为生物图像数据建立机构 OMERO 环境:机构工作人员和用户的观点

IF 1.5 4区 工程技术 Q3 MICROSCOPY
Anett Jannasch, Silke Tulok, Chukwuebuka William Okafornta, Thomas Kugel, Michele Bortolomeazzi, Tom Boissonnet, Christian Schmidt, Andy Vogelsang, Claudia Dittfeld, Sems-Malte Tugtekin, Klaus Matschke, Leocadia Paliulis, Carola Thomas, Dirk Lindemann, Gunar Fabig, Thomas Müller-Reichert
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引用次数: 0

摘要

研究机构的现代生物成像核心设施对于管理和维护高端仪器、为研究人员提供实验设计、图像采集和数据分析方面的培训和支持至关重要。这些设施的一项重要任务是对复杂的多维生物成像数据进行专业管理,这些数据通常数量庞大,文件格式千差万别。本文详细介绍了德累斯顿工业大学(TU Dresden)的细胞成像核心设施(CFCI)成功实施 OME 远程对象系统(OMERO)用于生物成像特定研究数据管理(RDM)的过程。在确保符合 FAIR(可查找、可访问、可互操作、可重用)原则的前提下,我们在此概述了在将数据处理和存储适应到新的 RDM 系统时所面临的挑战。这些挑战包括引入标准化的特定组命名规范、使用标签和键值对进行元数据整理,以及整合现有的图像处理工作流程。通过分享我们的经验,本文旨在为打算实施 OMERO 作为生物成像数据管理系统的研究人员和教育机构提供见解和建议。我们展示了量身定制的决策和结构化方法如何在 RDM 实践中取得成功。
本文章由计算机程序翻译,如有差异,请以英文原文为准。

Setting up an institutional OMERO environment for bioimage data: Perspectives from both facility staff and users

Setting up an institutional OMERO environment for bioimage data: Perspectives from both facility staff and users

Modern bioimaging core facilities at research institutions are essential for managing and maintaining high-end instruments, providing training and support for researchers in experimental design, image acquisition and data analysis. An important task for these facilities is the professional management of complex multidimensional bioimaging data, which are often produced in large quantity and very different file formats. This article details the process that led to successfully implementing the OME Remote Objects system (OMERO) for bioimage-specific research data management (RDM) at the Core Facility Cellular Imaging (CFCI) at the Technische Universität Dresden (TU Dresden). Ensuring compliance with the FAIR (findable, accessible, interoperable, reusable) principles, we outline here the challenges that we faced in adapting data handling and storage to a new RDM system. These challenges included the introduction of a standardised group-specific naming convention, metadata curation with tagging and Key–Value pairs, and integration of existing image processing workflows. By sharing our experiences, this article aims to provide insights and recommendations for both individual researchers and educational institutions intending to implement OMERO as a management system for bioimaging data. We showcase how tailored decisions and structured approaches lead to successful outcomes in RDM practices.

Lay description: Modern bioimaging facilities at research institutions are crucial for managing advanced equipment and supporting scientists in their research. These facilities help with designing experiments, capturing images, and analyzing data. One of their key tasks is organizing and managing large amounts of complex image data, which often comes in various file formats and are difficult to handle.

This article explains how the Core Facility Cellular Imaging (CFCI) at Technische Universität Dresden successfully implemented a specialized system called OMERO. With this system it is possible to manage and organize bioimaging data sustainably in a way that they are findable, accessible, interoperable and reusable according the FAIR principles. We describe the practical implementation process on exemplary projects within scientific research and medical education. We discuss the challenges we faced, such as creating a standard way to name files, organizing important information about the images (known as metadata), and ensuring that existing image processing methods could work with the new system.

By sharing our experience, we aim to offer practical advice and recommendations for other researchers and institutions interested in using OMERO for managing their bioimaging data. We highlight how careful planning and structured approaches can lead to successful data management practices, making it easier for researchers to store, access, and reuse their valuable data.

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来源期刊
Journal of microscopy
Journal of microscopy 工程技术-显微镜技术
CiteScore
4.30
自引率
5.00%
发文量
83
审稿时长
1 months
期刊介绍: The Journal of Microscopy is the oldest journal dedicated to the science of microscopy and the only peer-reviewed publication of the Royal Microscopical Society. It publishes papers that report on the very latest developments in microscopy such as advances in microscopy techniques or novel areas of application. The Journal does not seek to publish routine applications of microscopy or specimen preparation even though the submission may otherwise have a high scientific merit. The scope covers research in the physical and biological sciences and covers imaging methods using light, electrons, X-rays and other radiations as well as atomic force and near field techniques. Interdisciplinary research is welcome. Papers pertaining to microscopy are also welcomed on optical theory, spectroscopy, novel specimen preparation and manipulation methods and image recording, processing and analysis including dynamic analysis of living specimens. Publication types include full papers, hot topic fast tracked communications and review articles. Authors considering submitting a review article should contact the editorial office first.
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