ScanImage® Changes

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


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