the "Best-In-Class" software for controlling laser scanning microscopes built for scientists. Nothing comes even close.

New Features in ScanImage 2019b

Now with support for the new vDAQ, support for 3D-Shot, live motor updates and a new stack system.

Support for vDAQ

ScanImage now supports the vDAQ - a brand new Data Acquisition card developed by Vidrio specifically for microscope control. The vDAQ is an all in one solution for controlling scanners, Pockels cells, Piezo objective positioners, shutters and much more.

3D-Shot workflow

ScanImage now supports the 3D-Shot holographic optogenetics workflow.

Live Motor Update

ScanImage's new stage system automatically updates the position of the motors in the Motor Controls GUI (for selected stages only).

New Stack System

The new stack controls simplify the workflow for acquiring stacks and make the user experience more intuitive.

Premium Features

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

3-Photon Imaging

Lasers with low repetition rates (1-15MHz) are becoming more popular, especially for 3-Photon imaging. ScanImage can gate the acquisition in between laser pulses to reject electrical noise and increase the SNR. Read more.

Offline Data Viewer
The new ScanImage offline data viewer opens ScanImage multiple region of interest and arbitrary line scanning data. It can extract traces of fluorescent activity and render videos to AVI or TIFF. Read more.
Oscilloscope Mode
ScanImage's new oscilloscope mode helps identifying noise sources by visualizing and analyzing the raw digitizer data. Identify ground loops, noise from ambient light, electrical noise from stages and digitizer saturation. Read more.
Photon Counting

ScanImage's photon counting feature uses a high speed digitizer to detect individual photons and bin them according to their arrival time relative to the laser pulse. This technique can increase the signal to noise ratio in photon limited acquisitions by rejecting electrical noise. The flexible implementation can save images in photo current integration mode and photon counting mode at the same time. Read more.

3D Motion Correction
The 3D Motion Correction feature allows to detect and correct lateral and axial motion in real-time to retarget the imaging and photostimulation laser paths. A flexible API enables users to write custom motion estimation and correction functions to customize the feature to their needs. Read more.
Widefield Camera Imaging
The camera feature allows to use the microscope's widefield camera directly with ScanImage. The camera can be aligned to the scanner, and the scanned image can be overlayed onto the camera image. Additionally, a reference image from a previous session can be loaded to help finding the site. Read more.
Support for the 2p Mesoscope

The 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.
Read more.
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. Read more.
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.

ScanImage Remote Control

ScanImage can now be controlled from a remote Matlab instance via a TCP/IP network. This allows for easier setup of workflow that requires the synchronization of multiple systems such as Ephys and behavior control.

SLM Power Calibration

The diffraction efficieny of an SLM depends on the displayed phasemask. ScanImage now includes a tool to calibrate the diffraction efficiency for holographic points in a 3D volume. This calibration is used to provide even illumination of cells in optogenetic experiments.

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.

Don't Let the Microscope Control You!