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 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>3GHz |
| 16 GB memory |
| vDAQ for microscope control |
Light Beads Microscopy: A Breakthrough in Volumetric in vivo Brain Imaging
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Mini2P miniature microscope and ScanImage
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NYU scientists use ScanImage to monitor dopamine-induced brain activity in a model of Parkinson’s disease
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In Vivo Two-Photon Synaptic Imaging with ScanImage — New Findings Challenge the Hebbian Theory of Plasticity
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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 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 | ✘ | ✔ |
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 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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"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."
"Our experience with the MBF equipment and especially the MBF people has been outstanding. I cannot speak any higher about their professionalism and attention for our needs."
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.
