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)
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![]() | 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
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![]() | 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.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 GRAB or LOOP mode Acq Value can also be:
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![]() | 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.
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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.
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![]() | 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).
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![]() | Displays the current state of ScanImage. Can be one of the following:
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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 Regions of Interest/Stimulus 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. 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.![]() ![]() ![]() |
![]() | 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.
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MROI & PhotoStim Launch (SI2015 Only)
The Multiple Regions of Interest (MROI) and Photostimulation (Photostim) modes allow targeted laser scanning for imaging and stimulation within the scan volume, respectively
![]() | Launch Regions of Interest/Stimulus Editor for configuration of Multiple Regions of Interest (MROI) imaging. |
![]() | Launch Photostim Controls for configuration of photostimulation scans. |
![]() | Enable MROI imaging, for Grab/Loop modes.
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![]() | Enable MROI imaging, for Focus mode. |
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. |
![]() | 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.) |
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 ScanImage | Exits ScanImage and exits Matlab. |
Exit Matlab | Exits 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. |

MAIN CONTROLS Panel - View Menu
Raise Windows | Moves all currently open ScanImage windows to the foreground. |
Show All Windows | Launch all ScanImage windows (including those that have not been opened) and moves them to the foreground |
Alignment Controls | Launch the Alignment Controls window. (SI2015 Only) |
FastZ Controls | Launch the Fast Z Controls window. |
Image Controls | Launch the Image Controls window. |
Motor Controls | Launch the Motor Controls window. |
Photostim Controls | Launch the Photostim Controls window. (SI2015 Only) |
Power Controls | Launch the Power Controls window. |
Channel 1 Display | Launch the Channel 1 Display window. |
Channel 2 Display | Launch the Channel 2 Display window. |
Channel 3 Display | Launch the Channel 3 Display window. |
Channel 4 Display | Launch the Channel 4 Display window. |
Channel Merge Display | Launch the Channel Merge Display window. |