Main Controls (r3.7)

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• Overview
• Section A
• Section B
• Section C
• Section D
• Section E
• Section F
• Menus
  • File Menu
  • Settings Menu
  • View Menu

Overview

The MAIN CONTROLS panel is the main ScanImage window. It is the panel from which image acquisitions are initiated (Section C). Closing the MAIN CONTROLS panel causes ScanImage as a whole to exit (after confirming intent). The panel is broken into two halves. The left half (Sections A-C) is always visible, while the right half (Sections D-F) can be shown or hidden. During certain types of acquisitions, the right half is hidden automatically to prevent certain commands from being processed during an ongoing acquisition.

Section A

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  : (Read-Only) Displays the name of the currently loaded Configuration (CFG file). If none is loaded, this field is blank.

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  : (Read-Only) When in
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  acquisition mode, this indicates the number of repeat iterations that have been completed.

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  : (Read-Only) For
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  /
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  acquisitions, this keeps track of the number of slices that have been acquired (in the current repeat iteration, if using
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  ), counting up to the
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  value set in the
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  window.

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  : (Read-Only) For
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  /
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  acquisitions, this keeps track of the number of frames that have been acquired (in the current repeat iteration, if using
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  ), counting up to the
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  value set in the
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  window.

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  : For
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  /
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  acquisitions, this sets the stem of the filename to be saved for the next or ongoing acquisition. The
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  is appended to the specified
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  to create the full filename, e.g. beadTest3.tif in the example shown.

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  : For
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  /
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  acquisitions, this sets the number to append to the specified
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  to create the full filename. This value is automatically incremented at the end of each acquisition (repeat iteration, if using
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  ). The value can be manually edited, to affect the number that will be appended for the next acquisition.

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  : This displays a value in seconds, that depends on the current state and acquisition mode:
  • During
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    and
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    acquisitions, this displays a count-up value, in seconds, measuring the time elapsed for the ongoing acquisition.
  • For
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    acquisitions with External Triggering (
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    ) enabled, a count-up value is displayed while waiting for the external trigger to arrive before beginning the acquisition (or next Repeat, if using
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    ).
  • During LOOP acquisitions, the behavior of
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    is described in LOOP Mode

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  : This initiates a Snapshot acquisition, which is a specially configured
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  acquisition to acquire and display an average of the number of Frames specified in the adjoining text control.
  This is useful for quickly visualizing the specimen/field-of-view in between configured
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  acquisitions without adjusting the current ScanImage _Configuration nor risking overexposure with a
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  acquisition.

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  : (CFG Value) This checkbox activates a Line Scan acquisition, forcing the amplitude of the scan in the slow scan dimension to be zero.

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  : This control toggles the display of the right half of the MAIN CONTROLS window.

Section B

This section consists of three components, from left to right:

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  : This checkbox determines whether Auto Save functionality is enabled for
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  /
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  mode, causing image data to be automatically saved to disk during the acquisition
  A running buffer of the most recently acquired frames is maintained in the
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  variable. The size of the running data buffer is specified by the
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  values in the
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  . A separate value is used depending on whether
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  is selected or not.

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  : (Read-Only) This string displays status information regarding the state of ScanImage.
  When the Status String specifies an error has occurred, it is recommended to look at the Matlab Command window to obtain additional information.

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  : (CFG Value) This toggle-button enables/disables External Triggering for
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  /
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  modes. It has no effect on FOCUS mode acquisition. If no external trigger is configured in the INI file, this button is disabled.

Section C

This section allows the user to begin a ScanImage image acquisition, using one of the 3 available acquisition modes – [FOCUS, GRAB, and LOOP].

Upon selecting one of the buttons, acquisition begins (or is armed to wait for an External Trigger), and the corresponding button changes to read

, while the others are hidden. Pressing

stops acquisition immediately.

Section D

There are three groups of controls in this section –

,

, and

– which affect the scan command generated by ScanImage during acquisition.
These controls can be adjusted while live imaging in FOCUS mode.
The

,

, and

values all comprise part of the current ScanImage Configuration – i.e. their values are captured whenever a CFG file is saved.

In addition, this section contains:

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  controls in this section allow the
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  ,
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  , and
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  values to be rapidly restored to preset reference values.
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  controls on a docked sub-window, containing controls to facilitate beam and scan alignment.

Rotate Controls

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  : (CFG Value) Specifies angle, in degrees, by which the scan field-of-view is rotated.
  At this time, scan rotation is not supported when Bidirectional Scanning is activated. The Rotate control is disabled in this circumstance.

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  : Resets the rotation value to 0 degrees.

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  : Activates a Graphical Interaction Tool allowing the user to select a line on the target image display window. The angle of the line updates the
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  value accordingly; the center of the line updates the
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  values accordingly.
  As the control's name suggests, this control facilitates the configuration of scans for Line Scanning operation. Note however, that the updated
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  and
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  values apply regardless of whether Line Scanning is active or not.
  Note that the length of the selected line has no effect.

Shift Controls

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  : (CFG Value) Specifies an offset, in optical degrees, to apply to the scan command signals in the Fast and Slow dimensions, shifting the field-of-view.

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  : The arrows allow the
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  values to be adjusted without entering a new value. The value is adjusted (incremented or decremented) by the amount specified (in optical degrees) in the two nearby text edit controls – one each for horizontal and vertical adjustments.

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  : Resets the shift values to 0 degrees

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  : Activates a Graphical Interaction Tool allowing the user to select a point on the target image display window. The location of this point updates the
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  values accordingly.

Zoom Controls

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  : (CFG Value) The 4 numbers represent the currently configured zoom factor and allow independent adjustment of the 1s, 10s, and 100s digit of that value. In additional, fractional zoom values can be specified with one decimal digit.
  • ScanImage simply divides the
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    values (specified in the
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    window) by the currently configured zoom factor, to determine the current scan amplitude.
  • The
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    digits appear with a yellow background when the current zoom factor is below the Constant @ Zoom >= value specified in the
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    window.

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  : Resets the currently configured {factor (and the Zoom Indicator) to 1, or to the
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  value specified in the
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  window.

Reset Controls

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  : By default, resets the
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  ,
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  , and
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  values to the values stored in the currently specified Configuration (CFG file). In other words, the unsaved CFG changes made by adjusting
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  ,
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  , and
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  are undone.
  If a set of
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  ,
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  , and
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  values are cached using
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  , then
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  restores those cached values instead.

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  : Caches the current
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  ,
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  , and
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  values so that subsequently pressing
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  will restore these values.
  Note that this does not save the current
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  ,
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  , and
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  values to the current Configuration (CFG file).

Align Controls

Section E

This section consist of controls to define/manage/load Regions of Interest (ROIs) within the scan's field-of-view. A Region of Interest consists of four items of information:

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   value pair
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   value
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4. Motor position (if motor is active)

Together these specify a square (or rhombus, if

is nonzero) subregion within the most recently scanned field-of-view that can be scanned (at higher rates or pixel density, if desired).

The selected Region(s) of Interest are graphically depicted in the ROI Display window, with the current ROI displayed in red.

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  : Activates a Graphical Interaction Tool allowing the user to select a square region on the target image display window. The currently configured
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  and
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  values are updated to reflect the size and center of the selected region.
  At this time, ScanImage does not support rectangular regions-of-interest, although the box drawn with the ROI tool can be rectangular. The rectangular region is converted to a square region upon capturing the
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  and
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  values.
  
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  : Restores the
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  ,
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  , and
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  values prevailing prior to the previous Region of Interest selection with the
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  tool.

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  : Captures the current
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  ,
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  , and
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  values as well as the current motor position (if motor is active) and stores values as a numbered ROI in the ROI Selection Menu.

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  : Removes the currently selected numbered ROI in the ROI Selection Menu from the list. Updates the currently selected numbered ROI value to a valid value (if any are left).

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  : Selection of numbered ROI value in dropdown menu updates currently configured
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  ,
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  , and
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  values to match those stored with numbered ROI. If motor is active, the X/Y/Z stage position(s) are also updated accordingly.
  The left/right arrows to right of ROI Selection Menu can also be used to select the next lower/higher numbered ROI value.
  
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Section F

This section contains 6 toggle buttons corresponding to the 6 Fast Configurations which can be defined in ScanImage. These correspond to ScanImage configurations (CFG Files), which can be loaded, or started, by pressing the single numbered button.

The

dialog documentation describes how Fast Configurations are set up. When the current ScanImage configuration corresponds to one of the current Fast Configurations, that button appears depressed.

See Enhanced Fast Configurations for notes about Fast Configurations introduced in ScanImage 3.7
When

option is enabled for a particular Fast Configuration in the

dialog, the corresponding button appears green in the MAIN CONTROLS panel
The tooltip for each Fast Configuration button contains the name of the CFG file saved as that particular Fast Configuration, so it is easy to identify the 6 Fast Configuration names.

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  : This toggle button shows/hides the
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  window, which is used to set the majority of values specifying the ScanImage Configuration.

Menus

File Menu

Settings Menu

View Menu