ScanImage® Changes

This page is a collection of changes for each major release of ScanImage®.


New Universal Features

  • Incrementally shift the FOV of the Mini2P (Mirrorcle MEMS) when zoomed in from the main window

  • Add reference coordinate space option for defining arbitrary stack planes relative to the range of the fastZ device (e.g., to facilitate using the Thorlabs liquid crystal analog fastZ device)

  • The volume flyback trajectory is now configurable for FastZ devices. This is good for any custom field curvature correction.

  • Add pixel and line clock for NI LinScan imaging systems

  • In Beam Controls, split beam blanking checkbox into X axis blanking and Y axis blanking checkboxes

New Premium Features

Device Support

  • Add support for Thorlabs liquid crystal analog fastZ device present in the Prelude and increasingly in Bergamo micrsoscopes

  • Add support for Newport CONEX-CC Controllers

  • Add support for Scientifica Motion8 Motor Controllers

  • Implied with Stage scanning - support is added for Zaber stream API for supported controllers.

Each of the above is supported in basic ScanImage, though stage-scanning as a feature is not.

GUI Tweaks

  • For dual imaging and photostimulation microscopes using vDAQ, heavily recommend sharing photostim output triggers with imaging scanners’ auxiliary inputs to timestamp stimulations in concurrently recorded TIFFs

  • The Thorlabs ECU2 now only adds as many devices to the configuration as are required for a given system

  • Widgets are now minimizeable and hideable

  • Photostim hotkeys now work immediately after toggling the enable hotkeys checkbox

  • Disable GUI elements that are not applicable or risky for use with the Mini2P

  • Sample based power box display in the ROI Group Editor shifts with motion detection estimates

  • Give an edit table and mouse actions for editing previously placed tiles in Tile View.

  • Arbitrary Z slices can now be removed for the ROI Group Editor projection axes by shift-clicking on the slice to remove. This is helpful for stacks with the Thorlabs liquid crystal analog fastZ.

Bug fixes

  • Optimize frame acquired callbacks to eliminate display and processing lag

  • Fix configuration errors when reinitializing μManager Cameras

  • Improved hardware detection and identification for Thorlabs PMT2100 devices.

  • Fix loading of TIFFs for motion correction reference. Allow 100 nm tolerance for matching reference to live image Zs.

MATLAB Axes Toolbox
  • Remove MATLAB axes toolbox from ScanImage® GUIs including widgets in new (2023a and up) MATLAB versions


New Universal Features

  • Motion Estimation

  • Averaged frames can now be used as a basis for image correlation

  • The rate of Motion Estimation can now be throttled by a configurable number of averaged frames

New Premium Features

  • Power Box sample correction can now be compensated using Motion Estimation

  • The SLM diffraction efficiency can now be defined by supplying a function instead of requiring a substage camera alignment

  • Retain sample phase with the laser clock between imaging sessions with new automated laser phase tracking for low repetition rate lasers on the High Speed vDAQ.

  • The High Speed vDAQ now has a specialized bitfile that supports laser repetition rates down to 62 kHz

Device Support

GUI Tweaks

  • Overall
    • Bound the Home key to raise all ScanImage® GUIs if one of the ScanImage® windows have focus.

    • Pressing Shift + Home now raises all ScanImage® GUIs and places them in the default arrangement

  • Beam Controls
    • Beams not paired with the currently selected imaging scanner will now be grayed out

    • Power/Z adjustment mode now defaults to Exponential rather than None

  • Channel controls
    • Save and apply colormaps with configuration files

  • Display Controls
    • Live histograms

    • No longer closes after new acquisitions are started

    • Can select the channel, Z, and ROI of the image

  • ROI Group Editor
    • SLM Photostimulation

    • Now shows stimulations in the projection view outside of SLM point editing mode

    • Allow dragging all points at once

    • Points can now be copied from the projection view

    • Context Images and Live Images Z now reliably displays their true Z position in Sample Coordinates

    • Page Up and Page Down can now be used to scroll through ROIs

  • Motor Controls
    • Changes tilt button color to green if an objective tilt has been configured

  • Photostimulation Controls
    • Allow selection of photostimulation-enabled scanners from the window without having to restart ScanImage® first

    • Buttons/text boxes/pulldowns are now properly disabled depending on GUI state

  • Scanfield Display controls
    • Added autofill button to populate scanfields with all ROI and z combinations

    • Fixed resize behavior

  • SLM Alignment window
    • Added reset buttons for SLM spatial alignments

  • Signal Conditioning controls
    • The Apply Clock Settings button now remains green after locking to an external clock so long as the PLL is maintained. It will now turn pink if the PLL is disrupted.

  • RggScan
    • The Acquisition Engine number can now be configured in the configuration page

  • Stack Controls
    • Promoted to a default GUI

    • Added a new stack-enabled checkbox

Bug Fixes

  • Eliminated y-axis scrolling when acquiring Fast Z stacks of many slices/frames

  • Fixed file-incrementing issue when looping with a slow Z stack

  • Fixed invalid error when scanning Z stacks that only partially intersect ROIs outside of the first slice

  • ROI Group Editor’s ‘draw array’ checkbox is now available for RGG scanners

  • ROI Group Editor, Signal Conditioning Controls, Waveform Controls, and Channel Windows can now be properly raised by their corresponding button or menu item

  • The MCM5000 mirrors’ starting positions now account for position inversions set by the user


New premium features:

  • Sample tracking Power Boxes

  • Import Tile Manager images into the ROI Group Editor

  • Multiple Regions of Interest scanning support for polygonal scanning

  • VTK viewer can render a tapered, irregularly shaped ROI

Universal new features:

  • SI Coordinate System management for multiple objectives

  • Externally Triggerable Scripts

  • Support for Meadowlark Optics 1024 x 1024 SLM

  • Improved implementation for Thorlabs MCM6000

  • GUIs Recoloring implementation to save, load, and apply coloring to windows of ScanImage . Useful for dual acquisition engines.

Bug Fixes:

  • Improvement to sample clock synchronization on standard speed vDAQs

  • Improved fastZ stack with step waveform in RggScan

  • Improvements to the Data Recorder

  • Fix Photostim ROI Group Optimization button

  • NI LinScan Live Image from ROI Group Editor now pulls from correct channels

  • Pan and Zoom in Y while polygonal scanning



  • PMT widget coloring based on (filter) wavelength

  • Beam power display in mW added to beam controls GUI (if Power Output [W] configured in beams device)

  • PMT2100 can load configured gain, bandwidth, and offset settings

  • Can apply pmt settings with enter/return key press from pmt settings dialog.

Bug Fixes:

  • Configuration and user settings file saving and loading

  • Display frame averaging applied to ROI Group editor context images.

  • Double/Multiple click of PMT settings dialog will spawn one just one window

  • Roi Group Editor stack context images are now set at Zs set at beginning of acquisition

  • Live image Z is now tracked to the current sample position during focus acquisition

  • If rotation of a scanfield is applied between acquisitions, the ROI Group Editor live image is no longer improperly rotated on first volume of stack

  • Motorized halfwave plate device can accept angles less than zero or greater than 360, and update power fraction correctly for rotation stages that are not the first axis of a motor controller.

  • Adding beams to configuration while ScanImage is running will no longer break power boxes



  • Zaber stage display dragging control

  • Waveform Generator

  • Waveform Recorder

  • Polygonal scanning implemented for both vDAQ and NI systems

  • QLM License manager

Bug Fixes

  • Saturation protection on vDAQ acquisition pipeline

  • Laser gating window bound correction

  • Fixes to power boxes for better support of multiple beams


New Features

  • 3D visualization of stack data

Hardware Improvements

  • Galvo control: Add configurable voltage offset.

  • Meadowlark SLM 512×512 now end-of-life

  • Meadowlark SLM 1920 Linked to newest Meadowlark driver

  • Added Support for NI DAQmx 21.3.x

  • Stack controls: Modified behavior of actuator lag to only apply time shift control signal.

  • Shutters: Add safeguard option to prevent opening when pointing beams.

  • Arbitrary line scanning: Improved data processing performance.

  • vDAQ: Breakout display now visualizes IO pin values.

  • Sutter MP285-A: Velocity parameter now settable

Bug fixes

  • Fix arbitrary line scanning with multiple FastZ actuators

  • NI FlexRIO: Fix pixel value overflow when enabling laser trigger mask.

  • Beams, FastZ: fix controls when adding LUT values.

  • NI hardware: fix overflow case when exceeding 65,536 grabs per acquisition.


New Features

Hardware support


  • Faster startup time.

  • Zaber stages: drag live image to move stages. Example

  • Zaber stages: add support for lockstep

  • Channel histogram: add statistics (mean, std)

  • New Beams backend and GUI

  • Add advanced configuration settings for beam calibration

  • Galvos: allow to configure offset voltage

Bug fixes

  • Fix Photostim triggering

  • vDAQ + linear scanning: setting log average to > 1 corrupts saved Tiff files

  • Stability improvements

Known issues

  • vDAQ: photostim does not control piezo objective positioner

  • NI FlexRIO: laser trigger + sample masking returns incorrect data


ScanImage® Basic

  • Fix FastZ Optimization


  • Fix rare vDAQ init failure

  • Fix simulated vDAQ display

  • Fix looped slow stacks


ScanImage® Basic

  • Waveform test fixes

Bug Fixes

  • vDAQ setting input fixes

  • Slow stack loop fixes

  • Thorlab Kineses deinit fixes



  • Fix ADC init issue with daughter board ADCs


  • Fix overriding valid config in config editor

  • Fix missing file error in Newport folder.


  • Warn if floating control line opens digital shutter


PI Piezo Driver Changes

  • Default to closed loop.

vDAQ Fixes

  • Signal conditioning GUI

  • Uniform sampling with Resonant Scan

Thorlabs Kinesis Fixes

  • Benchtop motor controller

Misc Fixes

  • Remove Visual C++ runtime

  • Enforce Beam power limits

  • Motor movement after pointing scanners


  • Large stack start performance


High speed vDAQ support

  • Photon counting

  • Time Multiplexed Acquisition

Motor system

  • Software limits for Z motion

  • New driver for Thorlabs Kinesis motors

  • New Zaber stage driver (requires Matlab 2017b or later)

  • New Scientifica stage driver

  • New Marzhauser Tango driver


  • uManager 2.0 support

SLM photostimulation

  • improved workflow for SLM alignment

NOTE: when upgrading from an older ScanImage® version, the SLM alignment needs to be redone.


  • Fix triggering in Meadowlark SLMs

  • vDAQ: allow configuration of clock outputs

  • vDAQ: fix I2C configuration

  • vDAQ: improve performance on AMD processors

  • RggScan: fix saving/loading of alignment matrix

  • PicoQuant FLIM: fix stack acquisition

  • LinScan: crashes in Matlab 2020 when acquiring with NI RIO hardware

System requirements

  • Increase minimum supported Matlab version to R2017a


Enhanced user experience

  • New configuration editor

  • Apply configuration changes without restart

  • Breakout panel visualization for vDAQ

  • Device widgets

  • New beams system

  • USB connection for PI Piezos

National Instruments

  • NI DAQmx 20.1 support


  • LinScan + 6110: Fix synchronization issue

Compatibility Note

  • Machine Data Files and Configuration files

  • from SI versions before 2020 cannot be reused



  • NEW Support vDAQ firmware A1

  • Mirrorcle support

  • Improved DMA transfer

National Instruments

  • NI DAQmx 19.6 support


  • LinScan logging issues

  • Three photon feature bugs

  • Bounded stacks beam depth adjustment bug

  • Scan path alignment issues

  • SLM + Galvo alignment routine issues

Meadowlark SLM

  • Enable triggering support


  • vDAQ Support

  • Live Motor Updates

  • New Stack Controls

  • 3D Shot workflow



  • Thorlabs BScope microscope

  • SLM wavefront correction file

  • ‘smooth’ SLM LUT calibration



  • Various bug fixes

  • Improvements to Camera View GUI.




  • Motion Correction for Z

  • Improved Galvo Waveforms

  • Eliminated FastZ Volume Period Adjustment

  • Custom Header Properties

  • Data Overwrite Warning

  • Various fixes and overhauls

Bug Fixes

  • PZAdjust

  • Tile Display

  • Rolling Stripe Data

  • FastZ

  • Pure Analog Devices



  • SLM & Galvo/Galvo targeted Photostimulation


  • 2P Mesoscope

  • multi-ROI (mROI) imaging

  • FastZ step mode

  • Motion Correction

  • Online Analysis

  • Arbitrary Line Scanning


  • Optimization and caching of waveform AO’s