ScanImage provides researchers exquisite control of their microscopes and animal behavioral apparatus, providing precise synchronization between neuronal activity imaging and behavior observations. The software automates two-photon laser scanning microscope image collection and allows animal behavioral data to be correlated with neuronal activity.

The architecture of ScanImage has three layers: at the lowest level, images are acquired using a configurable FPGA. Data is then passed to a C++ layer that runs in its own thread and streams data to disk at 250 MB/sec. Data is also passed to a MATLAB^® layer, where images are displayed and optimized through a MATLAB UI. Users can code their own MATLAB user functions to further customize their data acquisition and analysis streams.