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

描述（由申请人提供）：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关键工具。它独特地允许在完整的脑组织深处以高分辨率进行三维成像。TPLSM在体内已经使得对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已被应用于行为动物，创造了一个新的实验范式，其中细胞脑活动的详细地图可以直接与测量的行为相关。TPLSM也与光遗传学兼容，允许光刺激靶向神经元。ScanImage是用于控制TPLSM实验的独立开源软件，一直处于TPLSM神经生物学应用的最前沿。ScanImage已被200多个实验室采用（并且还在增加）。ScanImage控件、自制和商用显微镜硬件以及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广泛需求。这一需求远远超过了单个实验室所能提供的，预计将进一步增长，多个大型研究机构和奥巴马总统的BRAIN计划将行为主体的细胞分辨率成像确定为高优先级研究领域。我们将把ScanImage改造成支持定制的强大的商业软件。新软件将支持闭环TPLSM：图像采集、图像分析和刺激生成均被插入到处理循环中。刺激可以是行为的，也可以涉及光遗传学。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，展示灵活的软件为闭环TPLSM实验提供动力的可行性。Vidrio将（1）将共振和检流计激光扫描模式-分别用于靶细胞的快速TPLSM成像和光遗传学光刺激-统一到单个包中;（2）展示一种允许自定义脚本中央处理器（CPU）计算的架构，以实现闭环实验;以及（3）演示了一个支持定制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。这些功能将为大脑活动和行为的精确和强大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.