Expanding access to open-source data acquisition software for next-generation silicon probes

扩大对下一代硅探针的开源数据采集软件的访问

• 批准号: 9910473
• 负责人: Joshua H Siegle
• 金额: $ 47.36万
• 依托单位: ALLEN INSTITUTE
• 依托单位国家: 美国
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-04-15 至 2024-03-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9910473
• 关键词: Action Potentials; Adoption; Architecture; Area; Brain; Code; Collaborations; Communities; Computer software; Data; Development; Devices; Documentation; Educational workshop; Electrophysiology (science); Ensure; Feedback; Foundations; Funding; Funding Agency; Future; Hair; Head; Human Resources; Institutes; Interview; Laboratories; Learning; Length; Linux; Measures; Mental Health; Mental disorders; Methods; Neurons; Neurosciences; Operating System; Plant Roots; Process; Research; Research Personnel; Resources; Rodent; Scientist; Services; Signal Transduction; Silicon; Site; Source Code; Standardization; Stream; Structure; Surveys; System; Technology; Testing; Time; Trust; Update; Visualization; base; brain cell; cost; data acquisition; data quality; data standards; density; design; experience; experimental study; extracellular; flexibility; improved; millisecond; nanoelectronics; next generation; open data; open source; relating to nervous system; repository; social media; software development; symposium; tool; voltage; volunteer; web site

We plan to provide software support services for Neuropixels probes, a groundbreaking new tool for recording electrical signals from the brain. These probes—which were created by IMEC, a world-renowned nanoelectronics research center, in collaboration with four funding agencies (HHMI, Allen Institute, Gatsby Foundation, and Wellcome Trust)—will become publicly available in July 2018. Each device consists of a single hair-like shank containing nearly 1000 recording sites, each of which can measure voltage changes with sub-millisecond precision. Not only can these probes simultaneously record action potentials from an order of magnitude more neurons than was previously possible, but the entire package is small enough to be mounted on the head of a freely moving rodent. Given the relatively low cost of these reusable probes, they will become a new standard for electrophysiology. In order to use Neuropixels for our own experiments, the Allen Institute made it possible to stream Neuropixels data into an existing open-source software package, Open Ephys. Funding for this proposal would allow us to hire personnel to provide community-wide support for the integration of Open Ephys and Neuropixels. Support functions would include responding to user requests, maintaining the source code, improving the documentation, and simplifying the processing of installing and upgrading the software. This would serve to make Neuropixels accessible to all laboratories, regardless of their prior experience with electrophysiology. In addition, we plan to gather software plugins developed by users, make them more robust, and disseminate them through a centralized repository. Open Ephys already has a global network of volunteer developers, which we plan to leverage to expand the features of this software. Throughout the process, we will engage with the community via interviews, surveys, conferences, and annual workshops. While our main focus will be on providing support services for Neuropixels users, our efforts will also benefit the broader electrophysiology community. The field is currently lacking open standards for data acquisition, analysis, and visualization, leading to a large amount of redundant development efforts across laboratories. Establishing long-term support for a flexible, powerful, and open-source software platform would provide a terrific foundation for future progress. Thanks to Open Ephys’ modular plugin architecture, it will be easy to adapt when the next technological breakthrough occurs.

我们计划为神经像素探测器提供软件支持服务，这是一种突破性的新记录工具 来自大脑的电信号。这些探测器-由世界知名的IMEC公司制造 纳米电子研究中心，与四个资助机构(HHMI、艾伦研究所、盖茨比)合作 基金会和惠康信托)-将于2018年7月公开提供。每个设备都包含一个 单个毛发状的小腿，包含近1000个记录点，每个记录点都可以测量电压变化 亚毫秒级精度。这些探头不仅可以同时记录来自一系列 比以前可能的更多的神经元，但整个包足够小，可以安装 在一只自由活动的啮齿动物的头上。鉴于这些可重复使用的探测器的成本相对较低，它们将成为 电生理学的新标准。为了将神经素用于我们自己的实验，艾伦研究所 使其能够将神经像素数据传输到现有的开源软件包Open Ephys中。 为这项提议提供资金将使我们能够聘请人员在整个社区范围内为 开放式Ephys和NeuroPixents的集成。支持功能将包括响应用户请求， 维护源代码，改进文档，并简化安装和 升级软件。这将有助于使所有实验室都可以访问神经像素，无论他们的实验室 有电生理学相关工作经验。此外，我们计划收集用户开发的软件插件， 使它们更健壮，并通过一个集中的存储库传播它们。Open Ephys已经有一个 全球志愿者开发人员网络，我们计划利用该网络来扩展该软件的功能。 在整个过程中，我们将通过访谈、调查、会议和年度 研讨会。虽然我们的主要重点将是为神经像素用户提供支持服务，但我们的努力将 也使更广泛的电生理学社区受益。该领域目前缺乏开放的数据标准 获取、分析和可视化，导致大量重复的开发工作 实验室。建立对灵活、强大和开源软件平台的长期支持将 为未来的进步提供了极好的基础。由于Open Ephys的模块化插件架构，它将成为 在下一次技术突破发生时易于适应。