Wolfson Bioimaging Facility, University of Bristol, Bristol, UK.

Department of Computer Science, University of Warwick, Coventry, UK.

Vivedia Ltd., Unit 29, Sheffield, UK.

ModularImageAnalysis (MIA) is an ImageJ plugin providing a code-free graphical environment in which complex automated analysis workflows can be constructed and distributed. The broad range of included modules cover all stages of a typical analysis workflow, from image loading through image processing, object detection, extraction of measurements, measurement-based filtering, visualisation and data exporting. MIA provides out-of-the-box compatibility with many advanced image processing plugins for ImageJ including Bio-Formats, DeepImageJ, MorphoLibJ and TrackMate, allowing these tools and their outputs to be directly incorporated into analysis workflows. By default, modules support spatially calibrated 5D images, meaning measurements can be acquired in both pixel and calibrated units. A hierarchical object relationship model allows for both parent-child (one-to-many) and partner (many-to-many) relationships to be established. These relationships underpin MIA's ability to track objects through time, represent complex spatial relationships (e.g. topological skeletons) and measure object distributions (e.g. count puncta per cell). MIA features dual graphical interfaces: the ‘editing view’ offers access to the full list of modules and parameters in the workflow, while the simplified ‘processing view’ can be configured to display only a focused subset of controls. All workflows are batch-enabled by default, with image files within a specified folder being processed automatically and exported to a single spreadsheet. Beyond the included modules, functionality can be extended both internally, through integration with the ImageJ scripting interface, and externally, by developing third-party Java modules that extend the core MIA framework. Here we describe the design and functionality of MIA in the context of a series of real-world example analyses. 中文翻译： ModularImageAnalysis (MIA) 是一个 ImageJ 插件，提供无代码图形环境，可以在其中构建和分发复杂的自动化分析工作流程。包含的模块范围广泛，涵盖典型分析工作流程的所有阶段，从图像加载到图像处理、对象检测、测量值提取、基于测量值的过滤、可视化和数据导出。MIA 提供与 ImageJ 的许多高级图像处理插件的开箱即用兼容性，包括 Bio-Formats、DeepImageJ、MorphoLibJ 和 TrackMate，允许这些工具及其输出直接合并到分析工作流程中。默认情况下，模块支持空间校准的 5D 图像，这意味着可以以像素和校准单位获取测量结果。分层对象关系模型允许建立父子（一对多）和伙伴（多对多）关系。这些关系支撑了 MIA 随时间跟踪对象、表示复杂空间关系（例如拓扑骨架）和测量对象分布（例如计算每个细胞的斑点）的能力。MIA 具有双图形界面：“编辑视图”提供对工作流程中模块和参数的完整列表的访问，而简化的“处理视图”可以配置为仅显示控件的重点子集。默认情况下，所有工作流程均启用批处理，指定文件夹中的图像文件会自动处理并导出到单个电子表格。除了包含的模块之外，功能还可以通过与 ImageJ 脚本接口集成进行内部扩展，以及通过开发扩展核心 MIA 框架的第三方 Java 模块进行外部扩展。在这里，我们通过一系列实际示例分析来描述 MIA 的设计和功能。