2014 |
Iyer, Vijay |
R24Activity Code Description: Undocumented code - click on the grant title for more information. |
Scanimage: Flexible Software For Laser Scanning Microscopy in Neuroscience @ Vidrio Technologies, Llc
DESCRIPTION (provided by applicant): Two-photon laser-scanning microscopy (TPLSM) is a critical tool for basic and biomedical neurobiology. It allows high-resolution, high-contrast three dimensional imaging within intact brain tissue. TPLSM allows detailed study of brain structure and function at the level of molecules, synapses, neurons, and circuits. Increasingly TPLSM is used to study brain disorders, such as stroke, epilepsy, Alzheimer's disease, Parkinson's disease, and spinal cord injury. This proposal aims to support and extend Scan-image - free, open-source software for controlling laser scanning microscopy instruments for neurobiology. Scan-image allows a rapidly growing number of scientists, technologists, and small manufacturers to develop home-built and/or specialized microscopes for brain research. Such standalone software for TPLSM control enables widespread and innovative uses of TPLSM for neurobiology. The flexibility to develop and deploy specialized microscope systems is increasingly needed to enable and propagate advanced approaches such as large-scale brain volume imaging, targeted manipulation of neurons via optogenetics, and imaging in awake, behaving animals. It is proposed to broaden the impact of TPLSM approaches and instruments used for neurobiology by: 1) integrating control and measurement of electrophysiology and behavioral data streams with Scan-image; 2) supporting a wider range of TPLSM microscopy hardware under Scan-image; 3) supporting additional existing and new modes of TPLSM with benefit to neurobiology; and 4) providing proactive and reactive support for Scan-image to the fast-growing user community. The resource will be comprised of software developer time to be allocated and prioritized among these goals towards neuroscientist user requirements, in consultation with an international Steering Committee of leading neuroscientists. The recent rapid growth of TPLSM adoption and publications in neurobiology reflects the great current and projected scientific value of high-resolution imaging in intact brain tissue. Maintaining Scan-image as a cutting-edge, dynamic, and flexible tool for TPLSM instrument and experiment control will surely lead to a new wave of important developments and discoveries in brain science.
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0.903 |
2014 |
Iyer, Vijay |
R43Activity Code Description: To support projects, limited in time and amount, to establish the technical merit and feasibility of R&D ideas which may ultimately lead to a commercial product(s) or service(s). |
Software to Study Brain Function During Behavior Using Laser-Scanning Microscopy @ Vidrio Technologies, Llc
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, Alzheimer's disease, Parkinson'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 200 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 Obama'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 1, Vidrio will create ScanImage 5, demonstrating the feasibility of flexible software to power closed-loop TPLSM experiments. Vidrio will (1) Unify resonant and galvanometer laser scanning mode - for fast TPLSM imaging and optogenetic photostimulation of targeted cells, respectively - into a single package; (2) demonstrate an architecture allowing custom scripted central processing unit (CPU) computation to implement closed-loop experiments; and (3) demonstrate a platform supporting custom low-level field-programmable-gate array (FPGA) computation to implement real-time, low latency closed-loop experiments. Phase 2 will build on these features to implement powerful new tools for interrogating brain function in behaving animals, including: real-time motion correction, 3d photostimulation, adaptive sampling for mapping activity in 3d. These features will provide a solution and product for precise and powerful inferential studies of brain activity and behavior.
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0.903 |