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.

我们提出的小项目的目标是：1）开发一个更有效，更方便，更准确的3D 使用虚拟现实（VR）和神经数据无国界（NWB）数据标准的结构分析工作流程， 和2）将这种软件/硬件生态系统实施到我们目前的SCI/D研究计划中， 疼痛和痉挛。通过开发这个3D-VR结构分析软件生态系统（3D-VR SASE），我们将 有力地扩大我们中心的实验范围和能力，在未来的转化研究。我们将 在两个具体目标中开展实验，以实现本项目的目标。 在具体目标1中，我们将建立一个基于VR的三维结构分析软件环境（3D-VR SASE）。 这将扩大我们的能力，调查动态变化的异常树突棘可塑性相关的 SCI/D。我们的VA中心已经运行成像系统，使我们能够执行多种 受损中枢神经系统的解剖学研究。然而，我们的项目轨迹现在已经严重超过了能力 这些系统中，没有商业工具，我们的需要是可用的或在开发中。因此，为了扩大 我们目前的硬件能力，我们将开发更快，更准确的重建/可视化 硬件/软件生态系统与我们中心已建立的NWB数据标准解决方案。 在Specific Aim 2中，我们将验证3D-VR SASE平台。我们使用公开可用的 神经元数据集，并使用转基因报告小鼠的脊髓组织进行树突棘的研究。 我们将使用该分析平台进行两项实验研究。首先，我们将重建神经元图像 DIADEM挑战赛是一项公共神经科学竞赛，旨在鼓励 改进神经元形态追踪的算法方法的发展。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 使用相对于“黄金标准”跟踪的准确度度量的跟踪。其次，我们将进行回顾性研究 死后收集的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。WDR神经元之所以引起人们的兴趣，是因为它们在上行神经元中投射纤维。 脊髓丘脑束，丘脑VPL伤害性处理区的主要疼痛通路。此外，本发明还 WDR神经元中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，以提高分析速度，3D 可视化和神经解剖重建，并实施NWB数据标准。的灵活性和 3D-VR SASE平台的广泛应用将促进我们目前的SCI/D研究计划以及研究 在美国退伍军人中也普遍存在的其他慢性疾病中的神经解剖病理学，例如， 老年痴呆症创伤后应激障碍多发性硬化症创伤性脑损伤总的来说，我们希望这项工作将有力地扩大我们中心的 实验范围和能力的翻译研究在未来。