ScanImage

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

New Features in ScanImage 2018a

Now with 3D motion correction, photon counting, support for low repetition rate lasers, and a brand new offline data viewer.

Photon Counting

ScanImage's new 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.

3D Motion Correction

The new 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.

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.

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.

Premium Features

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

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.
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.

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!