ScanImage

ScanImage is a sophisticated software package designed for controlling both custom built and commercially available multiphoton microscopes. It offers an extensive set of features that extend beyond simple 2D and stack acquisition, catering to a wide array of experimental needs. With its ability to be easily modified and the incorporation of advanced techniques, it positions microscopes at the forefront of microscopy.

The software provides a user-friendly, organized interface that facilitates advanced control of microscopes' components, allowing users to leverage existing microscopes to their fullest potential. It supports raster imaging and online motion correction, and enables customization through triggered responses to specific events. These premium features put conventional and unconventional microscopes on the cutting edge of imaging techniques.

Some of the sophisticated techniques employed by ScanImage include linear and resonant scanning, photostimulation, holography, and advanced applications like time correlated single photon counting and time multiplexed acquisition. The software supports control of 2-photon and 3-photon microscopes, along with laser scanning confocals.

Key Features

• Tiled Acquisition: Extends the microscope's field of view by moving and scanning the sample sequentially, allowing for volumetric montages.
• Multiple Region of Interest Scanning: Increases frame rate and spatial resolution by selectively scanning small sample patches.
• Photostimulation: Enables synchronized photoactivation during image acquisition, using customizable or predefined stimulation trajectories.
• Time Correlated Acquisition: Synchronizes data with laser pulses, allowing for isolation of specific fluorescence events.
• Arbitrary Line Scanning: Allows for flexible scanning pathways using galvanometer scanners, achieving high line rates.
• Motion Correction: Corrects for XYZ sample motion using live image data, improving alignment and targeting during experiments.
• Widefield Previewing: Utilizes a camera to aid in sample previewing and planning within the field of view.
• vDAQ Control: An all-in-one platform that synchronizes data acquisition with the laser clock, supporting advanced features.

ScanImage has been a professional standard in microscopy for over two decades, cited in more than 900 research papers. It runs on a MATLAB-based accessible source code, allowing for extensive automation and customization of experimental workflows. Supported by a dedicated engineering team, it receives regular updates to incorporate the latest techniques and hardware advancements.

The recommended hardware for running ScanImage includes a 64-bit Windows 11 operating system, a CPU greater than 3GHz, 16 GB of memory, and a vDAQ for microscope control.