ModularImageAnalysis (MIA): Assembly of modularised image and object analysis workflows in ImageJ

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 processin...

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Bibliographic Details
Published in:	Journal of microscopy (Oxford) Vol. 296; no. 3; pp. 173 - 183
Main Authors:	Cross, Stephen J., Fisher, Jordan D. J. R., Jepson, Mark A.
Format:	Journal Article
Language:	English
Published:	England Wiley Subscription Services, Inc 01-12-2024
Subjects:	automated analysis bioimage analysis Data transfer (computers) Graphical user interface Image acquisition image analysis Image processing ImageJ Information processing modular analysis Modules Object recognition Pattern recognition reproducible analysis Workflow ImageJ reproducible analysis bioimage analysis automated analysis image analysis modular analysis
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Description
Summary:	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.
Bibliography:	Correction added on 13 October 2023, after first online publication: Grant code added. ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23
ISSN:	0022-2720 1365-2818 1365-2818
DOI:	10.1111/jmi.13227