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 Neuropixels 探针提供软件支持服务，这是一种突破性的新记录工具 这些来自大脑的电信号——由世界知名的 IMEC 创建。 纳米电子学研究中心，与四个资助机构（HHMI、艾伦研究所、盖茨比 Foundation 和 Wellcome Trust）—将于 2018 年 7 月公开发布。每个设备都包含一个 单个毛发状柄包含近 1000 个记录位点，每个记录位点都可以测量电压变化 这些探头不仅可以同时记录亚毫秒级的动作电位。 神经元数量比以前多，但整个封装足够小，可以安装 鉴于这些可重复使用的探针的成本相对较低，它们将成为自由移动的啮齿动物的头部。 电生理学的新标准 为了将 Neuropixels 用于我们自己的实验，艾伦研究所 使得将 Neuropixels 数据流式传输到现有的开源软件包 Open Ephys 中成为可能。 该提案的资金将使我们能够雇用人员为社区提供支持 Open Ephys 和 Neuropixels 的集成支持功能包括响应用户请求、 维护源代码、改进文档并简化安装和处理过程 升级软件将使 Neuropixels 可供所有实验室使用，无论其实验室如何。 此外，我们计划收集用户开发的软件插件， 使它们更加强大，并通过 Open Ephys 已经拥有的集中存储库进行传播。 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、会议和年度活动与社区互动 虽然我们的主要重点是为 Neuropixels 用户提供支持服务，但我们的努力将是 也有利于更广泛的电生理学界，该领域目前缺乏开放的数据标准。 采集、分析和可视化，导致大量冗余的开发工作 为灵活、强大的开源软件平台建立长期支持。 得益于 Open Ephys 的模块化插件架构，它将为未来的进步奠定良好的基础。 当下一个技术突破发生时很容易适应。