations, to represent each of the imaging/experimental modes they use.
The new {report-info:data:FastConfigurations|render=wiki|source=SI3.7 Data} window is accessed via *Settings >> UserFast FunctionsConfigurations...* on the {report-info:data:MainControls|render=wiki|source=SI3.7 Data} menu:
h5. {toggle-cloak:id=FastConfigs} Show...
{cloak:id=FastConfigs}
{panel:title=Fast Configurations}{center}!Fast Configurations (r3.7)^FastConfigurations.bmp!{center}{excerpt-include:Fast Configurations (r3.7)|nopanel=true}{panel}
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h3. Continuous File Streaming Improvements
ScanImage 3.5 introduced [continuous file streaming|http://openwiki.janelia.org/wiki/display/ephus/Unlimited+and+Uninterrupted+Acquisition] as an option for non-stack *GRAB/LOOP* acquisitions (i.e. acquisitions where {blue:# Slices}=1). This feature saves files to disk as they are acquired, rather than waiting till the end of an acquisition to save the file. This permits unlimited, uninterrupted acquisitions.
{anchor:RunningDataBuffer}
ScanImage 3.7 now uses continuous file streaming for _all_ *GRAB/LOOP* acquisitions (when {blue:AutoSave} is enabled), including stack acquisitions. The {blue:Save During Acquisition} option in 3.5.x and 3.6.x has been removed.
As a consequence, ScanImage 3.7 no longer typically maintains a buffer in memory (RAM) of the entire acquisition. HoweverInstead, ita configurable cancircular berunning usefulbuffer toof maintainthe imagemost datarecently bufferedacquired inframes RAM, e.gis maintained. for online processing in _User Functions_. ScanImage 3.7 therefore maintains a circular buffer of the most recently acquired frames in the {vi-statevar:state.acq.acquiredData} state variable (in the Matlab global workspace). This is the same variable that was used in ScanImage 3.6 (and earlier) to maintain a buffer of the entire acquisition; however the variable is now somewhat differently structured. The variable was previously a cell-array of 3-d arrays; in ScanImage 3.7, it is now a nested cell array of 2-D images (frames), indexed as follows:
{panel:borderStyle=dashed}>> state.acq.acquiredData\{<FrameIndex>\}\{<ChannelIndex>\}(<lineIndex>,<pixelIndex>)
where <FrameIndex> counts from the most recent frame.{panel}
The {report-info:data:UserSettings|render=wiki|source=SI3.7 Data} dialog, accessed via *Settings >> User Settings...* from the {report-info:data:MainControls|render=wiki|source=SI3.7 Data}menu) allows this buffer to be configured:
h5. {toggle-cloak:id=UserSettings} Show...
{cloak:id=UserSettings}
{panel:title=User Settings}{center}!User Settings (r3.7)^UserSettings.bmp!{center}{multi-excerpt-include:name=MaxBufferedFrames|pageTitle=User Settings (r3.7)|nopanel=true}{panel}
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h3. DAQ Toolbox No Longer Required
ScanImage 3.7 no longer requires use of the DAQ toolbox. Instead, it uses a Matlab [class|http://www.mathworks.com/help/techdoc/matlab_oop/ug_intropage.html] which _wraps_ the NI DAQmx library. This approach has several advantages:
* Faster data read times are achieved (>4x faster), which increases amount of time available for user functions
* More comprehensive coverage of DAQmx features is achieved, compared to DAQ toolbox. For example, the DAQ toolbox does not support [counter/timer channels|http://zone.ni.com/devzone/cda/tut/p/id/9376#toc3] which underlie several of the new features in ScanImage 3.7.
h1. Other New Features
h3. Finite LOOP acquisitions
In earlier versions, [*LOOP*|SI3.6_AcqModes] mode acquisitions were indefinite -- the user was required to {blue:ABORT} the acquisition manually. In ScanImage 3.7, the {report-info:data:StandardControls|render=wiki|source=SI3.7 Data} panel contains a new control specifying the {blue:# Repeats}. *LOOP* acquisitions will automatically terminate after specified number of _Repeats_. The value _Inf_ (default) can be entered to mimic the original, indefinite looping behavior.
h3. Fractional zoom adjustment
In earlier versions, the {blue:Zoom} control in the {report-info:data:MainControls
The {report-info:data:UserSettings|render=wiki|source=SI3.7 Data} dialog, accessed via *Settings >> User Settings...* from the {report-info:data:MainControls|render=wiki|source=SI3.7 Data}menu) allows this buffer to be configured:
h5. {toggle-cloak:id=UserSettings} Show...
{cloak:id=UserSettings}
{panel:title=User Settings}{center}!User Settings (r3.7)^UserSettings.bmp!{center}{multi-excerpt-include:name=MaxBufferedFrames|pageTitle=User Settings (r3.7)|nopanel=true}{panel}
{cloak}
h3. DAQ Toolbox No Longer Required
ScanImage 3.7 no longer requires use of the DAQ toolbox. Instead, it uses a Matlab [class|http://www.mathworks.com/help/techdoc/matlab_oop/ug_intropage.html] which _wraps_ the NI DAQmx library. This approach has several advantages:
* Faster data read times are achieved (>4x faster), which increases amount of time available for user functions
* More comprehensive coverage of DAQmx features is achieved, compared to DAQ toolbox. For example, the DAQ toolbox does not support [counter/timer channels|http://zone.ni.com/devzone/cda/tut/p/id/9376#toc3] which underlie several of the new features in ScanImage 3.7.
h1. Other New Features
h3. Finite LOOP acquisitions
In earlier versions, [*LOOP*|SI3.6_AcqModes] mode acquisitions were indefinite -- the user was required to {blue:ABORT} the acquisition manually.
In ScanImage 3.7, the {report-info:data:StandardControls|render=wiki|source=SI3.7 Data} panel allows user to specify a finite number of _Repeats_ for a [*LOOP*|SI3.6_AcqModes] acquisition:
h5. {toggle-cloak:id=FiniteLoops} Show...
{cloak:id=FiniteLoops}
{panel:title=Standard Controls}{center}!Standard Controls (r3.7)^StandardControls.bmp!{center}{multi-excerpt-include:name=NumRepeats|pageTitle=Standard Controls (r3.7)|nopanel=true}{panel}
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h3. Fractional zoom adjustment
In earlier versions, the {blue:Zoom} control in the {report-info:data:MainControls|render=wiki|source=SI3.7 Data} panel allowed the zoom value to be specified in only integer increments. ScanImage r3.7 now allows fractional zoom values, providing greater control over the scan range directly from the {report-info:data:MainControls|render=wiki|source=SI3.7 Data} panel.
The {blue:Zoom} value simply represents a division of (both) the {blue:Angular Range Fast/Slow} values in the {report-info:data:Configuration|render=wiki|source=SI3.7 Data} panel.
(/) For most users, the {blue:Angular Range Fast/Slow} values should not require modification -- the {blue:Zoom} control, with fractional values, should now provide sufficient adjustment flexibility over the scanned image area.
h5. {toggle-cloak:id=FracZoom} Show...
{cloak:id=FracZoom}
{panel:title=Main Controls}
{center}!Main Controls (r3.7)^MainControls_FracZoomHighlight.png!{center}
(i) When a [Scan Parameter Array|Scan Configuration (r3.6)#FastScanDetails] is specified in the {report-info:data:Configuration|render=wiki|source=SI3.7 Data} panel, allowedany the zoom value to be specified in only integer increments. ScanImage r3.7 now allows fractional zoom values, providing greater control over the scan range directly from the {report-info:data:MainControls|render=wiki|source=SI3.7 Data} panel.
The {blue:Zoom} value simply represents a division of (both) the {blue:Scan Angular Range} values in thenon-integer {blue:Zoom} values are rounded to determine the scan parameters ({blue:Acquisition Delay}, {blue:Scan Delay}, and {blue:Fill Fraction}) in effect at specified {blue:Zoom}.
{panel}
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h3. Slider adjustment of power during FOCUS
In ScanImage 3.7, a new {blue:Live Adjust} control on the {report-info:data:ConfigurationPowerControls|render=wiki|source=SI3.7 Data} panel. Forallows most users, the {blue:Scan Angular Range} values do not require modification -- the {blue:Zoom} control should provide sufficient adjustment flexibility over the scanned range.
(i) When a [Scan Parameter Array|Scan Configuration (r3.6)#FastScanDetails] is specified inslider to be adjusted during [*FOCUS*|SI3.6_AcqModes], if selected:
h5. {toggle-cloak:id=LiveAdjust} Show...
{cloak:id=LiveAdjust}
{panel:title=Power Controls}{center}!Power Controls (r3.7)^PowerControls.bmp!{center}
{multi-excerpt-include:name=LiveAdjust|pageTitle=Power Controls (r3.7)|nopanel=true}
(i) The {blue:Verify Power} control (rarely used) previously on the {report-info:data:ConfigurationPowerControls|render=wiki|source=SI3.7 Data} panel, anyhas non-integer {blue:Zoom} values are rounded to determine the scan parameters ({blue:Acquisition Delay}, {blue:Scan Delay}, and {blue:Fill Fraction}) in effect at specified {blue:Zoom}.
h3. Slider adjustment of power during FOCUSbeen relocated to the {report-info:data:UserSettings|render=wiki|source=SI3.7 Data} dialog.
{panel}
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{set-data:ColormapLink|hidden=true}[colormap|http://www.mathworks.com/help/techdoc/ref/colormap.html]{set-data}
h3. More image display colormap options
In ScanImage 3.7, a new {blue:Live Adjust} control on the6.x and earlier, the [Image Display windows|SI3.6_ImageDisplay] are always displayed with a grayscale {report-info:data:PowerControlsColormapLink|render=wiki|source=SI3.7 Data} panel allows the slider to be adjusted during [*FOCUS*|SI#.6_AcqModes], if selected:
{panel:title=POWER CONTROLS}{multi-excerpt-include:name=LiveAdjust|pageTitle=Power Controls (r3.7)|nopanel=true}{panel}
(i) The {blue:Verify Power} control (rarely used) previously on the}, with a few options to display pixels at or near saturation as colored.
ScanImage 3.7 offers a wider range of standard {report-info:data:ColormapLink|render=wiki} options, and also provides users the ability to specify their own {report-info:data:ColormapLink|render=wiki} .
The {report-info:data:PowerControlsImageControls|render=wiki|source=SI3.7 Data} panel hasprovides been relocated to thethe standard {report-info:data:UserSettingsColormapLink|render=wiki|source=SI3.7 Data} dialog.options:
{anchor:Colormap}
h3. More image display colormap options
In earlier versions, the [Image Display windows|SI3.6_ImageDisplay] are always displayed with a grayscale colormap, with the possibility of displaying
In ScanImage 3.7, most Colormap controls are moved to the {report-info:data:ImageControls|render=wiki|source=SI3.7 Data} panel. The {blue:Colormap} menu allows a wider selection of colormaps, including the Matlab [jet colormap|http://www.mathworks.com/help/techdoc/ref/colormap.html] and options to display Channels 1 and 2 as red & green (in either order).
In addition, a user-specified colormap can be specified, for each Channel, in theh5. {toggle-cloak:id=ImageControls} Show...
{cloak:id=ImageControls}
{panel:title=Image Controls}{center}!Image Controls (r3.7)^ImageControls.bmp!{center}{multi-excerpt-include:name=ColormapSettings|pageTitle=Image Controls (r3.7)|nopanel=true}{panel}
{cloak}
The {report-info:data:Channels|render=wiki|source=SI3.7 Data} dialog provides the capability for a user-defined/configured {report-info:data:ChannelsColormapLink|render=wiki|source=SI3.7 Data} dialog. }:
h5. {toggle-cloak:id=Channels} Show...
{cloak:id=Channels}
{panel:title=Channels}{center}!Channels (r3.7)^Channels.bmp!{center}{excerpt-include:Channels (r3.7)|nopanel=true}{panel}
{cloak}
h3. Option to average binned samples
To date, ScanImage has summed the input samples obtained at each pixel of the scanned image (see [Input Data Processing|SI3.6_ImageDigitization]). The number of samples at each pixel is computed as the {blue:Bin Factor}, displayed on the {report-info:data:Configuration|render=wiki|source=SI3.7 Data} panel; its value is determined by the {blue:Nominal Ms/Line}, {blue:Pixels/Line}, and {blue:Input Sample Rate}.
Some users may preferScanImage 3.7 adds the option to average, rather than sum, the samples obtained at each pixel. This makes the intensity values for each [Image Display window|SI3.6_ImageDisplay] (and hence the {blue:White} and {blue:Black} levels that are appropriate) independent of the {blue:Bin Factor} (and hence the {blue:Nominal Ms/Line}, {blue:Pixels/Line}, and {blue:Input Sample Rate} values).
ScanImage 3.7 adds an {blue:Average Samples} control to select this option. See the {report-info:data:ImageControls|render=wiki|source=SI3.7 Data} panel documentation.
. This is available from the {report-info:data:ImageControls|render=wiki|source=SI3.7 Data} panel:
h5. {toggle-cloak:id=AverageSamples} Show...
{cloak:id=AverageSamples}
{panel:title=Image Controls}{center}!Image Controls (r3.7)^ImageControls.bmp!{center}
{multi-excerpt-include:name=AverageSamples|pageTitle=Image Controls (r3.7)|nopanel=true}{panel}
{cloak}
{anchor:ShutterBeforeEOM}
h3. Support for shutter located before Pockels
The [Shutter control signal|SI3.6_Shutter] feature in earlier ScanImage versions assumed that shutter is located after any/all Pockels/modulators in system -- i.e. a single shutter is used for all the [_Beams_|SI3.6_PockelsCell] in use.
ScanImage 3.7 adds option for the Pockels/EOM to be located _before_ the Pockels. This is most commonly used when there is only one _beam_. To select this option, the {vi-statevar:state.shutter.shutterBeforeEOM} value in the [INI file|SI_INIFile] should be set to 1.
(i) The one & only effect of selecting this option is that shutter is opened/closed at start/end of [Pockels calibration|SI3.6_PockelsCell#PockelsCalibration]
(!) One effect of the {vi-statevar:state.shutter.shutterBeforeEOM} value is that the beam is transmitted through to scope, and potentially specimen, during Pockels calibration. Careful attention should be paid to the {vi-statevar:state.init.parkAngleX/Y} INI file values; the scanner is directed to this angle during Pockels calibration.
h3. Ability to set root save file path
ScanImage requires that user select save path, via *File >> Set Save Path...* dialog on the {report-info:data:Main Controls|render=wiki|source=SI3.7 Data} panel before a {blue:GRAB/LOOP} acquisition with {blue:AutoSave} selected.
h3. Ability to set root save file path
ScanImage 3.7 speeds this folder selection by allowing the {blue:Root Save Path} to be specified as a [User Setting|SI3.6_UserSettings] inmakes it faster to select the _save path_, which is typically required at the start of each ScanImage session. The option is available from the {report-info:data:UserSettings|render=wiki|source=SI3.7 Data} dialog:
h5. This path is used as the starting point for the folder selection dialog in *File >> Set Save Path...*. For instance, 'c:\data' or 'c:\data\<username>' might be specified as the {blue:Root Save Path}.{toggle-cloak:id=RootSavePath} Show...
{cloak:id=RootSavePath}
{panel:title=User Settings}{center}!User Settings (r3.7)^UserSettings.bmp!{center}
{multi-excerpt-include:name=RootSavePath|pageTitle=User Settings (r3.7)|nopanel=true}{panel}
{cloak}
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