GReD, CNRS, INSERM, Université Clermont Auvergne, Clermont-Ferrand, France.
Université Côte d'Azur, CNRS, IPMC, Valbonne, France.
F1000Res. 2022 Apr 5;11:392. doi: 10.12688/f1000research.110385.2. eCollection 2022.
The Open Microscopy Environment Remote Objects (OMERO) is an open-source image manager used by many biologists to store, organize, view, and share microscopy images, while the open-source software ImageJ/Fiji is a very popular program used to analyse them. However, there is a lack of an easy-to-use generic tool to run a workflow on a batch of images without having to download them to local computers, and to automatically organize the results in OMERO. To offer this functionality, we have built (i) a library in Java: "Simple OMERO Client", to communicate with an OMERO database from Java software, (ii) an ImageJ/Fiji plugin to run a macro-program on a batch of images from OMERO and (iii) a new set of Macro Functions, "OMERO Macro extensions", dedicated to interact with OMERO in macro-programming. The latter is intended for developers, with additional possibilities using tag criteria, while the "Batch OMERO plugin" is more geared towards non-IT scientists and has a very easy to use interface. Each tool is illustrated with a use case.
OMERO 远程对象（Open Microscopy Environment Remote Objects）是一种开源的图像管理器，被许多生物学家用于存储、组织、查看和共享显微镜图像，而开源软件 ImageJ/Fiji 则是一个非常流行的程序，用于分析这些图像。然而，目前缺乏一种简单易用的通用工具，可以在不将图像下载到本地计算机的情况下对一批图像运行工作流程，并自动将结果组织到 OMERO 中。为了提供此功能，我们构建了（i）一个 Java 库：“Simple OMERO Client”，用于从 Java 软件与 OMERO 数据库进行通信，（ii）一个用于从 OMERO 运行批处理图像的 ImageJ/Fiji 插件，以及（iii）一组新的 Macro Functions，“OMERO Macro extensions”，专门用于在宏编程中与 OMERO 进行交互。后者面向开发人员，使用标签标准提供了更多可能性，而“Batch OMERO 插件”则更面向非 IT 科学家，具有非常易于使用的界面。每个工具都通过用例进行了说明。
