Public archiving and data integration in the era of multi-modal imaging

多模态成像时代的公共归档和数据集成

• 批准号: MR/P019544/1
• 负责人: Gerard Kleywegt
• 金额: $ 120.62万
• 依托单位: European Bioinformatics Institute
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2017
• 资助国家: 英国
• 起止时间: 2017 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=MR%2FP019544%2F1
• 关键词: Public; archiving; data; integration; era

Consider a scenario in which one could image a whole organism, and then progressively zoom in to the level of organs, tissue, cells, molecules and finally atoms, at each step revealing more detail. Although the prospect of scaling from the level of organisms to atoms may seem far-fetched, there now do exist imaging techniques to cover almost all of these imaging scales. There is a growing body of biomedical research where information from different imaging techniques at different scales are combined, i.e., multi-modal imaging, to piece together a more comprehensive understanding of a problem than can be obtained from one technique alone. However the wider integration of imaging data is hampered by the lack of public accessibility to this data and commonly used formats for representing the information required to bring the different modalities into register. To address all scales of imaging at once would be extremely challenging given the enormous scope of the problem, the disparate user communities and the resources required.In the field of molecular structural biology, which involves the study of the 3D structure of molecules, the concept of public archiving of structures is well established with archives such as the PDB (atomic model data) and EMDB (3D volumes derived from electron microscopy (EM) experiments including electron tomography) enjoying widespread community support. Our strategy has therefore been to first consider the integration between the cellular and molecular imaging scales in consultation with the relevant communities. We organized two 'expert' workshops inviting key specialists and community representatives which resulted in concrete recommendations including - exploring public archiving of large EM image datasets, the development of visualisation tools that provide an integrated, problem-centric view of structures piecing together information from the different imaging modalities, the imaging modalities which should be targeted first - 3D scanning electron microscopy (3DSEM), soft X-ray tomography (SXT) and correlative light and electron microscopy (CLEM) , and the development of a format to facilitate data integration. In an on-going MRC-funded project (grant MR/L007835; MOL2CELL) we have successfully developed EMPIAR - a public archive for raw EM image data, which is capable of handling data-sets in the terabyte range. We are developing a web-based visualisation tool (Volume browser) that provides an openly accessible integrated view of 3D biological data at the cellular and molecular scales derived from the EMDB and PDB archives, and a format that supports one form of integration between these scales. In the proposed project we want to build upon the work started in the MOL2CELL project and a) extend archiving in EMPIAR to include full support for the proposed imaging modalities, b) extend format support to represent the information required to bring the different modalities into register and use this to improve and extend the Volume browser, and c) develop software and data pipelines from major microscopy centres to facilitate data deposition to EMDB and EMPIAR and to improve the quality and quantity of the information collected.While the scope of the project is limited to the molecular and cellular imaging scales, the outcomes are potentially applicable to other imaging modalities. The inclusion of the new imaging modalities into EMPIAR can serve as one model for how public archiving can be organized and established, the format developed can be used for data integration between other imaging modalities and the Volume browser for integrated visualisation with other imaging scales. Furthermore developers of resources for multi-modal imaging data stand to gain from open access to the software developed in the project and the data in EMPIAR.

考虑这样一个场景：人们可以对整个生物体进行成像，然后逐步放大到器官、组织、细胞、分子，最后是原子的水平，每一步都能揭示更多的细节。虽然从生物体到原子的尺度的前景看起来很遥远，但现在确实存在着几乎涵盖所有这些成像尺度的成像技术。生物医学研究的主体越来越多，其中来自不同尺度的不同成像技术的信息被组合，即，多模态成像，拼凑出一个更全面的了解一个问题，比可以从一个技术单独获得。然而，由于公众无法获取成像数据，也无法使用通用格式来表示登记不同模式所需的信息，因此成像数据的更广泛整合受到阻碍。考虑到问题的巨大范围、不同的用户群体和所需的资源，一次解决所有尺度的成像将是极具挑战性的。在分子结构生物学领域，涉及分子的3D结构的研究，公共结构档案的概念已经在PDB等档案馆中得到了很好的确立（原子模型数据）和EMDB（来自电子显微镜（EM）实验的3D卷，包括电子断层扫描），享有广泛的社区支持。因此，我们的策略是首先考虑与相关团体协商，整合细胞和分子成像尺度。我们组织了两次“专家”研讨会，邀请了主要专家和社区代表，提出了具体建议，包括-探索大型EM图像数据集的公共存档，开发可视化工具，提供整合的，以问题为中心的结构视图，将不同成像模式的信息拼凑在一起，应首先针对的成像方式--三维扫描电子显微镜（3DSEM）、软X射线断层摄影（SXT）和相关光学和电子显微镜（CLEM），以及开发一种便于数据整合的格式。在一个正在进行的MRC资助的项目（赠款MR/L007835; MOL 2CELL），我们已经成功地开发了EMPIAR -原始EM图像数据的公共存档，这是能够处理数据集的TB范围。我们正在开发一个基于网络的可视化工具（卷浏览器），它提供了一个开放的三维生物数据的综合视图，在细胞和分子尺度上来自EMDB和PDB档案，以及一种格式，支持这些尺度之间的一种形式的集成。在提议的项目中，我们希望以MOL 2CELL项目中开始的工作为基础，a）扩展EMPIAR中的存档，以包括对提议的成像模态的全面支持，B）扩展格式支持，以表示将不同模态纳入配准所需的信息，并使用该信息来改进和扩展容积浏览器，以及c）开发软件和主要显微镜中心的数据管道，以方便将数据存入EMDB和EMPIAR，并提高所收集信息的质量和数量。虽然该项目的范围仅限于分子和细胞成像尺度，结果可能适用于其他成像方式。将新的成像模式纳入EMPIAR可以作为如何组织和建立公共存档的一个模型，开发的格式可以用于其他成像模式之间的数据集成，容积浏览器用于与其他成像尺度集成可视化。此外，多模态成像数据资源的开发人员可以从开放获取项目中开发的软件和EMPIAR中的数据中获益。

项目成果

EMPIAR: the Electron Microscopy Public Image Archive.

• DOI: 10.1093/nar/gkac1062
• 发表时间: 2023-01-06
• 期刊: NUCLEIC ACIDS RESEARCH
• 影响因子: 14.9
• 作者: Iudin, Andrii;Korir, Paul K.;Somasundharam, Sriram;Weyand, Simone;Cattavitello, Cesare;Fonseca, Neli;Salih, Osman;Kleywegt, Gerard J.;Patwardhan, Ardan
• 通讯作者: Patwardhan, Ardan

Methods in Cell Biology

• DOI: 10.1016/s0091-679x(15)00182-x
• 发表时间: 2012
• 作者: A. Asthagiri;A. Arkin

Volume EM: a quiet revolution takes shape.

• DOI: 10.1038/s41592-023-01861-8
• 发表时间: 2023-06
• 期刊: Nature methods
• 影响因子: 48
• 作者: Collinson LM;Bosch C;Bullen A;Burden JJ;Carzaniga R;Cheng C;Darrow MC;Fletcher G;Johnson E;Narayan K;Peddie CJ;Winn M;Wood C;Patwardhan A;Kleywegt GJ;Verkade P
• 通讯作者: Verkade P

Volume electron microscopy.

• DOI: 10.1038/s43586-022-00131-9
• 发表时间: 2022-07-07
• 期刊: Nature reviews. Methods primers
• 作者: Peddie CJ;Genoud C;Kreshuk A;Meechan K;Micheva KD;Narayan K;Pape C;Parton RG;Schieber NL;Schwab Y;Titze B;Verkade P;Aubrey A;Collinson LM
• 通讯作者: Collinson LM

Image archiving at EMBL-EBI - EMPIAR and the BioImage Archive

EMBL-EBI 的图像存档 - EMPIAR 和 BioImage Archive

• DOI: 10.1017/s1431927621009892
• 发表时间: 2021
• 期刊: Microscopy and Microanalysis
• 影响因子: 2.8
• 作者: Kleywegt G