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This documentation is for a legacy ScanImage version. The current documentation is ScanImage 2019.

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User Settings / Config

Displays name of currently loaded User Settings (USR) file. If none loaded, field is blank.

Launch dialog to select new USR file to load

Save current user settings to currently loaded USR file. (Use File >> Save User Settings As... from menubar to save current user settings to a new USR file)

Displays name of currently loaded Configuration (CFG) file. If none loaded, field is blank.

Launch dialog to select new CFG file to load.

Save current configuration to currently loaded Configuration (CFG) file. (Use File >> Save Configuration As... from menubar to save current configuration to a new CFG file).

Acquisition Parameters

For more information on the relationship between Frames, Slices, and Acqs, please consult the Imaging Guide.

For GRAB/LOOP acquisitions, number of frames acquired/to-acquire at current slice - for the current Repeat (if using LOOP).
For GRAB/LOOP acquisitions, number of slices acquired/to-acquire - for the current Repeat (if using LOOP) and for the current volume (if using FastZ imaging).
For LOOP acquisitions, number of times to repeat acquisition of specified # Frames & # Slices.
For LOOP acquisitions, specifies time, in seconds, between start (trigger) of each Repeat. Value is ignored when external triggering is used.
For FOCUS/GRAB acquisitions, displays time, in seconds, since start of acquisition. For LOOP acquisitions self-triggered by ScanImage, displays countdown from specified Repeat Period to start of next Repeat. For LOOP acquisitions with external triggering, displays time since last Repeat was externally triggered.


Sets stem of filename to be saved for next or ongoing GRAB/LOOP acquisition. The Acquisition# is appended to specified Basename to create the full filename, e.g.test0515_001.tif in example shown.
Sets number to append to specified Basename  to create the full filename. Value is automatically incremented at end of each acquisition (or Repeat) when using LOOP. Value can be manually edited as well. By default, value is incremented
Increment Acquisition# by 1.
Launch dialog to select save directory to which files are saved.
Determines whether disk logging functionality is enabled during GRAB/LOOP acquisitions.
Specifies # of frames to average together before appending single (averaged) frame to current log file. Value > 1 implies file averaging is enabled. Note this implies data reduction: file size is reduced and raw data is lost. File averaging capability is separate from the display Rolling Average specified in Image Controls.

Acquisition Control

Enables/disables external triggering for GRAB/LOOP acquisitions (no effect on FOCUS acquisitions).

External Triggering


This button is only available when external start trigger is configured in Triggers window. This button cannot be selected unless an external trigger is defined. 

Start image acquisition in one of the 3 supported ScanImage modes, described below. Acquisition begins (or is armed to wait for an external trigger) and corresponding button changes to ABORT. Pressing ABORT stops the ongoing acquisition.

Continuous imaging until ABORT is pressed (or focusDuration is reached, as specified in User Settings without file-saving, external-triggering, etc. Used for searching specimen, panning & focusing, etc.
Start (or arm) single acquisition, with file-logging and/or external triggering if enabled, for specified #Frames and #Slices, and specified #Volumes in Fast Z Controls if FastZ imaging is enabled.
Start (or arm) sequence of GRAB acquisitions, termed Repeats, either for specified #Repeats if using self-triggering or for each supplied external start trigger until ABORT. Also, LOOP mode is used for continuous multi-trigger acquisition modes allowed with next triggering, configured in the Triggers window.

Displays the current state of ScanImage. Can be one of the following:

  • Idle: Not currently in any acquisition mode, waiting for user.
  • Grab: Currently executing a single Grab acquisition.
  • Loop: Currently executing a Grab acquisition as part of a looped sequence of Grab acquisitions.
  • Loop_Wait: Currently in "Loop mode", not currently grabbing frames, but waiting for a trigger to start the next Grab acquisition.
  • Point: Currently in "Point mode", with the pockels cell on (if configured), shutters on (if configured), and the Y-axis galvanometer pointed to the center of its range.

ROI Scan Parameters

The Zoom, Shift Fast/Slow, and Scan Angle Multiplier Fast/Slow controls specify the ROI Scan Parameters in ScanImage parlance - they affect the scan generated by ScanImage during acquisition.


Each of these control values are part of the current ScanImage Configuration, i.e. these values are saved/loaded to/from CFG files.

Specifies factor by which scan angular range is reduced, for both fast & slow dimensions. Adjusting zoom factor will set value to nearest allowed zoom increment.
Resets Zoom value to ROOT ROI value of 1.0 - i.e. to full scan angular range supported by scanning hardware.
Specifies scan angle offset in specified scan dimension; this effectively shifts scan pattern laterally in the microscope's plane of focus. This value is in degrees. Adjustment is only allowed in slow scan dimension.
Displays the reduction factor for scan angle (lateral scan extent in microscope focal plane) in specified scan dimension, i.e. displays the aspect ratio of the scanned area.
(tick) A Scan Angle Multiplier Slow value = 1 specifies a square area scan
(tick) A Scan Angle Multiplier Slow value ≠ 1 specifies a rectangular area scan
(tick) A Scan Angle Multiplier Slow value = 0 specifies a line scan
Toggle button switching Scan Angle Multiplier Slow between 0 (line scan mode) and the current Base ROI value.
Points scanner at center of field-of-view (following specified Shift values). Can be used for scanner alignment purposes. Button renamed to PARK while scanner is pointed to field center. Scanner remains pointed until PARK  is pressed.
(tick) While scanner is pointed, beam power is adjusted to specified level and shutter is opened (if such hardware is configured in Machine Data File)

Fast Configuration Buttons

The Fast Configurations window, from File >> Settings >> Fast Configurations..., allows specified CFG files to be associated with buttons on Main Controls (and keyboard shortcuts) for one click (press) access to frequently-used configurations.

Load specified Fast Configuration, i.e. settings of CFG file specified in Fast Configurations window.

Fast Config Buttons


These buttons will not be active unless they have been associated with a config file using the Fast Configurations window.

By default, the F1-F6 keys correspond to Fast Configuration 1-6 (respectively). The Fast Configurations window has an option which changes the fast configuration keys to Ctrl-<F1-F6>.

Toggle on/off display of the Configuration Controls window

MAIN CONTROLS Panel - File Pulldown

Load User Settings...Displays name of currently loaded User Settings (USR) file. If none loaded, field is blank.
Save User Settings...Save current user settings to currently loaded USR file.
Save User Settings As...Launch dialog to select new USR file to save.
Load Configuration...Displays name of currently loaded Configuration (CFG) file. If none loaded, field is blank.
Save Configuration...Save current configuration to currently loaded Configuration (CFG) file.
Save Configuration As...Launch dialog to save current configuration to a new CFG file).
Fast Configurations...Launch the Fast Configurations window. 
Set Save Path...Launch dialog to select save directory to which files are saved. (Identical in function to the DIR... button in the main window.)
Save Last Acquisition As...Launch dialog to save images from currently displayed channels to TIF format. Only actual image data is saved - the merge window and any tiled images are not saved.
Exit ScanImageExits ScanImage and exits Matlab.
Exit MatlabExits ScanImage and exits Matlab.

MAIN CONTROLS Panel - Settings Pulldown

Triggers...Launch the Trigger Window.
Channels...Launch the Channels Window.
Fast Configurations...Launch the Fast Configurations window. 
User Functions...Launch the User Functions window. 
User Settings...Launch the User Settings window. 

MAIN CONTROLS Panel - View Pulldown

Raise WindowsMoves all currently open ScanImage windows to the foreground.
Show All WindowsLaunch all ScanImage windows (including those that have not been opened) and moves them to the foreground
Image ControlsLaunch the Image Controls Window.
Power ControlsLaunch the Power Controls Window.
Motor ControlsLaunch the Motor Controls Window.
FastZ ControlsLaunch the Fast Z Controls Window.
Channel 1 DisplayLaunch the Channel 1 Display window.
Channel 2 DisplayLaunch the Channel 2 Display window.
Channel 3 DisplayLaunch the Channel 3 Display window.
Channel 4 DisplayLaunch the Channel 4 Display window.
Channel Merge DisplayLaunch the Channel Merge Display window.