Don’t let the microscope control you! ScanImage is a software package for controlling custom built or commercially available multiphoton microscopes. It is packed with a multitude of features beyond planar and stack acquisition to satisfy a plethora of experimental needs, and is easily modified to adapt to new needs. Its premium features enable advanced techniques which puts conventional and unconventional microscopes alike on the cutting edge of microscopy.
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 decades, it has been cited in more than 14,00 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 11 operating system |
| CPU>3GHz |
| 16 GB memory |
| vDAQ for microscope control |
Download ScanImage brochure here.
ScanImage® 2026.1.0
Released: July 2026
New Features & Enhancements
SLM Photostimulation Returns
SLM photostimulation has been completely rebuilt around the viewport interface introduced in ScanImage® 2026.0.0, bringing pattern editing, hologram generation, and system alignment into a single, intuitive workspace.
Highlights include:
Mini vDAQ™ Support for Mini2P
ScanImage® 2026.1.0 adds support for the new Mini vDAQ™, designed specifically for the standard Mini2P miniscope. Dedicated hardware templates and built-in distortion correction make setup faster and easier.
More Flexible Data Logging
Gain greater control over how imaging data is saved with expanded logging options:
Interactive Waveform Generator
Create and edit analog output waveforms directly from the Auxiliary panel using the new integrated waveform editor.
The updated waveform generator also simplifies the creation of synchronized TTL pulses, making it easier to design complex experimental protocols.
For a complete list of new features, enhancements, bug fixes, and improvements, visit the ScanImage Changelog.
ScanImage’s Tiling tool extends the microscope’s field of view by sequentially moving and scanning the sample. ScanImage controls the microscope stage to automatically move to different locations in the sample. The tiling tool can be combined with a stack acquisition to produce volumetric montages.
In a full field of view raster scan, acquisition time is spent in regions that might not provide any insightful data. To get around this limitation, ScanImage’s multiple region of interest scanning feature selectively scans small patches in the sample. This increases the frame rate and the spatial resolution of the collected data. An example using this technique is the 2p-RAM mesoscope developed in the Svoboda lab at the Janelia research campus.
ScanImage’s Photostimulation workflow enables selective photoactivation of a region in the brain during a simultaneous image acquisition. Stimulation trajectories can be selected from a predefined library, or user customized. A photostimulation experiment consists of a predefined sequence of stimulation targets, which can be precisely synchronized to the image acquisition and/or a behavioral experiment with hardware triggers.
ScanImage works with the vDAQ’s clocking feature to synchronize acquisition to the laser clock so there is a fixed number of samples per laser pulse. With this, subranges of samples between laser pulses can be separated into multiple virtual channels. This technique can be used to ignore sample ranges outside of the fluorescence lifetime (3P imaging), or it can be used to isolate fluorescence events occurring between laser pulses (Light Beads Microscopy).
Resonant raster scanning typically achieves frame rates of ~30FPS, but can be an inflexible way to image. Arbitrary line scanning uses galvanometer scanners to allow any path you prefer to scan. Depending on the geometry and overall length of the scan line, line rates of up to 2kHz are achievable, especially when used in combination with the waveform optimization feature. ScanImage provides a convenient graphical tool to define, visualize, and scan complex trajectories.
ScanImage is capable of both continuously detecting and correcting XYZ sample motion from live image data with respect to a reference plane or volume. Corrections can be made via combination of galvo, motorized stage, or fast Z scanning devices. Estimations can be made from planar, stack, and/or rapid multi-region scans.
Detected motion (with or without correction) can be put to further use by:
Utilizing a camera in ScanImage can aid in the previewing of a sample and enhance the process of 2P scanning. Although the optical sectioning ability of 2P microscopy can be advantageous, it can also pose a challenge in locating the precise depth of the sample to scan. If the camera is parfocal with the scanner, ScanImage can provide a live widefield camera view which can aid in identifying the plane of interest with greater ease.
Beyond finding the appropriate scanning depth, a camera can further be used to plan acquisition or stimulation within the field of view. Premium ScanImage incorporates alignment tools which help register the camera image to the scanned image. This enables you to draw the area(s) to be scanned over top of the particular features of the sample as they are depicted from the live camera feed. Other supported cameras are listed here.
vDAQ is an all-in-one data acquisition platform to control all aspects of a laser scanning microscope. It controls scanners, beam modulators, shutters, photodetectors, fast focusing devices and much more. The simplified breakout box greatly reduces the wiring complexity of the microscope compared to traditional data acquisition solution. Its clocking features enable synchronization to the laser clock for advanced features such as time correlated acquisition. vDAQ is powered by a field upgradable FPGA to future proof your microscope.
| Category | Feature Description | ScanImage BASIC | ScanImage PREMIUM |
|---|---|---|---|
| Actively developed and maintained & includes one year of technical support | ✔ | ✔ | |
| Scanning | Resonant-Galvo and Galvo-Galvo Frame Scanning | ✔ | ✔ |
| Polygonal scanner support | ✔ | ✔ | |
| Beam control and selective power delivery via FOV-bound power boxes | ✔ | ✔ | |
| Beam modulation with motorized half-wave plates | ✔ | ✔ | |
| Custom power depth adjustment profiles | ✔ | ✔ | |
| Volume acquisition with motorized stages or fast-focusing devices(ETL, Piezo, etc) | ✔ | ✔ | |
| FastZ-actuator tuning & Independent Z-control for multiple scanners | ✔ | ✔ | |
| Live motor position update in GUI (for selected stages) | ✔ | ✔ | |
| Multiple region of interest (mROI) scanning | ✘ | ✔ | |
| Simultaneous imaging and photostimulation | ✘ | ✔ | |
| Arbitrary line scanning using two galvos | ✘ | ✔ | |
| Command waveform optimization | ✘ | ✔ | |
| Tiling Tool for mosaic imaging and FOV relocation | ✘ | ✔ | |
| Sample-tracking power boxes | ✘ | ✔ | |
| New! Global Curvature Correction GUI | ✘ | ✔ | |
| Software Features | Big Tiff file creation | ✔ | ✔ |
| Scriptability in Matlab, extensibility via user functions | ✔ | ✔ | |
| Externally triggerable scripts | ✔ | ✔ | |
| Online 3D Motion Correction & Oscilloscope Mode for Noise Analysis | ✔ | ✔ | |
| Online analysis (ROI Integration) | ✘ | ✔ | |
| ScanImage remote control | ✘ | ✔ | |
| Configuration, Alignment, and Characterization | Resource store architecture with device widgets | ✔ | ✔ |
| Support for vDAQ & high-speed vDAQ | ✔ | ✔ | |
| ScanImage coordinate system management for multiple objectives | ✔ | ✔ | |
| Alignment of scanners and stage | ✔ | ✔ | |
| Perspective alignment between multiple scanner | ✘ | ✔ | |
| SLM diffraction efficiency calibration | ✘ | ✔ | |
| 3D Shot holographic targeting workflow | ✘ | ✔ | |
| Display | Live histogram for imaging channels | ✔ | ✔ |
| Offline data viewer | ✔ | ✔ | |
| Synchronization | Custom waveform generator (vDAQ only) | ✔ | ✔ |
| Synchronization to laser clock (vDAQ) | ✔ | ✔ | |
| Ancillary signal recorder (vDAQ only) | ✔ | ✔ | |
| Auxiliary Timestamp Recording to TIFF | ✘ | ✔ | |
| Timestamped I2C Data Recording to TIFF | ✘ | ✔ | |
| Acquisition gating for low rep rate Lasers | ✘ | ✔ | |
| Synchronization with PicoQuant FLIM Systems | ✘ | ✔ | |
| Temporal Demultiplexing of signals (vDAQ only) | ✘ | ✔ | |
| Recommended Version by Microscope | Galvanometers only Microscope (Make use of Arbitrary Line Scanning, Photostimulation, and Multiple Regions of Interest Scanning) | ✔ | ✔ |
| Mini2P | ✔ | ✔ | |
| Mesoscope (for MROI imaging) | ✘ | ✔ | |
| 3P (for gating signal) | ✘ | ✔ | |
| SLM mediated Optogenetics (for Photostim) | ✘ | ✔ | |
| Camera support for widefield alignment | ✘ | ✔ | |
| Light Beads | ✘ | ✔ |
This study presents a live brain-slice model that enables high-resolution imaging and quantitative analysis of blood–brain barrier permeability and transporter function at the level of individual capillaries.
A model-guided two-photon optical design enables high-resolution retinal imaging and functional calcium recordings without the need for adaptive optics.
A multiphoton imaging approach using infrared excitation enables non-invasive, deep-tissue visualization with preserved resolution in highly scattering tissues.
Multiphoton excitation at 1700 nm enables high-resolution visualization of lymphatic structure and dynamics in strongly scattering skin tissue.
Chronic two-photon imaging reveals that loss of stable hippocampal place cells underlies memory impairment following microvascular injury.
Two-photon–guided electrophysiology reveals that inhibitory synaptic activity increases with song learning and suppresses sensory input to HVC premotor neurons.
Cell-type-specific calcium imaging revealed distinct and spatially organized activity patterns in the dorsal pons across sleep–wake states. Glutamatergic neurons were predominantly active during REM sleep, while GABAergic neurons were biased toward wakefulness, highlighting specialized subpopulations involved in sleep regulation.
A holographic two-photon imaging system enables simultaneous multi-plane recording of neuronal activity across cortical layers with single-cell precision. Multiplexed excitation and synchronized acquisition capture fast, correlated calcium dynamics beyond the limits of sequential two-photon scanning.
Adaptive excitation enables high-speed, deep two-photon voltage imaging of multiple neurons while staying below tissue heating limits. By boosting signal collection and supporting simultaneous dual-plane recordings, this approach captures rapid neuronal activity at depths and speeds not achievable with conventional two-photon microscopy.
An integrated multiphoton system enabled large field-of-view, single-cell imaging deep into cortical and subcortical regions. Simultaneous two- and three-photon imaging captured activity across thousands of neurons, extending depth and coverage beyond conventional approaches.
A dual-engine two-photon mesoscope enabled high-resolution, simultaneous imaging across widely separated cortical regions. Independent scan control and adaptive optics supported flexible, large-scale recording of thousands of neurons in vivo, overcoming traditional field-of-view limitations in two-photon microscopy.
ScanImage enables real-time control of laser scanning microscopes using standard data acquisition hardware, eliminating the need for complex, custom electronics. It delivers high-quality, multi-channel imaging with microsecond-level precision while offering the flexibility researchers need to build and adapt advanced confocal and two-photon microscopy systems.
A resonant-scanning two-photon microscope is used to enable high-speed direct laser writing, allowing accurate micron-scale 3D printing while maintaining sub-micron feature resolution.
ScanImage is used across the globe by the most prestigious laboratories.
MBF Bioscience and Phaseform are delighted to announce a breakthrough collaboration that integrates Phaseform’s advanced Adaptive Optics (AO) solutions into MBF
In their recent publication, Jeffrey Demas and co-authors introduced “Light Beads Microscopy”, an important technological breakthrough in 2 photon microscopy. The
ScanImage software from MBF Bioscience, along with the accompanying vDAQ acquisition and control card with analog to digital, digital to analog,
The utility of ScanImage is underscored by the number of references it receives in the world’s leading scientific publications. See examples below:
Wu, M., X. Zhang, et al.
Dopamine pathways mediating affective state transitions after sleep lossView Publication
Radulescu, C. I., N. Doostdar, et al.
Age-related dysregulation of homeostatic control in neuronal microcircuitsView Publication
Zhang, X., C. Wang, et al.
Analysis of Error Sources in the Lissajous Scanning Trajectory Based on Two-Dimensional MEMS MirrorsView Publication
Wilton, D. K., K. Mastro, et al.
Microglia and complement mediate early corticostriatal synapse loss and cognitive dysfunction in Huntington’s diseaseView Publication
Uribe-Arias, A., R. Rozenblat, et al.
Radial astrocyte synchronization modulates the visual system during behavioral-state transitionsView Publication
Wang, A. Y. M., M. M. Kulkarni, et al.
An ON-type direction-selective ganglion cell in primate retinaView Publication
Nasu, Y., A. Aggarwal, et al.
Lactate biosensors for spectrally and spatially multiplexed fluorescence imagingView Publication
Jovanoski, K. D., L. Duquenoy, et al.
Dopaminergic systems create reward seeking despite adverse consequencesView Publication
Chia, X. W., J. K. Tan, et al.
Emergence of cortical network motifs for short-term memory during learningView Publication
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.
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.
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.
ScanImage requires Matlab 2017a or later. A Matlab license needs to be obtained separately.
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 Nature, Thumb-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.
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 between laser pulses.
ScanImage offers powerful triggering schemes that allow to precisely align the image acquisition with a behavioral experiment.
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.
I was genuinely impressed by how effortlessly I was able to start using NeuroInfo, and the registration precision is outstanding. I have trialed many different automated counting pipelines but found that the anatomical alignment within NeuroInfo was exceptionally reliable. This tool’s intuitive interface paired with such accurate output has truly streamlined our neuroanatomical analysis.
"I rarely have encountered a company so committed to support and troubleshooting as MBF."
"The NeuroInfo software is so good. It compensates for students’ inexperience. They always lay down sections in the wrong order and have trouble recognizing the anatomy. This solves that problem."
"MBF Bioscience is extremely responsive to the needs of scientists and is genuinely interested in helping all of us in science do the best job we can."
"I am so happy to be a customer of your company. I always get great help related with your product or not. With the experienced members, you are the best team I've ever met. All of your staff are very kind and helpful. Thank you for your great help and support all the time."
"We’ve been very happy for many years with MBF products and the course of upgrades and improvements. Your service department is outstanding. I have gotten great help from the staff with the software and hardware."
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:
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.
The vDAQ is an all-in-one card and breakout box that’s engineered to provide the most advanced and dependable microscope control and data acquisition.
A revolutionary new microscope based on a technological breakthrough called Scanned Line Angular Projection (SLAP) two photon laser scanning microscopy.
The Light Beads Microscopy, an add-on for 2-photon microscopes, allows capturing a volume with a depth of about 0.5 mm as fast as capturing a single plane in a conventional microscope.