• Created by Unknown User (iyerv), last modified on Oct 09, 2013
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IMAGE CONTROLS Panel

Levels

For each channel, these specify input digitizer levels that are displayed as full and zero brightness (i.e. white and black, for standard grayscale colormap) on the Channel display figures.

(info) Digitizer levels are 14-bit signed integers encoding average voltage value, measured during dwell time at each pixel, within range specified in CHANNELS dialog
(tick) The levels do NOT affect data logged to TIF files. However, these values are stored in the /channelsLUT/ property logged to the TIF file header; thus, it is possible to recover the display used at the time of ScanImage acquisition

Settings Menu

  • : (Not applicable in SI 4.2)
  • : If enabled, a crosshair is shown in all the Channel Display figures marking the center of the scanned field-of-view
  • : Save current user settings to currently loaded user (.USR) file
  • : Save current user settings to user-selected user (.USR files)
  • : Opens/raises the USER SETTINGS window showing all the ScanImage properties saved to user (.USR) files, allowing each of their values to be edited

Frame Averaging & Selection

  • : Specify the number of last-acquired frames to be averaged together on Channel Display figures, i.e. to reduce image noise. This has no effect on data logged to TIF files.
  • : Constrain value to be equal to value specified on MAIN CONTROLS (which indicates number of frames to average into each logged frame to TIF file)

ScanImage allows selecting which of every N acquired frames are displayed in Channel Display figures.

  • : Specify that a selected subset of every N frames will be displayed
  • : Specify which of each batch of N frames to display. If more than one frame is selected, the Channel display figure will be subdivided to allow each selected frame to be visualized simultaneously.
    (tick) Setting Selected Frames equal to 1:N (i.e. display /all/ frames in the subset) is useful for Volume Imaging specified in FAST Z CONTROLS. See picture below.
    (tick) Setting Selected Frames equal to N corresponds to display decimation, i.e. displaying every Nth frame acquired. This reduces CPU processing time spent on frame display. Note this decimation is in addition to any reported in the CONFIGURATION panel.
  • : Constrains to equal .
    (tick) Selecting this option suppresses appearance of live rolling average, i.e. shows only the averaged result at reduced display rate
  • : Constrains to equal value of
    (tick) Selecting this option allows one to view every N'th frame in Channel Display figures

The use of =8 with =[1:7] is depicted here - the user can 'simultaneously' visualize several planes at once:

Image Tools

This section contains tools that involve graphical user interaction with one of the ScanImage Channel Display figures.

: Selects which Channel Display figure or Channel Merge Display figure, user will interact with upon selecting one of the Image Tools. If /None/ is selected, user must first click in a particular Image Display figure before initiating user interaction.
(tick) Selecting a allows user to skip the first click to select a window, i.e. if interaction is always done in a particular Channel Display



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
(tick) This is helpful for investigating a subregion of an image without actually scanning the smaller subregion, which may cause excessive photodamage/photobleaching.
(tick) This capability is particularly useful for fine optimization of bidirectional scan alignment (see CONFIGURATION)

The Matlab zoom tool remains active on the targeted Channel 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.


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.

The Matlab data cursor tool remains active on the targeted Channel 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.


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

The computed histogram depends on the levels selected for the given Channel.

(tick) This tool is useful for visually determining the quality the colormap mapping determined by the levels chosen
(info) This tool cannot be used with the Channel Merge Display figure


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 Channel Display Figure, as mapped to colormap entries in that target.

The computed statistics depends on the levels selected for the given Channel.

(info) This tool cannot be used with the Channel Merge Display figure

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