The most advanced software for controlling laser scanning microscopes. Don't let the microscope control you!
MBF Bioscience > ScanImage®

Product Overview

Don’t let the microscope control you! ScanImage is a software package for controlling multiphoton and laser scanning microscopes. It enables advanced techniques such as time multiplexed acquisition and single photon counting. ScanImage uses the powerful vDAQ hardware for controlling all aspects of the microscope. ScanImage runs on custom-built microscopes and on commercial microscopes from Scientifica, Sutter Instruments, Prospective Instruments, and Thorlabs.

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Key Benefits

ScanImage software is the professional’s tool of choice for controlling multi-photon laser scanning microscopes. Enabling cutting-edge microscopy solutions for more than 2 decade, it has been cited in more than 900 research papers. ScanImage can be used to control 2-photon and 3-photon microscopes and laser scanning confocals using techniques such as, linear scanning, resonant scanning, photostimulation, holography, and has advanced techniques such as time correlated single photon counting and time multiplexed acquisition. Using MATLAB based accessible source code, it can be customized and adapted by the microscope user to enable new workflows. The rich scripting API allows users to fully automate experiment workflows. ScanImage is supported by a team of engineers who work with leading microscopy experts and commercial entities to ensure the latest techniques and hardware are incorporated in its regular software updates.

Recommended Hardware Requirements
64-bit Windows 10 or 11 operating system
16 GB memory
vDAQ for microscope control

Light Beads Microscopy: A Breakthrough in Volumetric in vivo Brain Imaging
>>Learn More

Mini2P miniature microscope and ScanImage
>>Learn More

NYU scientists use ScanImage to monitor dopamine-induced brain activity in a model of Parkinson’s disease
>>Learn More

In Vivo Two-Photon Synaptic Imaging with ScanImage — New Findings Challenge the Hebbian Theory of Plasticity
>>Learn More

ScanImage Enables Cutting Edge Visual Cortex Research
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Visit our blog to read more case studies

Download ScanImage product sheet here.


Released December 2023

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

  • Introduce stage scanning for mesoscale image tiling using an XY stage to scan perpendicular to the resonant axis.

Visit the ScanImage changelog to see all of the changes in this version

Compare ScanImage Versions

Feature Description

ScanImage BASIC


Resonant-Galvo and Galvo-Galvo Frame Scanning
Synchronization to laser clock (vDAQ)
Beam control and selective power delivery via power boxes
Volume acquisition with motorized stages or fast-focusing devices (ETL, Piezo, etc)
Scriptability in Matlab, extensibility via user functions
ScanImage coordinate system management for multiple objectives
Externally triggerable scripts
Big Tiff file creation
FastZ-actuator tuning & Independent Z-control for multiple scanners
Live histogram for imaging channels
Custom power depth adjustment profiles
Integration with the electrophysiology package WaveSurfer
Offline data viewer, Online 3D Motion Correction & Oscilloscope Mode for Noise Analysis
Live motor position update in GUI (for selected stages)
New resource architecture with device widgets
Beam modulation with motorized half-wave plates
Support for vDAQ & high-speed vDAQ
Actively developed and maintained & includes one year of technical support
Custom waveform generator (vDAQ only)
Ancillary signal recorder(vDAQ only)
MCM-6000 redbox support
Galil DMC-4040 stage support
Sample-tracking power boxes
Import tile manager images into the ROI group editor
Low rep-rate laser support
Polygonal scanner support
Synchronization with PicoQuant FLIM Systems
Multiple region of interest (mROI) scanning
Online analysis (ROI Integration)
Perspective alignment between multiple scanner
Alignment of scanners and stage
Simultaneous imaging and photo stimulation
Arbitrary line scanning using two galvos
Command waveform optimization
Support for 2P mesoscope & 3- photon imaging
SLM support for targeted photostimulation
Acquistion gating for low rep rate Lasers
Camera support for widefield alignment
SLM diffraction efficiency calibration
ScanImage remote control
Tiling Tool for mosaic imaging and FOV relocation
3D Shot holographic targeting workflow
Support for Scientifica HoloStim-3D

Who Is Using ScanImage?

ScanImage is used across the globe by the most prestigious laboratories. 

News About ScanImage

Cited in Peer Reviewed Scientific Publications

ScanImage’s utility is underscored by the number of references it receives in the worlds most important scientific publications. See examples below: 

Frequently Asked Questions (FAQ)

Which microscopes can ScanImage control?

ScanImage can control custom built and commercial microscopes from Scientifica, Sutter Instruments, Prospective Instruments and Thorlabs. ScanImage uses the powerful vDAQ data acquisition hardware to control all aspects of the microscope. For legacy systems, data acquisition systems from National Instruments are also supported.

Is ScanImage customizable?

ScanImage is written in Matlab and is source accessible. ScanImage is fully scriptable and automatable in Matlab, and is extensible through user functions. Our expert engineers are also available to perform custom software development as a service.

Which microscope hardware does ScanImage control?

ScanImage supports numerous devices, including: resonant and linear scanners, galvos, beam modulators, motor controllers, fast focus, shutters, cameras, and spatial light modulators. A complete list of supported microscope hardware can be found in the ScanImage documentation

Does ScanImage require a Matlab license?

ScanImage requires Matlab 2017a or later. A Matlab license needs to be obtained separately.

Does ScanImage support the Mini2P?

The Mini2P was designed for use with ScanImage software and the vDAQ data acquisition card. Weighing <3g, the Mini2P enables 2-photon microscopy of freely moving mice. It can image hundreds of neurons in a volume, with temporal resolution suitable for GCaMP6-labeled mice.


For more information, see the research article that introduces the Mini2P, Large-scale two-photon calcium imaging in freely moving mice and the Technology Feature on the Mini2P in NatureThumb-sized microscope captures images deep inside the brains of active animals.


To use the Mini2P with ScanImage, see the build protocol and software installation documents included in the MINI2P toolbox GitHub repository.

Does ScanImage support 3P microscopy?

ScanImage offers tools to optimize the SNR for 3P acquisitions. Since 3P lasers typically have a lower repetition rate, ScanImage can mask out the noise signal between laser pulses.

How does ScanImage integrate with my experiment?

ScanImage offers powerful triggering schemes that allow to precisely align the image acquisition with a behavioral experiment.

What is the maximum acquisition speed that ScanImage supports and the maximum duration of an image acquisition?

ScanImage supports resonant scanners with line rates of up to 100kHz. The vDAQ acquires data with a sample rate of up to 125MHz. The high speed add-on for the vDAQ acquires data with up to 2.7GHz. vDAQ allows synchronizing the digital data conversion to the laser to enable techniques such as time correlated photon counting and time multiplexed acquisition.

ScanImage supports acquisitions of arbitrary durations. The only practical limit to the acquisition length is the size of the hard drive.



Robust Professional Support

As part of our Premium Support services, our ScanImage® software engineers can assist you troubleshooting computer imaging issues.


We’ve also developed a host of additional support services, including:


  • Forums
    We have over 25 active forums where open discussions take place.
    >> Learn More
  • On-Site/Training
    We’ve conducted over 750 remote software installations.
    >> Learn More
  • Webinars
    We’ve created over 55 webinars that demonstrate our products & their uses.
    >> Learn More

Request an Expert Demonstration

We offer both a free demonstration and a free trial copy of ScanImage. During your demonstration you’ll also have the opportunity to talk to us about your hardware, software, or experimental design questions with our team of Ph.D. neuroscientists and experts in microscopy, neuron tracing, and image processing.

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Recorded Webinars and Videos

ScanImage Workshop Talk with Director, Bruce Kimmel

Webinar: Accelerating Neuroscience Research with ScanImage with Dr. Bruce Kimmel

Workshop: MINI2P and ScanImage