Software to study brain function during behavior using laser-scanning microscopy

DESCRIPTION provided by applicant Two photon laser scanning microscopy TPLSM is a critical tool for basic and biomedical neurobiology It uniquely allows three dimensional imaging deep within intact brain tissue and at high resolutions TPLSM in vivo has enabled ground breaking studies of normal brain function and disorders of the brain including stroke traumatic brain injury epilepsy Alzheimerandapos s disease Parkinsonandapos s disease and spinal cord injury Recently TPLSM has been applied to behaving animals creating a new experimental paradigm where detailed maps of cellular brain activity can be directly correlated with measured behavior TPLSM is also compatible with optogenetics allowing photostimulation of targeted neurons ScanImage is standalone open source software for controlling TPLSM experiments that has been at the forefront of TPLSM applications for neurobiology ScanImage has been adopted by over labs and counting ScanImage controls home built and commercial microscope hardware and entire neurophysiology experiments Vidrio Technologies has been formed to meet strong and widespread demand for commercial support and development service for ScanImage The demand vastly exceeds what a single laboratory can provide and is expected to grow further with multiple large research institutes and President Obamaandapos s BRAIN Initiative identifying cellular resolution imaging in behaving subjects as a high priority research area We will rework ScanImage into robust commercial software that supports customization The new software will support closed loop TPLSM Image acquisition image analysis and stimulus generation are each inserted into a processing loop The stimuli can be behavioral or can involve optogenetics The closed loop paradigm will allow investigators to establish causality not just correlation between brain activity and behavior In Phase Vidrio will create ScanImage demonstrating the feasibility of flexible software to power closed loop TPLSM experiments Vidrio will Unify resonant and galvanometer laser scanning mode for fast TPLSM imaging and optogenetic photostimulation of targeted cells respectively into a single package demonstrate an architecture allowing custom scripted central processing unit CPU computation to implement closed loop experiments and demonstrate a platform supporting custom low level field programmable gate array FPGA computation to implement real time low latency closed loop experiments Phase will build on these features to implement powerful new tools for interrogating brain function in behaving animals including real time motion correction d photostimulation adaptive sampling for mapping activity in d These features will provide a solution and product for precise and powerful inferential studies of brain activity and behavior PUBLIC HEALTH RELEVANCE Two photon laser scanning microscopy is a tool that allows three dimensional imaging with cellular resolution within the brain or spinal cord of living animals It allows for instance the study of brain wiring and rewiring of observing brain activiy in individual cells and synapses and observing blood vessels and blood flow These capabilities are used for studies of healthy brain function learning and memory stroke traumatic brain injury epilepsy Alzheimerandapos s disease and Parkinsonandapos s disease We propose to develop instrument control software to allow two photon microscopy to be more widely and flexibly used for neurobiology This software will particularly support advanced experiments in awake not anaesthetized animals that observe the correlation between brain activity and behavior with cellular details It will further allow incorporating the tools of optogenetics parallel computing and programmable hardware to probe causal relationships between brain activity and behavior These studies will provide greater understanding of basic brain function and brain disorders