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

项目摘要 生物体利用化学元素的通量来控制基本过程，如新陈代谢， 稳态、细胞周期和受精。在人体内可以检测到多达60种化学元素， 其中25个是必不可少的。必需元素的失调支持神经系统疾病、血管生成 和癌症中的肿瘤形成，以及对感染性疾病的免疫反应。化学元素用于 疾病诊断和治疗;钆是一种常见的磁共振造影剂，金属基 纳米颗粒显示出药物递送的前景，铂和砷化合物是化学治疗剂。 元素成像（EI）提供多种化学元素的浓度和分布数据 以图像的形式原位;加速对多种生物金属机制的理解， 从环境到生物医学EI进一步推进NIGMS的目标，以支持基础研究，提高我们的 了解生物过程，并为疾病诊断，治疗， 和预防然而，EI技术是具有挑战性的访问和掌握。激光剥蚀电感 耦合等离子体质谱（LA-ICP-MS）是一种基于实验室的电子轰击技术， 适用于生物医学应用，与其他EI技术相比具有相当或更低的检测限。的 达特茅斯微量元素分析核心（TEAC）是一个既定的和高度重视的共享资源， 支持美国各地的研究人员，由EI和ICP-MS方面经验丰富的研究人员组成，使用州- 最先进的仪器，并与行业合作伙伴建立了良好的联系。2021年，TEAC扩大了 目前的特设服务，以建立一个专门的生物医学EI用户设施;生物医学国家元素 成像资源（BNEIR）（1R24GM141194）。我们的目标是拓宽EI技术在生物医学中的应用 通过建立在TEAC现有的基础设施，管理，仪器和专业知识。我们咨询 与山姆韦伯博士，斯坦福大学同步辐射光源，以进一步适应他的免费提供EI 软件，微分析工具包，为LA-ICP-MS。 与MicroAnalysis Toolkit的创建者合作，以扩大这种流行的EI软件的互操作性， 本管理补充文件旨在完成过渡《微分析工具包》所需的基础工作 到基于Web的界面，用户可以从本地源或在线存储库访问他们的数据， 在设备独立平台上执行数据可视化和分析。运行微量分析的能力 在线界面的工具包将（1）消除BNEIR的财务障碍，并简化其数据处理 EI经验有限的用户;（2）简化大量X射线数据源的数据管道;（3）使 FAIR数据库为遗留EI数据提供可能：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的互操作性，以及（5）为在线接口铺平道路， 其他EI软件应用程序。

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.