QUAREP-LiMi. Development of quality control tools and methodologies for light microscopy: improving image data quality, reliability & reproducibility.

背景资料：自从在世纪晚期引入和广泛使用以来，显微镜已经从定性的图像收集工具发展为能够获取信息丰富的图像的自动化的复杂仪器。事实上，显微镜现在支撑着许多生物医学研究，并被用来为许多新兴的“组学”技术提供空间背景。观察一个样本往往是不够的;有必要备份这些观察与定量信息回答往往复杂的生物医学问题。这些观察结果和数据的质量与用于制作它们的显微镜的质量一样好：因此，重要的是要了解，记录和提供显微镜的“质量”。有了这些信息，研究人员和公众将对这些仪器收集、解释和发布的成像数据充满信心。问题：荧光显微镜的标准化在科学界并没有得到广泛实践：最近的一项大型（来自大约200个成像实验室）由联合会成员进行的全球显微镜用户社区调查，我的团队强调了在选择记录哪些显微镜质量控制（QC）指标以及执行频率方面的不一致性。解决方案：我们已经建立了一个由显微镜学家和其他相关用户/团体组成的国际联盟，QUAREP-LiMi（光学显微镜中仪器和图像的质量评估和再生），其最初目标是在显微镜界获得共识，并确定一套应在定义的时间间隔内对显微镜进行的QC测试。我们希望，这将使这一主题“神秘化”，并鼓励良好的显微镜维护实践，促进实验室和研究设施之间采用光学显微镜的标准化。与显微镜和显微镜组件制造商合作，我们将寻求自动化QC数据采集和分析过程，目的是将此“显微镜质量”信息存储在图像元数据（描述图像如何采集的图像信息）中。我们将确保所有开发的协议，样品和图像分析工具免费提供给经验丰富和缺乏经验的显微镜工作者。QUAREP-LiMi的工作将提高光学显微镜内更好的质量控制的知名度和需求，因此，我们希望能够影响政策制定者，并确保所有已发布的显微镜图像都可以使用描述显微镜“质量”的最小元数据集。为此，我们正在与出版商、图像数据库和资助机构合作。资金需求：QUAREP-LiMi已经迅速发展到270多名来自学术和商业背景的成员，并且完全由志愿成员组成。组织和管理这样一个庞大而分散的集团是困难和耗时的，通过此次融资投标，我们将聘请一名技术项目经理来管理，协调和有效地沟通联合体的工作。影响：如果QUAREP-LiMi的目标得以实现，许多社区和利益相关者将受益：1.研究科学家和成像科学家将利用QC程序的统一和简化。2.科学出版商和公众将受益于对科学出版物的价值和可复制性的全面增强的信任。资助机构将受益于质量控制实践的计划改进，这无疑将提高图像数据的可靠性、可重复性和开放性，从而提高科学产出的整体价值和质量。核心成像设施和显微镜保管人和用户，他们将受益于对其图像数据准确性的信心增强以及所执行的QC测量的适用性，以回答他们的科学问题。

Background: since their introduction and widespread use in the late 17th Century, microscopes have moved from qualitative, image-collecting tools to automated, complex instruments capable of acquiring information-rich images. Indeed, microscopy now underpins a lot of biomedical research and is being used to provide the spatial context to many emerging 'omics' techniques. Observing a sample is often insufficient; there is a need to back-up these observations with quantitative information to answer often complex biomedical questions. The quality of these observations and data are only as good as the quality of the microscope used to make them: thus, it is important that microscope 'quality' is understood, documented and made available. With this information to hand, researchers and the public will have full confidence in the imaging data collected, interpreted and published from such instruments.The problem: standardisation for fluorescence microscopy is not widely practised in the scientific community: a recent large (from approximately 200 imaging labs) global microscopy-user community survey performed by members of the Co-I team have highlighted the inconsistencies when it comes to choosing which microscope Quality Control (QC) metrics to record and how frequently they are performed. The solution: we have established an international consortium of microscopists and other related users/ groups, QUAREP-LiMi (QUality Assessment and REProducibility for Instruments & Images in Light Microscopy) with an initial aim to gain consensus across the microscopy community and identify a set of QC tests that should be performed on microscopes at defined intervals. This will, we hope, 'demystify' the subject and encourage good practise for microscope maintenance and promote standardisation between labs and research facilities employing light microscopy. Working with microscope and microscope component manufacturers, we will seek to automate the process of QC data capture and analysis with an intent to store this 'microscope quality' information in the image metadata (information about an image that describes how that image was captured). We will ensure that all developed protocols, samples and image analysis tools are made freely available and accessible to both experienced and inexperienced microscopists. The work of QUAREP-LiMi will raise the profile of, and the need for, better quality control within light microscopy and as a result, we hope will influence policy makers and ensure that a minimal set of metadata that describes microscope 'quality' are made available with all published microscopy images. For this, we are working with publishers, image data repositories and funding bodies.The need for funding: QUAREP-LiMi has grown rapidly to over 270 members from both academic and commercial backgrounds and consists entirely of voluntary members. Organising and managing such a large and disparate group is difficult and time consuming, with this funding bid, we will employ a technical project manager to manage, coordinate and effectively communicate the work of the consortium.Impact: if the aims of QUAREP-LiMi are realised, a number of communities and stakeholders will benefit:1. Research scientists and imaging scientists will take advantage of the harmonization and simplification of the QC procedures.2. Scientific publishers and the general public will profit from an overall enhanced trust in the value and reproducibility of scientific publications.3. Funding bodies will benefit from the planned improvement of QC practices that will undoubtedly improve image data reliability, reproducibility, and openness, increasing overall the value and quality of scientific output.4. Core imaging facilities and microscope custodians and users, who will profit from heightened confidence in the accuracy of their image data and the suitability of performed QC measurements to answer their scientific questions.