What is ScanImage?

ScanImage is a “Best-In-Class” software application for controlling a laser scanning microscope built for scientists. Nothing comes even close.

We engineered ScanImage to make complex experiments happen quickly in a smooth workflow.  We remember the bad old days: painstaking post-experimental analysis that took hours or even days to complete.  Since 2016, ScanImage incorporates on-line real-time analysis so you can adjust your imaging parameters and experimental paradigm while the animal is still on the microscope.

New Features in ScanImage 2016b

Now even more powerful

Now with support for the 2p-RAM and spatial light modulators.  Adds motion correct, online analysis, arbitrary line scanning and much more!  Parallel scan paths have been supported since ScanImage 2015.

Support for the 2p Mesoscope

This new large field of view random access two-photon microscope (2p-RAM) provides the largest field of view in the industry and is near diffraction limited.  Vidrio helped develop the 2p-RAM and ScanImage is the only software that will run the microscope.  The region of interest/stimulus group editor gives you random access to the massive 5 mm field of view available on this cutting edge microscope.

Spatial Light Modulator 

Spatial light modulators (SLM) are a powerful new tool for two-photon microscopy.  Nikolenko et. al. demonstrated the power of the "scanless" microscope and performed optogenetic experiments using an SLM.  Simultaneously image or photostimulate neurons in distinct regions using ScanImage in combination with your favorite SLM device.


Parallel Scan Paths

Perform simultaneous imaging and photostimulation.  Each scanner path has it’s own field of view and ScanImage provides easy methods for scanner alignment on the two paths.   Our alignment algorithms provide knowledge of the precise position of individual neurons in the field of view so your photostimulation pulse will hit the target.  Both resonant and galvo scanners are supported.

Online Motion Correction

Photostimulation and online analysis experiments rely on knowledge of the precise position of indivdual neurons in the field of view.  ScanImage features online motion correction that tracks the sample and retargets the photostimulation laser and integration region of interest for online analysis.


Waveform Optimization

The actual trajectory of mechanical actuators (Galvos, Piezos, voice coils...) lags behind the commanded trajectory, which results in a warped image geometry. ScanImage implements optimization routines to measure the actuator response and compensates for inaccuracies in the actuator trajectory.


Base Features

Built for scientists, by scientists

Highly Optimized Acquisition Engine

ScanImage utilizes the power of FPGAs for real-time image formation, while the CPU is free for your analysis code! Even at frame rates greater than 2kHz!

Best in Class Image Quality

ScanImage lets you choose the optimal signal conditioning method for your setup: Select from a variety of digitizer input ranges, anti-aliasing filters, or synchronize your acquisition directly to the laser pulses. How about photon counting? ScanImage does it all!

Runs On Any Microscope

Have a microscope you want to upgrade? Want to build your own super-advanced scope? ScanImage will be able to run it! How about an off the shelf scope featuring ScanImage? Check out our hardware partners.

Flexible Scanner Configurations

ScanImage supports a variety of scanner configurations including standard linear Galvo-Galvo and Resonant-Galvo combinations.  The software also supports Resonant-Galvo-Galvo and SLM scanning options.  

Volume Imaging

ScanImage supports stack acquisitions using your stage or a Fast-Z focusing device. We support a variety of stages, piezos and electrically tunable lenses.  If your hardware isn't on our long list of supported devices we'd be happy to work with you to add your device.  Just ask.

Synchronization to Behavioral Experiments

ScanImage supports sub-microsecond synchronization with third party hardware and software. This allows you to run imaging and behvioral experiments in tandem. This is important to correlate behavior events and image data to another during analysis.

Scriptability in Matlab

Don't let the microscope control you!  With ScanImage you can automate your imaging experiments the way you want.  The ScanImage API empowers you to take back control by easily writing Matlab scripts that perform the operations you want, when you want them. You want to synchronize across your experimental apparatus?  How does sub-microsecond synchronization sound?

Big Tiff File Support

Ever hit the maximum Tiff file size when you have a great imaging session in progress?  Not any more, because ScanImage now supports the Big Tiff file format.  Gone are the days of splitting up your experiments into large numbers of smaller files so you can record all your data.  

Laser Power Modulation

ScanImage provides multiple ways to control laser power including selective regions of increased/decreased power and a customizable z-depth power control. Excellent imaging experiments require laser power management flexibility so that you can deliver the right amount power at the right time and place.

Premium Features

When you want to do complex cutting edge
never been done before experiments, with ScanImage Premium, you can.

Arbitrary Line Scanning

ScanImage provides a new method to utilize a linear scanning (galvo-galvo) microscope for fast imaging. Building upon the robust ScanImage multi ROI core, arbitrary line scanning enables high speed sampling of desired ROIs by reducing time spent scanning areas of little interest in the sample. If the locations of desired ROIs are already known and you are only interested in how the fluorescence at specified points is changing over time, an arbitrary path can be configured to sample the desired points at high speed.

Multiple Region of Interest (mROI) Scanning

ScanImage allows the microscope's full field of view to be subdivide into multiple smaller regions of interest (ROIs).  This feature can be used to trace complex structures in 3D volumes, optimize imaging frame rates and reduce tissue exposure to the laser.  Although this feature works with a pair of linear galvo scanners,  a resonant/galvo/galvo triple scanner combination provides the most imaging flexibility.   Read more.

Real-time Online Analysis

After defining regions of interest (ROI) in the field of view or volume, ScanImage monitors pixel intensities with the ROI providing real-time online analysis capability.  You can monitor up to 200 ROIs simultaneously and produce analog and digital output signals in response to pixel intensity thresholds set for each ROI.  This feature is particularly useful when performing closed-loop experiments.

Multiple Scanner Alignment

When using a dual scan path microscope for photostimulation it is often desirable to image and identify cells for stimulation with one scan path, then stimulate the cells using the other scan path. For this targeting to be accurate, alignment between the scanners is critical.  Once you achieve rough alignment in physical space, ScanImage provides a best-in-class method to fine tune the alignment in software space.

Scanner to Stage Alignment

Similar to the scanner alignment, ScanImage can align the stage (motors) to the laser scanners. This process is semi-automated and takes advantage of ScanImage's motion correction framework.  After a successful calibration, ScanImage can perform measurements in stage units and can move the stage to defined positions.  Read more.

Simultaneous Imaging and Photostimulation

ScanImage features a photostimulation module. If your microscope has two independent scan heads, they can be used for simultaneous and independent imaging and photostimulation.  The scan path and stage alignment features of ScanImage make sure you hit your target with high precision.  Flexible options are provided to trigger photostimulation pulses from software events or external signals.

Don't Let the Microscope Control You!