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OME-Zarr:具有国际社区支持的云优化生物成像文件格式。

OME-Zarr: a cloud-optimized bioimaging file format with international community support.

机构信息

German BioImaging-Gesellschaft für Mikroskopie und Bildanalyse e.V., Constance, Germany.

Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK.

出版信息

Histochem Cell Biol. 2023 Sep;160(3):223-251. doi: 10.1007/s00418-023-02209-1. Epub 2023 Jul 10.

Abstract

A growing community is constructing a next-generation file format (NGFF) for bioimaging to overcome problems of scalability and heterogeneity. Organized by the Open Microscopy Environment (OME), individuals and institutes across diverse modalities facing these problems have designed a format specification process (OME-NGFF) to address these needs. This paper brings together a wide range of those community members to describe the cloud-optimized format itself-OME-Zarr-along with tools and data resources available today to increase FAIR access and remove barriers in the scientific process. The current momentum offers an opportunity to unify a key component of the bioimaging domain-the file format that underlies so many personal, institutional, and global data management and analysis tasks.

摘要

一个不断壮大的社区正在构建下一代生物成像文件格式 (NGFF),以克服可扩展性和异构性方面的问题。由开放显微镜环境 (OME) 组织,面临这些问题的来自不同模态的个人和机构设计了一种格式规范流程 (OME-NGFF) 来满足这些需求。本文汇集了众多社区成员,描述了云优化格式本身——OME-Zarr,以及当前可用的工具和数据资源,以提高 FAIR 访问并消除科学过程中的障碍。当前的势头为统一生物成像领域的一个关键组件提供了机会——该格式是许多个人、机构和全球数据管理和分析任务的基础。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5e11/10492740/912460607972/418_2023_2209_Fig1_HTML.jpg

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