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!ImageControls_compact.bmp!  !ImageControls.bmp!
*IMAGE CONTROLS Panel*
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The *IMAGE CONTROLS* panel contains controls related to the ScanImage [_Image Display Figures_|SI3.6_ImageDisplay] -- MATLAB figure windows which present, in various manners, the most recently acquired image data obtained by ScanImage on each of its up to 4 input _Channels_. These figures are: the _Channel 1-4_ displays, _Channel 1-4 Max Projection_ displays, and the _Channel Merge_ display. 

h3. Section A: {blue:White/Black} Levels
These input values, entered directly as numeric values or by using the slider controls, specify  the pixel data values of the [processed input data|SI3.6_InputDigitization] for each input _Channel_ that will be mapped to the highest and lowest entries, respectively in the 256-level _colormap_ used to display each _Channel's_ data on the [_Image Display Figures_|SI3.6_ImageDisplay]. 
* Pixel data values above the {blue:White} level are mapped to the highest entry in the _colormap_
* Pixel data values below the {blue:Black} levels are mapped to the lowest entry in the _colormap_
* Pixel data values between the {blue:White} and {blue:Black} levels are mapped linearly to entries within the _colormap_.

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(/) Refer to [Enhanced colormap options|SI3.7Doc#Colormap] and the {report-info:data:Channels|render=wiki|source=SI3.7 Data} dialog documentation for information about the [colormap|http://www.mathworks.com/help/techdoc/ref/colormap.html] used for the _Image DisplayFigures_
(/) The {blue:White/Black} levels do not affect the data stored to the stored [_Image Files_|SI3.6_ImageFiles] which remain the original pixel data value without remapping. However the {blue:White/Black} levels are stored to the [_Image Header_|SI3.6_ImageFiles#ImageHeader], so it is possible to recover the display used at the time of ScanImage acquisition.
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{comment}Consider including an excerpt about colormap issues here{comment}

h3. Section B: Image Display Interactive Tools
This section consists of {blue:Image Tools} that involve graphical user interaction with one of the ScanImage [_Image Display_|SI3.6_ImageDisplay] figures.

{anchor:GraphInteractionTools}
The {blue:Default Target} control selects the target of these and other _graphical interaction tools_ in ScanImage:
{panel:title=SCANIMAGE CONCEPT: Graphical Interaction Tools}{include:Graphical Interaction Tools (r3.6)}{panel}

{anchor:DisplayZoomTool}
{blue:Display Zoom} !DisplayZoom.bmp!
This button toggles on/off the Matlab [zoom tool|http://www.mathworks.com/access/helpdesk/help/techdoc/creating_plots/f4-44425.html] in the target figure. With the zoom tool, it is possible to zoom in on selected areas of the image, _without affecting the scan command signals_ generated -- ScanImage continues to scan the larger scan area determined by the current [_Configuration_|SI3.6_Config].
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(/) This is helpful for investigating a subregion of an image without actually scanning a smaller subregion, which often causes excessive photodamage/photobleaching. 
(/) This capability is particularly useful for [optimizing bidirectional scan configurations|SI3.6_FastScanDetails#BidiOptimization] at low {blue:Zoom} levels.
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The Matlab zoom tool remains active on the targeted [_Image Display Figure_|SI3.6_ImageDisplay] until the button is pressed again, toggling the feature off. While the feature remains active, the tool's context menu (right-click menu) can be used to zoom back out of regions. Thus the tool allows one to change the selected subregion repeatedly.

{blue:Display Data Tips} !DisplayDataTip.bmp!
This button toggles on/off the Matlab [data cursor tool|http://www.mathworks.com/access/helpdesk/help/techdoc/creating_plots/f4-44221.html] in the target figure. With the data cursor tool, one or more 'datatips' can be added to the target figure, allowing the pixel value at any position in the image to be displayed as a small note. Once added, datatips can be moved freely throughout the image figure, with the noted value updating to reflect the image pixel location.

{comment}Show datatip figure here?{comment}
The Matlab data cursor tool remains active on the targeted [_Image Display Figure_|SI3.6_ImageDisplay] until the button is pressed again, toggling the feature off. While the feature remains active, the tool's context menu (right-click menu) can be used to add further datatips, as well as to remove datatips. Note that datatips left active when the tool is toggled off will remain displayed -- it is often recommended to _Delete All Datatips_ via the context menu before toggling the tool off.

{blue:Display Histogram} !DisplayHistogram.bmp!
This button will compute and display a Matlab figure containing a histogram of the pixel data values.
* The histogram _bins_ correspond to the 256 _colormap_ entries in the targeted [_Image Display Figure_|SI3.6_ImageDisplay].
* The histogram _counts_ correspond to the number of pixels assigned to each entry

The computed histogram depends on the {blue:White/Black} levels selected for the given _Channel_.

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(/) This tool is useful for visually determining the quality the _colormap_ mapping determined by the {blue:White/Black} levels chosen
(i) This tool cannot be used with the _Channel Merge_ figure
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{blue:Display Statistics} !DisplayStatistics.bmp!
This button will compute and display to the Matlab command line basic statistics (max, min, median, mean, mode) of the pixel data values in the targeted [_Image Display Figure_|SI3.6_ImageDisplay], as mapped to _colormap_ entries in that target.

The computed statistics depends on the {blue:White/Black} levels selected for the given _Channel_.

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(i) This tool cannot be used with the _Channel Merge_ figure
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h3. Advanced Image Display Settings

These settings can be shown/hidden with the {color:blue}*/\*{color}/{blue:\\/} control at bottom right of main panel

{multi-excerpt:name=AverageSamples}
{blue:Average Samples}: If selected, the {blue:Bin Factor} input samples collected for each pixel are averaged, rather than summed, for purposes of both image display and file saving. 
(/) Enabling this option makes 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 independent of the {blue:Nominal Ms/Line}, {blue:Pixels/Line}, and {blue:Input Sample Rate} values. 

(i) No information is lost when averaging samples, since the {blue:Bin Factor}, and the {blue:Average Samples} option itself, are stored to the [Image File Header|SI3.6_ImageFiles#FileHeader]. The _summed_ and _averaged_ forms of data display/saving can then readily be computed from the other.
{multi-excerpt}

{blue:Draw Crosshairs on Images}: If selected, two lines crossing the center of each _Image Display Window_ are shown, to allow ready visualization of the image center. 
(i) When this option is selected, then {blue:Disable Image Striping} should also be selected in the {report-info:data:Configuration|render=wiki|source=SI3.7 Data} panel

{multi-excerpt:name=ColormapSettings}
{blue:Colormap}: A listbox containing several standard options for the [Colormap|http://www.mathworks.com/help/techdoc/ref/colormap.html] to be used for each of the _Image Display Windows_. After making a selection, the {blue:Apply} button must be pressed for change to take effect.
(i) The selection in the {report-info:data:ImageControls|render=wiki|source=SI3.7 Data} panel is just a macro to update the values entered into the {blue:Colormap} entries in the {report-info:data:Channels|render=wiki|source=SI3.7 Data} dialog. 
(i) Users can create their own custom colormap instead, as further described in the {report-info:data:Channels|render=wiki|source=SI3.7 Data} dialog documentation.
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_Colormap_ Options:
* *Gray*: (Default) An 8-bit grayscale colormap is used for all image display figures
* *GrayHighSat*: An 8-bit grayscale colormap is used for all image display figures. Pixels with values occupying upper 5% of the range specified by current {blue:Black/White} values (for each channel) are colored red.
* *GrayLowSat*: An 8-bit grayscale colormap is used for all image display figures. Pixels with values occupying lower 5% of the range specified by current {blue:Black/White} values (for each channel) are colored green.
* *GrayBothSat*: An 8-bit grayscale colormap is used for all image display figures. Pixels with values occupying upper/lower 5% of the range specified by current {blue:Black/White} values (for each channel) are colored red/green, respectively.
* *Jet*: The Matlab [jet colormap|http://www.mathworks.com/help/techdoc/ref/colormap.html] is used with 256 levels (8-bit).
* *Red/Green/Gray/Gray*: Channels 1 and 2 use monochrome 8-bit red and green colormaps, respectively. Channels 3 & 4 use 8-bit grayscale colormaps.
* *Green/Red/Gray/Gray*: Channels 1 and 2 use monochrome 8-bit green and red colormaps, respectively. Channels 3 & 4 use 8-bit grayscale colormaps.
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{multi-excerpt}

{blue:Get PMT Offsets}: Pressing this button will read the baseline level on each of the PMT input channels. ScanImage stores the most recently measured _offset_ values to the [image file header|SI3.6_ImageFiles#FileHeader] for each acquisition. 
(i) The offset values are _not_ applied (subtracted) to the image data displayed and stored to the image file.