ImageJ is a widely‐used open‐source software that allows users to visualize, inspect, quantify, and validate scientific image data. Therefore, we also discuss the contributions of ImageJ2 to enhancing multidimensional image processing and interoperability in the ImageJ ecosystem. These new tools have been facilitated by profound architectural changes to the ImageJ core brought about by the ImageJ2 project. Moreover, new capabilities for deep learning are being added to ImageJ, reflecting a shift in the bioimage analysis community towards exploiting artificial intelligence. These plugins and tools have been developed to address user needs in several areas such as visualization, segmentation, and tracking of biological entities in large, complex datasets. Here we review the core features of this ecosystem and highlight how ImageJ has responded to imaging technology advancements with new plugins and tools in recent years. We refer to this entire ImageJ codebase and community as the ImageJ ecosystem. It is available in many forms, including the widely used Fiji distribution. ImageJ consists of many components, some relevant primarily for developers and a vast collection of user‐centric plugins. The close collaboration between programmers and users has resulted in adaptations to accommodate new challenges in image analysis that address the needs of ImageJ's diverse user base. ImageJ is an open‐source image analysis software platform that has aided researchers with a variety of image analysis applications, driven mainly by engaged and collaborative user and developer communities. As techniques for acquiring images increase in complexity, resulting in larger multidimensional datasets, imaging software must adapt. The author, Wayne Rasband ( is at the Research Services Branch, National Institute of Mental Health, Bethesda, Maryland, USA.For decades, biologists have relied on software to visualize and interpret imaging data. ImageJ is being developed on Mac OS X using its built in editor and Java compiler, plus the BBEdit editor and the Ant build tool. User-written plugins make it possible to solve almost any image processing or analysis problem. Custom acquisition, analysis and processing plugins can be developed using ImageJ's built in editor and Java compiler. ImageJ was designed with an open architecture that provides extensibility via Java plugins. Density or gray scale calibration is also available. Spatial calibration is available to provide real world dimensional measurements in units such as millimeters. The program supports any number of windows (images) simultaneously, limited only by available memory. All analysis and processing functions are available at any magnification factor. Image can be zoomed up to 32:1 and down to 1:32. It does geometric transformations such as scaling, rotation and flips. It supports standard image processing functions such as contrast manipulation, sharpening, smoothing, edge detection and median filtering. It can create density histograms and line profile plots. It can calculate area and pixel value statistics of user-defined selections. It is multithreaded, so time-consuming operations such as image file reading can be performed in parallel with other operations. It supports "stacks", a series of images that share a single window. It can read many image formats including TIFF, GIF, JPEG, BMP, DICOM, FITS and "raw". It can display, edit, analyze, process, save and print 8-bit, 16-bit and 32-bit images. Downloadable distributions are available for Windows, Mac OS, Mac OS X and Linux. ![]() It runs, either as an online applet or as a downloadable application, on any computer with a Java 1.4 or later virtual machine. ImageJ is a public domain Java image processing program inspired by NIH Image for the Macintosh.
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