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.
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 |
| CPU>2GHz |
| 16 GB memory |
| vDAQ for microscope control |
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Download ScanImage product sheet here.
ScanImage®2023.1.0
Released December 2023
New Universal Features
New Premium Features
Compensate for sample motion in photostimulation with vDAQ using Motion Detection without any additional hardware or software configuration
Visit the ScanImage changelog to see all of the changes in this version
ScanImage’s Tiling tool extends the microscope’s field of view by sequentially moving and scanning the sample. ScanImage automatically 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 enable synchronizing the acquisition to the laser clock to establish a precise temporal relationship between the acquired electrical signal and the laser pulse rate. With this information, a single signal trace from a detector can be split up into multiple virtual channels, where each channel defines a window in time relative to the last laser pulse. This technique can be used to suppress electrical background noise by masking out time windows without relevant data, or it can be used to time demultiplex data from multiple locations in the sample.
Resonant raster scanning typically achieves rates of ~30Hz. If data from only a small number of sites in the sample needs to be collected, it can be more efficient to plan a closed scan trajectory so that each site is visited once. Depending on the geometry and the overall length of the scan line, line rates of up to 2kHz are achievable. 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 volume while an active acquisition is ongoing. Corrections can be made via combination of galvo, motorized stage, or fast Z scanning devices. Estimations can be made from planar, stack, or rapid multi-region scanning modalities – even able to correct for motion of separate ROIs independently using the galvos and fastZ scanners.
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.
| Feature Description | ScanImage BASIC | ScanImage PREMIUM |
|---|---|---|
| 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 |
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,
ScanImage’s utility is underscored by the number of references it receives in the worlds most important 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 signal 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.
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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.
