Laying the Groundwork for Web-based Elemental Imaging Software: The MicroAnalysis Toolkit

为基于网络的元素成像软件奠定基础：微观分析工具包

• 批准号: 10609200
• 负责人: Brian P Jackson
• 金额: $ 24.49万
• 依托单位: DARTMOUTH COLLEGE
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-05-01 至 2026-04-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10609200
• 关键词: Ablation; Administrative Supplement; Arsenicals; Basic Science; Biological Process; Cell Cycle; Chemicals; Collaborations; Communicable Diseases; Consult; Contrast Media; Data; Data Analyses; Data Sources; Databases; Devices; Drug Delivery Systems; Elements; Fertilization; Foundations; Gadolinium; Goals; Homeostasis; Human body; Image; Imaging Techniques; Immune response; In Situ; Inductively Coupled Plasma Mass Spectrometry; Infrastructure; Laboratories; Lasers; Link; Magnetic Resonance; Malignant Neoplasms; Metabolism; Metals; National Institute of General Medical Sciences; Online Systems; Organism; Platinum Compounds; Prevention; Process; Research Personnel; Resource Sharing; Resources; Roentgen Rays; Running; Services; Source; Trace Elements; angiogenesis; base; computerized data processing; data pipeline; data visualization; detection limit; disease diagnosis; experience; imaging software; industry partner; instrumentation; interoperability; metallicity; nanoparticle; nervous system disorder; online repository; platform-independent; prevent; success; synchrotron radiation; tumor; web based interface

PROJECT SUMMARY Living organisms use fluxes in chemical elements to control fundamental processes such as metabolism, homeostasis, the cell cycle, and fertilization. Up to 60 chemical elements can be detected in the human body, 25 of which are essential. Dysregulation of essential elements underpins neurological disorders, angiogenesis and tumor formation in cancer, and immune response to infectious disease. Chemical elements are used in disease diagnosis and treatment; gadolinium is a common magnetic resonance contrast agent, metal-based nanoparticles show promise for drug delivery and platinum and arsenic compounds are chemotherapeutics. Elemental imaging (EI) provides data for both the concentration and distribution of multiple chemical elements in situ in the form of an image; accelerating understanding of a diverse range of bio-metallic mechanisms from environmental to biomedical. EI furthers the NIGMS goal to support basic research that increases our understanding of biological processes and lays the foundation for advances in disease diagnosis, treatment, and prevention. However, EI techniques are challenging to both access and master. Laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) is a laboratory-based EI technique that it is increasingly applied to biomedical applications with comparable or lower detection limits than other EI techniques. The Dartmouth Trace Element Analysis Core (TEAC) is an established and highly regarded shared resource that supports researchers throughout the US, is staffed by experienced researchers in EI and ICP-MS, using state- of-the-art instrumentation and has excellent links to industry partners. In 2021 the TEAC expanded upon the current ad hoc service to establish a dedicated biomedical EI user facility; the Biomedical National Elemental Imaging Resource (BNEIR) (1R24GM141194). Our aim is to broaden access to EI techniques in biomedicine by building upon the TEAC’s existing infrastructure, administration, instrumentation, and expertise. We consult with Dr Sam Webb, Stanford Synchrotron Radiation Lightsource, to further adapt his freely available EI software, the MicroAnalysis Toolkit, for LA-ICP-MS. Building upon the success of BNEIR and the collaboration with the creator of the MicroAnalysis Toolkit to broaden interoperability of this popular EI software, the aim of this administrative supplement is to complete the groundwork necessary to transition the MicroAnalysis Toolkit to a web-based interface, where users can access their data from local sources or online repositories and perform data visualization and analysis on a device independent platform. The ability to run the MicroAnalysis Toolkit from an online interface would (1) remove financial barriers to, and simplify data processing for, BNEIR users with limited experience in EI; (2) streamline the data pipeline for numerous X-ray data sources; (3) make FAIR databases for legacy EI data possible: preventing legacy data from being lost; (4) establish a standard for EI software interoperability in a rapidly growing analytical field, and (5) pave the way for online interfaces for other EI software applications.

项目概要 生物体利用化学元素的通量来控制新陈代谢等基本过程， 在人体内可以检测到多达 60 种化学元素， 其中 25 种重要元素的失调是神经系统疾病和血管生成的基础。 化学元素用于癌症的肿瘤形成以及对传染病的免疫反应。 疾病诊断和治疗；钆是一种常见的金属磁共振造影剂 纳米颗粒显示出药物输送的前景，铂和砷化合物是化疗药物。 元素成像 (EI) 提供多种化学元素的浓度和分布数据 以图像形式进行原位研究；加速对各种生物金属机制的理解； EI 进一步推动了 NIGMS 的目标，即支持基础研究，从而提高我们的能力。 了解生物过程，为疾病诊断、治疗、 然而，EI 技术对于感应激光消融来说是具有挑战性的。 耦合等离子体质谱 (LA-ICP-MS) 是一种基于实验室的 EI 技术，其应用日益广泛 适用于生物医学应用，其检测限与其他 EI 技术相当或更低。 达特茅斯微量元素分析核心 (TEAC) 是一种成熟且备受推崇的共享资源， 支持美国各地的研究人员，由 EI 和 ICP-MS 领域经验丰富的研究人员组成，使用国家- TEAC 拥有最先进的仪器，并与行业合作伙伴建立了良好的联系。 当前的临时服务是建立一个专门的生物医学 EI 用户设施； 成像资源 (BNEIR) (1R24GM141194) 我们的目标是扩大生物医学中 EI 技术的使用范围。 我们以 TEAC 现有的基础设施、管理、仪器和专业知识为基础进行咨询。 与斯坦福同步辐射光源 Sam Webb 博士合作，进一步调整他的免费 EI LA-ICP-MS 的微量分析工具包以 BNEIR 的成功和合作为基础。 与 MicroAnalysis Toolkit 的创建者合作，扩大这款流行 EI 软件的互操作性，目的是 本行政补充文件旨在完成微分析工具包过渡所需的基础工作 到基于网络的界面，用户可以从本地来源或在线存储库访问数据， 在独立于设备的平台上执行数据可视化和分析能够运行微观分析。 在线界面的工具包将 (1) 消除 BNEIR 的财务障碍并简化数据处理 EI 经验有限的用户；(2) 简化众多 X 射线数据源的数据管道；(3) 遗留 EI 数据的 FAIR 数据库成为可能：防止遗留数据丢失 (4) 建立标准； EI 软件在快速发展的分析领域中的互操作性，以及 (5) 为在线界面铺平道路 其他 EI 软件应用程序。