Enabling Shared Analysis and Processing of Large Neurophysiology Data

项目概要/摘要 了解大脑功能是改善医疗保健和推进许多科学举措的关键。 阿尔茨海默氏症、帕金森氏症和肌萎缩性侧索硬化症等脑退行性疾病的治疗正在成为 随着当前美国人口老龄化和预期寿命的增加，这一点越来越重要。的费用 据估计，仅在2016年，阿尔茨海默氏症和其他痴呆症就超过2000亿美元，更不用说人类了。 这些疾病带来的灾难。自闭症、成瘾、抑郁、癫痫、创伤性脑损伤和疼痛 治疗只是与大脑功能相关的一些至关重要的健康问题。认知 科学也处于计算和自治系统研究的最前沿，有可能 彻底改变人机交互并应对新出现的全球挑战。由于这些和 BRAIN（Brain Research through Advancing Innovative Neurotechnologies） 总统倡议的目的是改善国家未来的健康和竞争力， 加速大脑研究的根本目标。 为了实现这一目标，大脑研究界开发了神经数据无国界： 神经生理学（NWB）文件格式和规范，以支持大规模的合作和研究。这 开放格式创建于2014年，已经对基于细胞的神经生理学产生了影响， 诸如艾伦脑科学研究所之类的组织生成和共享诸如艾伦 脑观察站和艾伦细胞类型数据库。虽然这一初步工作很有希望， 由于缺乏便于浏览、处理、分析和可视化的软件工具，研究团体的工作进展缓慢 NWB数据，同时促进可复制性。因此，这项工作的目的是生产这样的工具，以支持大脑 倡议和其他大规模的大脑研究计划，通过支持和发展NWB社区。 这里提出的工作解决了基于细胞的神经生理学中的三个重要工作流程： 生理学来成像刺激下的神经元，硅探针记录来检测来自表面的尖峰事件， 皮层下穿深层结构，体外切片电生理记录时变刺激 和神经元的电反应。将创建新颖的多尺度软件工具， 浏览、处理、分析和可视化基于NWB的大脑数据;将实验刺激与 观察到的反应。还将开发转换实用程序，将现有数据转换为NWB格式。为 数据庞大、复杂，可能分布在许多站点，软件工具将基于网络， 使研究人员能够以可复制的方式远程访问和处理数据，并使用可扩展的云 计算资源。该软件将在开源许可证下发布，并将被放置在 正式的软件流程，以促进整个研究社区的共享。这些工具将被构思出来， 在艾伦科学家的帮助下创建，他们还将使用这三个工作流程进行最终验证。

Project Summary / Abstract Understanding brain function is key to improving health care and advancing a number of scientific initiatives. The treatment of degenerative brain diseases such as Alzheimer's, Parkinson’s, and ALS is becoming increasingly important as the current US population ages and life expectancies increase. The costs of Alzheimer's and other dementias is estimated at over $200 billion in 2016 alone, not to mention the human devastation that these diseases incur. Autism, addiction, depression, epilepsy, traumatic brain injury, and pain treatment are just a few more of the critically important health concerns related to brain function. Cognitive science is also at the forefront of research into computational and autonomous systems, with the potential to revolutionize human computer interaction and tackle emerging global challenges. As a result of these and other significant opportunities the BRAIN (Brain Research through Advancing Innovative Neurotechnologies) Presidential initiative was created to improve the future health and competitiveness of the nation, with the fundamental goal of accelerating brain research. Consistent with this goal, the brain research community has developed the Neurodata Without Borders: Neurophysiology (NWB) file format and specification to support large-scale collaboration and research. This open format was created in 2014 and is already making an impact on cellular-based neurophysiology, with organizations such as the Allen Institute for Brain Science generating and sharing datasets such as the Allen Brain Observatory and the Allen Cell Types Database. Although this preliminary work is promising, progress in the research community is slowed by a lack of software tools to readily browse, process, analyse, and visualize NWB data, while promoting replicability. Thus this work aims to to produce such tools in support of the BRAIN initiative and other large-scale brain research programs by supporting and growing the NWB community. The work proposed here addresses three important workflows in cellular-based neurophysiology: o​ ptical physiology to image neurons under stimuli, silicon probe recordings to detect spike events from the surface of the cortex down through deeps​ structures, and​ in vitro slice electrophysiology to record t​ ime-varying stimulus and electrical response from a neuron​. Novel multiscale software tools will be created to enable efficient browsing, processing, analysis, and visualization of NWB-based brain data; linking experimental stimuli to observed responses. Conversion utilities will also be developed to convert existing data into NWB form. As the data is large, complex, and may be distributed across many sites, the software tools will be web-based, enabling researchers to remotely access and process data in a reproducible manner, and to use scalable cloud computing resources. The software will be released under open source licences and will be placed under formal software process to facilitate sharing across the research community. The tools will be conceived and created with the help of Allen scientists, who will also perform final validation using these three workflows.