ScanImage: Flexible software for operating laser scanning microscopes

We describe a simple, software-based approach to operating a laser scanning microscope without the need for custom data acquisition hardware. Data acquisition and control of laser scanning are achieved through standard data acquisition boards. The entire burden of signal integration and image processing is placed on the CPU of the computer. We quantitate the effectiveness of our data acquisition and signal conditioning algorithm under a variety of conditions. We implement our approach in an open source software package (ScanImage) and describe its functionality.We present ScanImage, software to run a flexible laser scanning microscope that allows easy custom design.Laser scanning microscopies (LSM) include some of the most important imaging modalities in biology. For example, confocal laser scanning microscopy (CLSM) is the tool of choice for high-resolution fluorescence microscopy in cultured and fixed tissue preparations [1-3]. Two-photon excitation laser scanning microscopy (2PLSM) is ideal for fluorescence microscopy in scattering media, such as living skin and brain tissue [4,5].Historically, new developments and applications of laser scanning microscopy have been limited primarily by the availability of new hardware. The development of suitable laser light sources and powerful data acquisition systems running on desktop computers brought CLSM to fruition [3]. In the case of 2PLSM, the development of mode-locked pulsed light sources operating in the red and near IR spectral range [6] made it practical [5].Several lines of commercial CLSMs and 2PLSMs are available. A manufacturer typically will offer one principal model and allow the customer to choose between different versions and options. Fundamentally, in terms of optics and software, a single general purpose design is offered. However, exciting applications demand specialized design. Often these applications include some of the most promising experimental developments. Currently, most hardware components of