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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

ScanImage can be configured to collect a specified number of 2D image Frames, at each of a number of axial (Z) Slices. In Loop mode, these are repeated for a given number of Acqs (Acquisitions).

For Grab/Loop modes: number of Frames acquired/to-acquire at current Slice for the current Acq (if using LOOP)


For Grab/Loop modes: number of Slices acquired/to-acquire for the current Acq (if using LOOP)

For Fast Z Imaging, the number of Slices pertains to the current Volume (and Acq)

For Loop mode: the number of times to repeat an Acq of the specified number of Frames & Slices

For Loop mode: specifies time, in seconds, between the start of each Acq

For Focus/Grab modes: displays time, in seconds, since start of acquisition.

For Loop mode (self-triggered): displays countdown from specified Interval to start of next Acq

For Loop mode (external Start Triggering): displays time since last Acq was externally triggered.


Logging Controls

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. file_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 GRAB or LOOP mode Acq

Value can also be:


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.

(tick) File averaging capability is separate from the display Rolling Average specified in Image Controls

(info) File averaging implies data reduction: raw data is lost and file size is reduced

Specifies the number of frames to be saved to a single .tif file. Appends full filename to indicate the number of files associated with a set of frames, e.g. file_001_001.tif, file_001_002.tif if the frames from a single acquisition are saved to two separate files.

Sets and maintains the number of frames per file to the number of frames per acquisition.
Toggles on/off overwrite warning message. By default the acquisition counter will update based on the highest number detected on the end of file already located in the logging directory. There is nothing stopping users from changing this number to something lower which will overwrite data already present with the same base name and acquisition number. Enabling this warning will cause a dialog box to appear if you change the base name or acquisition # in such a way that you might overwrite data.

Acquisition Start Controls

ScanImage has 3 Acquisition Modes - FOCUS, GRAB, and LOOP.

The corresponding buttons start each mode, beginning or arming an acquisition, and the button changes to ABORT.
Pressing ABORT stops the mode and any ongoing acquisition.

FOCUS mode: Continuous acquisition without file-saving, until ABORT is pressed. Used for searching specimen, panning & focusing, etc.

During FOCUS, the following are disabled: file saving, external triggering, volume imaging, multi-ROI imaging.


GRAB mode: Start (or arm) a single acquisition.

LOOP mode: Start (or arm) a sequence of acquisitions (for up to the specified number of Acqs).

Globally enables/disable all external acquisition triggering signals for Grab/Loop modes (no effect on FOCUS mode).

(tick) The external acquisition triggering signals are configured in the Trigger Controls. If none is configured, this button is disabled.

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.

ScanField Parameters

The Zoom, Shift Fast/Slow, and Scan Angle Multiplier Fast/Slow controls specify the default ScanImage ScanField - a single two-dimensional area region of interest (ROI) for imaging.

If Multi-ROI (MROI) Imaging is enabled, these settings are ignored in favor of the configured mutiple 3D ROI/Stimulus Group Editor


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 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.

Shift corresponds to the fast (X) axial dimension.

Shift Slow corresponds to the slow (Y) axial dimension.

Specifies scan rotation angle Only functional with Linear Scanner. This value is in degrees.
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), changing button to PARK.

Scanner remains pointed to field center until PARK  is pressed.

(tick) Used for scanner alignment

(info) While scanner is pointed, beam power is adjusted to specified level and shutter is opened (if such hardware is configured in Machine Data File)

MROI & PhotoStim Launch

The Multiple Regions of Interest (MROI) and Photostimulation (Photostim) modes allow targeted laser scanning for imaging and stimulation within the scan volume, respectively

Launch ROI/Stimulus Group Editor for configuration of Multiple Regions of Interest (MROI) imaging.
Launch Photostim Controls for configuration of photostimulation scans.

Enable MROI imaging.


Launches the Integration Control window.

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 Menu

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.)
Machine Configuration...

Launch the ScanImage Machine Configuration Editor to edit machine configuration for the ScanImage system.

If new updates are applied and saved, ScanImage must be restarting for updated settings to take place.

Generate Support Report
Generate Support Report for a running ScanImage instance. This is useful for troubleshooting issues.
Reset DAQ Devices
Hardware reset of of DAQ devices. ScanImage will close and needs to be restarted.
Factory Reset ScanImageDeletes modified .mat class files and restores them to initial installation settings. ScanImage will close and needs to be restarted.
Exit ScanImageExits ScanImage and exits Matlab.
Exit MatlabExits ScanImage and exits Matlab.

MAIN CONTROLS Panel - Settings Menu

Beams...Launch the Beams Window.
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. 
Yoke WavesurferSet/Unset Yoke Wavesurfer function. 

MAIN CONTROLS Panel - View Menu

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
Status WindowLaunch and focuses on the Status Window.
Cycle ControlsLaunch the Cycle Controls window.
Alignment ControlsLaunch the Alignment Controls window.
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.
PMT ControlsLaunch the PMT Controls window.
Photostim ControlsLaunch the Photostimulation Controls window.
Integration ControlsLaunch the ROI Integration Control
Motion CorrectionLaunch the Motion Correction 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.