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IMAGE CONTROLS Panel

The IMAGE CONTROLS panel contains controls related to the ScanImage Image Display Figures – 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.

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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 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.

  • Pixel data values above the
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    level are mapped to the highest entry in the colormap
  • Pixel data values below the
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    levels are mapped to the lowest entry in the colormap
  • Pixel data values between the
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    and
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    levels are mapped linearly to entries within the colormap.
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Refer to Image Display Figures for further information about the colormap used by each of the figures, the pixel data mapping, and some further display options.
The

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levels do not affect the data stored to the stored Image Files which remain the original pixel data value without remapping. However the

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levels are stored to the Image Header, so it is possible to recover the display at the time of ScanImage acquisition.

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Consider including an excerpt about colormap issues here

Section B: Image Display Interactive Tools

This section consists of

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that involve graphical user interaction with one of the ScanImage Image Display figures.


The

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control selects the target of these and other graphical interaction tools in ScanImage:

SCANIMAGE CONCEPT: Graphical Interaction Tools
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This button toggles on/off the Matlab zoom tool 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.

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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 at low

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levels.

The Matlab zoom tool remains active on the targeted Image Display Figure 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.

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This button toggles on/off the Matlab data cursor tool 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.

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Show datatip figure here?

The Matlab data cursor tool remains active on the targeted Image Display Figure 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.

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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.
  • The histogram counts correspond to the number of pixels assigned to each entry

The computed histogram depends on the

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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

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levels chosen
This tool cannot be used with the Channel Merge figure

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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, as mapped to colormap entries in that target.

The computed statistics depends on the

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levels selected for the given Channel.

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This tool cannot be used with the Channel Merge figure

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