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

描述（申请人提供）：双光子激光扫描显微镜（TPLSM）是基础和生物医学神经生物学的重要工具。它独特地允许在完整脑组织深处以高分辨率进行三维成像。活体TPLSM使正常脑功能和脑疾病的突破性研究成为可能，包括中风、创伤性脑损伤、癫痫、阿尔茨海默病、帕金森病和脊髓损伤。最近，TPLSM被应用于有行为的动物，创造了一种新的实验范式，其中细胞大脑活动的详细地图可以直接与测量的行为相关联。TPLSM还与光遗传学兼容，允许对目标神经元进行光刺激。ScanImage是控制TPLSM实验的独立开源软件，一直处于神经生物学TPLSM应用的前沿。ScanImage已经被超过200个实验室采用（并且还在不断增加）。ScanImage控件，自制和商用显微镜硬件和整个神经生理学实验。Vidrio Technologies的成立是为了满足对ScanImage的商业支持和开发服务的强烈而广泛的需求。这一需求远远超出了单个实验室所能提供的，而且随着多个大型研究机构和奥巴马总统的BRAIN倡议将行为主体的细胞分辨率成像确定为一个高度优先的研究领域，预计还会进一步增长。我们将把ScanImage重新制作成支持定制的强大商业软件。新软件将支持闭环TPLSM：图像采集，图像分析和刺激生成都插入到处理回路中。刺激可以是行为性的，也可以是光遗传学的。闭环范式将允许研究人员在大脑活动和行为之间建立因果关系，而不仅仅是相关性。在第一阶段，Vidrio将创建ScanImage 5，演示灵活软件为闭环TPLSM实验提供动力的可行性。Vidrio将(1)将共振和振镜激光扫描模式（分别用于快速TPLSM成像和光致光刺激靶细胞）统一到一个封装中；(2)演示一种架构，允许自定义脚本化的中央处理器（CPU）计算实现闭环实验；(3)演示了一个支持自定义低级现场可编程门阵列（FPGA）计算的平台，以实现实时、低延迟的闭环实验。第二阶段将建立在这些功能的基础上，实现强大的新工具，用于询问行为动物的大脑功能，包括：实时运动校正，3d光刺激，3d映射活动的自适应采样。这些特征将为大脑活动和行为的精确而有力的推理研究提供解决方案和产品。

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.