Development of a 3D-VR Structural Analysis Software Ecosystem for SCI/D Research

开发用于 SCI/D 研究的 3D-VR 结构分析软件生态系统

• 批准号: 10482499
• 负责人: Andrew Michael Tan
• 金额: --
• 依托单位: VA CONNECTICUT HEALTHCARE SYSTEM
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-07-01 至 2024-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10482499
• 关键词: 3-Dimensional; 3D virtual reality; Address; Alzheimer' s Disease; American; Anatomy; Archives; Autopsy; Behavior assessment; Chronic Disease; Computer Workstations; Computer software; Data Analytics; Data Set; Databases; Dendritic Spines; Development; Ecosystem; Electrophysiology (science); Environment; Fiber; Future; Goals; Gold; Image; Image Analysis; Institutes; Longitudinal Studies; Mediating; Methodology; Modeling; Morphology; Mus; Neuroanatomy; Neurons; Neurosciences; Nociception; Output; Pain; Pathology; Pathway interactions; Peripheral nerve injury; Positioning Attribute; Post-Traumatic Stress Disorders; Posterior Horn Cells; Process; Reporter; Research; Research Project Grants; Retrieval; Retrospective Studies; Speed; Spinal; Spinal Cord; Spinal cord injury; Spinothalamic Tracts; System; Thalamic structure; Tissues; Transgenic Organisms; Veterans; Visualization; Work; algorithm development; algorithmic methodologies; base; cell type; central nervous system injury; clinically significant; data acquisition; data standards; design; digital; dorsal horn; experience; experimental study; file format; flexibility; imaging system; improved; in vivo; interest; light microscopy; microscopic imaging; open source; painful neuropathy; programs; reconstruction; spasticity; spinal cord and brain injury; three-dimensional visualization; tool; translational study; user-friendly; virtual reality

The goal of our proposed Small Project is: 1) to develop a more efficient, accessible, and accurate 3D structural analysis workflow using virtual reality (VR) and the Neurodata Without Borders (NWB) data standard, and 2) to implement this software/hardware ecosystem into our current SCI/D research program in neuropathic pain and spasticity. By developing this 3D-VR Structural Analysis Software Ecosystem (3D-VR SASE), we will powerfully expand our Center's experimental reach and capacity for translational studies in the future. We will carry out experiments in two Specific Aims to address the goal of this Project. In Specific Aim 1, we will establish a VR-based 3D structural analysis software environment (3D-VR SASE) that will expand our ability to investigate the dynamic changes in abnormal dendritic spine plasticity associated SCI/D. Our VA Center already operates imaging systems that have allowed us to perform a multitude of anatomical studies of the injured CNS. However, our project trajectory has now severely outpaced the capacity of these systems, and no commercial tools for our needs are available or in-development. Thus, to expand the capabilities of our current hardware, we will develop a faster, more accurate reconstruction/visualization hardware/software ecosystem with the established NWB data standard solution in our Center. In Specific Aim 2, we will validate the 3D-VR SASE platform. We demonstrate its utility using publicly available neuronal datasets and perform a study of dendritic spines using spinal cord tissue of transgenic reporter mice. We will perform two experimental studies with the analysis platform. First, we will reconstruct neuronal image stacks from the DIADEM challenge, which is a public neuroscience competition designed to encourage the development of algorithmic methods for improved neuron morphological tracing. The DIADEM challenge provides high-quality light-microscopy images with established specifications that allow us to score our VR traces using metrics of accuracy against a “gold standard” trace. Second, we will perform a retrospective study of dendritic spines in wide-dynamic range (WDR) dorsal horn neurons in post-mortem spinal tissue collected from our previous study. WDR neurons have been of interest because they project fibers in the ascending spinothalamic tract, a major pain pathway to the thalamic VPL nociceptive processing region. Additionally, dendritic spine dysgenesis in WDR neurons has been associated with neuropathic pain. In summary, this project will develop the 3D-VR SASE workflow that increases analytical speed, 3D visualization and neuroanatomical reconstruction, and implements the NWB data standard. The flexibility and broad utility of the 3D-VR SASE platform will facilitate our current SCI/D research program as well as the study of neuroanatomical pathologies in other chronic diseases that are also prevalent among US Veterans, e.g., Alzheimer's disease, PTSD, MS, TBI. Overall, we expect this work will powerfully expand our Center's experimental reach and capacity for translational studies in the future.

我们提出的小型项目的目标是：1) 开发更高效、更易于访问且更准确的 3D 使用虚拟现实 (VR) 和无国界神经数据 (NWB) 数据标准的结构分析工作流程， 2) 将该软件/硬件生态系统实施到我们当前的神经病理学 SCI/D 研究项目中 通过开发这个 3D-VR 结构分析软件生态系统 (3D-VR SASE)，我们将 我们将在未来有力地扩大我们中心的实验范围和转化研究能力。 在两个具体目标中进行实验，以实现该项目的目标。 在具体目标1中，我们将建立一个基于VR的3D结构分析软件环境（3D-VR SASE） 这将扩大我们研究与异常树突棘可塑性相关的动态变化的能力 我们的 SCI/D 中心已经运行了成像系统，使我们能够执行多种操作。 然而，我们的项目轨迹现在已经严重超出了能力。 这些系统，并且没有可用或正在开发的商业工具来满足我们的需求。 根据我们当前硬件的能力，我们将开发更快、更准确的重建/可视化 硬件/软件生态系统，并在我们中心建立了NWB数据标准解决方案。 在具体目标 2 中，我们将验证 3D-VR SASE 平台，并使用公开可用的工具来演示其实用性。 神经数据集并使用转基因报告小鼠的脊髓组织进行树突棘研究。 我们将使用分析平台进行两项实验研究，首先，我们将重建神经图像。 DIADEM 挑战赛的堆栈，这是一项公共神经科学竞赛，旨在鼓励 开发改进神经元形态追踪的算法方法 DIADEM 挑战。 提供具有既定规格的高质量光学显微镜图像，使我们能够对 VR 进行评分 其次，我们将进行一项回顾性研究。 收集的死后脊髓组织中宽动态范围 (WDR) 背角神经元的树突棘 我们之前的研究中，WDR 神经元引起了人们的兴趣，因为它们投射上行纤维。 脊髓丘脑束，丘脑 VPL 伤害性处理区域的主要疼痛通路。 WDR 神经元的树突棘发育不全与神经性疼痛有关。 总之，该项目将开发 3D-VR SASE 工作流程，提高分析速度、3D 可视化和神经解剖重建，并实现了NWB数据标准的灵活性和灵活性。 3D-VR SASE 平台的广泛实用性将促进我们当前的 SCI/D 研究计划以及研究 其他慢性疾病中的神经解剖学病理学在美国退伍军人中也很普遍，例如 总的来说，我们预计这项工作将有力地扩展我们中心的治疗范围。 未来转化研究的实验范围和能力。