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ImageJ
ImageJ
ImageJ
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ImageJ
DeveloperWayne Rasband (retired from NIH)
Stable release
1.54r[1] Edit this on Wikidata / 25 September 2025
Repository
Operating systemAny (Java-based)
TypeImage processing
LicensePublic Domain, BSD-2
Websiteimagej.net

ImageJ is a Java-based image processing program developed at the National Institutes of Health and the Laboratory for Optical and Computational Instrumentation (LOCI, University of Wisconsin).[2][3] Its first version, ImageJ 1.x, is developed in the public domain, while ImageJ2 and the related projects SciJava, ImgLib2, and SCIFIO are licensed with a permissive BSD-2 license.[4] ImageJ was designed with an open architecture that provides extensibility via Java plugins and recordable macros.[5] Custom acquisition, analysis and processing plugins can be developed using ImageJ's built-in editor and a Java compiler. User-written plugins make it possible to solve many image processing and analysis problems, from three-dimensional live-cell imaging[6] to radiological image processing,[7] multiple imaging system data comparisons[8] to automated hematology systems.[9] ImageJ's plugin architecture and built-in development environment has made it a popular platform for teaching image processing.[10][11]

ImageJ can be run as an online applet, a downloadable application, or on any computer with a Java 5 or later virtual machine. Downloadable distributions are available for Microsoft Windows, the classic Mac OS, macOS, Linux, and the Sharp Zaurus PDA. The source code for ImageJ is freely available.[12]

The project developer, Wayne Rasband, retired from the Research Services Branch of the NIH's National Institute of Mental Health in 2010, but continues to develop the software.

Features

[edit]

ImageJ can display, edit, analyze, process, save, and print 8-bit color and grayscale, 16-bit integer, and 32-bit floating point images. It can read many image file formats, including TIFF, PNG, GIF, JPEG, BMP, DICOM, and FITS, as well as raw formats. ImageJ supports image stacks, a series of images that share a single window, and it is multithreaded, so time-consuming operations can be performed in parallel on multi-CPU hardware. ImageJ can calculate area and pixel value statistics of user-defined selections and intensity-thresholded objects. It can measure distances and angles. It can create density histograms and line profile plots. It supports standard image processing functions such as logical and arithmetical operations between images, contrast manipulation, convolution, Fourier analysis, sharpening, smoothing, edge detection, and median filtering. It does geometric transformations such as scaling, rotation, and flips. The program supports any number of images simultaneously, limited only by available memory.

History

[edit]

Before the release of ImageJ in 1997, a similar freeware image analysis program known as NIH Image had been developed in Object Pascal for Macintosh computers running pre-OS X operating systems. Further development of this code continues in the form of Image SXM, a variant tailored for physical research of scanning microscope images. A Windows version – ported by Scion Corporation (now defunct), so-called Scion Image for Windows – was also developed. Both versions are still available but – in contrast to NIH Image – closed-source.[13]

On January 25, 2017, AstroImageJ (AIJ) was published by Karen Collins, John Kielkopf, Keivan Stassun, and Frederic Hessman. AIJ built upon the ImageJ processing pipeline, streamlining the software to excel at time-series differential photometry, light curve detrending and fitting, and ultra-precise light curve plotting. AIJ reads and write FITS files, generates master frames, and handles dark, bias, and flat-field subtraction all within the software. AIJ is used for multi-aperture differential photometry and exoplanet transit modeling, with built-in support for modifying aperture and annulus radii, choosing target and comparison objects simply by clicking, adjusting transit priors, and exporting data as a FITS and/or XML file.[14]

See also

[edit]
  • Eclipse ImageJ Plugin - An plugin which integrates ImageJ in a flexible tabbed view interface and also offers a powerful macro editor with a debugging interface.[15]
  • Bitplane - producers of image processing software with ImageJ compatibility
  • CellProfiler, a software package for high-throughput image analysis by interactive construction of workflow. The workflow could include ImageJ macro
  • CVIPtools A complete open-source GUI-based Computer Vision and Image Processing software, with C functions libraries COM based dll along with two utilities program for algorithm development and batch processing.
  • Fiji (software), an image processing package based on ImageJ
  • KNIME - an open-source data mining environment supporting image analysis developed in close collaboration with the next generation of ImageJ
  • List of free and open-source software packages
  • Microscope image processing

References

[edit]
[edit]
Revisions and contributorsEdit on WikipediaRead on Wikipedia

ImageJ

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ImageJ is a , Java-based image processing program designed for the acquisition, analysis, and visualization of scientific s, serving as a cross-platform successor to the original NIH Image software for Macintosh. Developed by Wayne Rasband at the (NIH) starting in 1997, ImageJ has evolved into a versatile tool supporting multithreaded operations and a broad ecosystem of plugins contributed by a global community of researchers. Key features include the ability to display, edit, process, and analyze 8-bit, 16-bit, and 32-bit images in formats such as TIFF, , , , and , with built-in tools for measurements like pixel statistics, histograms, distance calibrations, and geometric transformations including scaling, , and filtering. Its open architecture enables extensibility through plugins, macros, and scripts, allowing users to customize functionality for specialized applications in fields like , , and . Derivatives such as ImageJ2 (initiated in 2010 for enhanced modularity) and (a bundled distribution with pre-installed plugins) extend its capabilities while maintaining with the original ImageJ 1.x codebase.

Introduction

Overview

ImageJ is a , Java-based image processing program developed by Wayne Rasband at the (NIH). It has been actively maintained and extended with contributions from the Laboratory for Optical and Computational Instrumentation (LOCI) at the University of Wisconsin, focusing on enhancing its capabilities for scientific applications. The program's core purpose is to facilitate the processing and analysis of scientific , with particular emphasis on multidimensional datasets such as those generated by techniques. This includes tools for image display, editing, filtering, and quantitative measurements, making it a versatile platform for researchers in , , and related fields. As of November 2025, the current stable version is 1.54s6, released on October 2, 2025. ImageJ is available for download from its official NIH-hosted site and operates cross-platform on Windows, macOS, and through its Java foundation, requiring Java 8 or later. ImageJ serves as a foundational component within the broader SciJava ecosystem, which encompasses shared libraries and frameworks for extensible scientific computing.

Purpose and Scope

ImageJ serves as an open-source platform for processing and analyzing scientific images, primarily targeting researchers in , , and related fields who handle visual data from , , and other experimental sources. It accommodates users ranging from novices, through its accessible , to advanced practitioners who leverage scripting capabilities for automated workflows and custom analyses. This broad appeal extends to educators and students in scientific disciplines, facilitating both research and teaching applications in quantitative image evaluation. The scope of ImageJ encompasses the management of 2D, 3D, and higher-dimensional images, including multidimensional stacks that represent spatial, temporal, and spectral dimensions such as x, y, z, time, and channels. It supports a variety of common image formats, including TIFF, , and , enabling core analysis tasks like precise of features, application of filters for enhancement, and interactive visualization of data. These capabilities focus on static and for scientific inquiry, emphasizing accuracy in tasks such as and segmentation without delving into real-time operations. While versatile, ImageJ has defined boundaries: it is not designed for real-time image processing, and handling very large datasets may require community-developed extensions to avoid performance bottlenecks. Its operation relies on the (JVM), which can introduce overhead depending on system resources and Java version compatibility. These limitations highlight its orientation toward offline, research-oriented analysis rather than high-speed or industrial-scale applications. ImageJ's status underscores its open-source ethos, permitting unrestricted free use, modification, and redistribution worldwide. This framework empowers a global community to contribute plugins, scripts, and improvements, ensuring ongoing evolution tailored to diverse scientific needs while maintaining accessibility without licensing costs.

History

Origins and Early Development

The precursor to ImageJ was NIH Image, a public-domain image processing program developed by Wayne Rasband at the U.S. (NIH) in 1987 specifically for the Macintosh platform. Designed as a low-cost tool for biological image analysis, it built upon Rasband's earlier PDP-11-based program named "Image," which analyzed gels, autoradiographs, and medical images. NIH Image was first distributed on floppy disks in spring 1987 and rapidly adopted by the scientific community through promotion on Macintosh forums. By the late 1990s, the growing prevalence of personal computers and the waning dominance of Macintosh systems exposed the platform-specific limitations of NIH Image, prompting Rasband to develop ImageJ as a cross-platform successor. Released in 1997, ImageJ was implemented in to capitalize on the language's portability, enabling it to run seamlessly on Windows, Unix, and Macintosh systems from a single codebase. This transition was driven by the need for open, extensible software to support scientific imaging research at NIH, addressing the demand for broader accessibility beyond proprietary hardware. ImageJ initially ported key functionalities from NIH Image, including basic image capture, display, enhancement, measurements, and filters, while incorporating a straightforward interface for user interaction. It also retained NIH Image's macro language, introduced in 1989 for automation, and the plugin system added in 1993 to enhance extensibility. The first public release, version 0.50, occurred on September 23, 1997, with version 1.0 following in 1998; both were distributed freely via the NIH website.

Key Milestones and Evolution

In the early , ImageJ's development emphasized extensibility, building on the plugin system from NIH Image to enable seamless integration of user-contributed extensions for specialized image processing tasks. The macro language, ported from NIH Image, provided a simple scripting tool for automating repetitive workflows and recording user actions as executable code. This foundation supported the growth of a dedicated plugin repository, where community developers began sharing tools for tasks like filtering and analysis, laying the groundwork for ImageJ's expansive ecosystem. In 2006, the distribution was initiated as a bundled version of ImageJ with pre-installed plugins, enhancing accessibility for life sciences applications. The 2010s marked a pivotal shift toward modernizing ImageJ for complex datasets, beginning with the introduction of ImageJ2 in 2011 as a ground-up rewrite designed to handle multidimensional scientific images more efficiently while preserving compatibility with legacy plugins. By 2014, ImageJ2 integrated with the SciJava Common framework, which standardized plugin development, , and across related projects, enhancing overall and collaborative maintenance. These advancements were driven by community hackathons and contributions, reflecting ImageJ's evolution from a standalone tool to a flexible platform. Community involvement surged during this decade, culminating in over 1,000 plugins available by , many bundled in distributions like to streamline access for life sciences users. In 2017, reflections on the 25-year legacy of the NIH Image family—including ImageJ—underscored its open-source impact, noting widespread adoption in scientific image analysis and the role of free accessibility in fostering innovation. Into the 2020s and up to 2025, development has focused on sustaining the legacy ImageJ1 codebase through regular updates, such as version 1.54r (released September 25, 2025), while prioritizing compatibility bridges to ensure seamless operation of older plugins within newer environments. This dual-track approach maintains accessibility for long-term users amid ongoing enhancements to ImageJ2. ImageJ's enduring influence is evident in its citations across thousands of scientific papers annually, spanning , , and beyond.

Technical Architecture

Core Components

ImageJ's core architecture is built upon a set of foundational libraries and frameworks that ensure , extensibility, and efficient handling of scientific image data. These components, developed under the SciJava umbrella, provide the essential infrastructure for image processing, operations, and user interaction, forming the backbone for both ImageJ1 and ImageJ2 implementations. SciJava Common serves as the dependency injection framework that promotes across ImageJ projects. It encapsulates program state within an application , enabling multiple contexts to coexist in the same (JVM), in contrast to singleton patterns used in earlier designs. This framework facilitates automatic plugin discovery through classpath scanning and annotations, allowing developers to extend core functionality via services such as event handling and display management. By providing a layered menuing system and extensible services, SciJava Common ensures that ImageJ remains adaptable to diverse scientific workflows. At the heart of ImageJ's data model lies ImgLib2, a general-purpose library for multidimensional image processing that supports arbitrary data types, including 8-bit unsigned integers and 32-bit floating-point values. ImgLib2 enables the representation of N-dimensional images through an interface-driven design, accommodating various data sources such as primitive arrays or on-demand disk reads. A key feature is its caching mechanism, which stores N-dimensional array cells to and from disk as needed, facilitating efficient handling of large datasets that exceed available memory. This library underpins ImageJ's ability to process complex, high-dimensional scientific images without rigid constraints on dimensionality or data structure. SCIFIO, the Scientific Image IO framework, handles the reading and writing of diverse image formats, extending the capabilities of Bio-Formats through a dedicated plugin that supports over 100 life sciences formats. Built atop SciJava Common, SCIFIO operates on N-dimensional data independently of underlying storage mechanisms, enabling seamless integration with ImageJ's File > Open and File > Export commands. It includes native support for formats like TIFF, JPEG-2000, and OME-TIFF, with fallback mechanisms to legacy ImageJ I/O for unsupported files. This framework ensures robust interoperability with proprietary and standard scientific imaging data. ImageJ's user interface is implemented using a Swing-based (GUI), featuring a , , , and , without a central work area; instead, elements like images and results appear in separate, draggable windows. The provides quick access to over 60 tools for selections, annotations, zooming, and scrolling, with customizable toolsets accessible via right-click menus. Menus organize commands into categories such as File, Edit, and , while the command system executes operations through these menus, displaying outputs in tables or dedicated windows. This design supports intuitive interaction while maintaining compatibility with plugin extensions.

ImageJ1 and ImageJ2

ImageJ1 represents the original legacy version of ImageJ, initially released in 1997 as a Java-based, cross-platform successor to NIH Image. It employs a flat image model centered on 2D images via the ImageProcessor class and extends to 3D through image stacks, with hyperstacks providing limited support for additional dimensions like channels or time. This architecture supports pixel data in 8-bit unsigned integer, 16-bit unsigned integer, and 32-bit floating-point formats, alongside color modes such as 24-bit RGB and 32-bit ARGB, but imposes constraints like a 2-gigapixel limit per image due to its array-based storage. In contrast, ImageJ2 constitutes a complete object-oriented rewrite initiated in to address the limitations of ImageJ1 for handling modern multidimensional datasets. It leverages the ImgLib2 library to model images as n-dimensional structures with arbitrary axes—such as spatial dimensions, time, spectral channels, or user-defined metadata—enabling and out-of-core processing for datasets exceeding available memory. This design supports virtually unlimited (up to ~2^31) and pixel sizes (up to ~2^63 per dimension), facilitating scalability for on contemporary hardware like multi-core processors and GPUs. ImageJ2's extensibility is enhanced through the SciJava Common framework, which provides modular plugins, , and a , diverging from ImageJ1's more ad-hoc plugin system. The first alpha release occurred on April 1, 2011, with the initial stable version following in 2014. The core design philosophies of ImageJ1 and ImageJ2 reflect evolving needs in scientific imaging: ImageJ1 prioritized simplicity and rapid feature addition through a procedural plugin interface, fostering a vast ecosystem of over 2,000 plugins but struggling with higher-dimensional or massive datasets. ImageJ2, however, emphasizes future-proof modularity and interoperability, integrating libraries like SCIFIO for flexible I/O and breaking ImageJ1's size barriers to accommodate terabyte-scale volumes common in fields like . To bridge these versions, ImageJ2 incorporates the ImageJ Legacy layer, which dynamically translates ImageJ1's flat model and plugins into its n-dimensional framework at runtime, ensuring 100% for macros, scripts, and legacy code without modification. An automatic updater, inherited from distributions like , further eases transitions by handling dependency updates seamlessly.

Features

Image Processing Capabilities

ImageJ provides a suite of built-in tools for fundamental image manipulation, enabling users to open, duplicate, crop, and resize images efficiently. These operations support a variety of image types, including 8-bit and 16-bit , 32-bit floating-point, RGB color, and hyperstack formats that handle multidimensional data such as z-stacks, color channels, and . For instance, images can be opened from common formats like TIFF, , , and , while cropping and resizing allow selection of regions of interest or scaling with options to maintain quality. Duplication preserves metadata and selections, facilitating non-destructive workflows. The software includes native filtering and enhancement algorithms to improve image quality and extract features. Convolution-based filters, such as for noise reduction and median filtering for removal, apply kernel-based smoothing with configurable parameters like for Gaussian. is supported via the , which computes gradients to highlight boundaries using a 3x3 kernel. Additionally, frequency-domain processing is available through the (FFT), enabling tasks like filtering and ; the discrete FFT is defined by the equation
Xk=∑n=0N−1xne−2πikn/NX_k = \sum_{n=0}^{N-1} x_n e^{-2\pi i kn / N}
for k=0,1,…,N−1k = 0, 1, \dots, N-1, where xnx_n are the input samples. Measurement tools in ImageJ allow quantitative analysis of image properties and objects. Built-in functions compute metrics such as area, perimeter, , and shape descriptors like circularity from selections or regions. Intensity histograms display the distribution of values, aiding in contrast assessment and thresholding decisions. The particle analyzer processes thresholded images to detect and measure multiple objects, incorporating watershed segmentation to separate touching particles and outputting results in tables for further statistical analysis. Visualization capabilities enhance interpretation of complex datasets. Lookup tables (LUTs) map pixel intensities to colors, with over 100 predefined options like or for pseudocoloring images. For 3D volumes, orthogonal slice views display x-y, x-z, and y-z projections interactively. Time-series data in hyperstacks can be animated as frame sequences, supporting playback controls to visualize dynamic processes.

Extensibility and Customization

ImageJ's extensibility is primarily achieved through plugins, which are Java-based extensions that can be loaded dynamically to add new functionality. These plugins leverage the SciJava Common plugin framework, allowing developers to create custom commands, tools, and interfaces that integrate seamlessly with the core application. Over a thousand plugins are available, distributed via the built-in updater, which enables users to install, update, and manage extensions without manual intervention. A prominent example is TrackMate, a plugin for single-particle tracking that supports detection, linking, and visualization of particle trajectories in multidimensional images. In addition to plugins, ImageJ supports macros written in its dedicated ImageJ Macro Language (IJM), a simple, typeless scripting system designed for automating repetitive tasks and creating custom workflows. Macros can be recorded directly from user interactions or authored manually, featuring straightforward syntax for variables, loops, conditionals, and calls to built-in functions or plugins. This language is particularly accessible for non-programmers, enabling quick automation of image processing sequences without requiring compilation. For more advanced scripting, ImageJ integrates multiple languages through its extensible scripting framework, including BeanShell, , Python via , and Ruby via . These allow users to write scripts that access the full ImageJ , perform complex computations, and interact with external libraries, with support for running in headless mode or integrating with environments like Jupyter notebooks via packages such as pyimagej. Scripts can be executed from the menu, toolbar, or editor, providing flexibility for both ad-hoc analysis and . Customization in ImageJ extends to user interface modifications, such as reconfiguring the to include custom tools or macros and adding new menu items through plugin implementations. Developers utilize the ImageJ API, which provides annotated interfaces for plugin types, to build these extensions, ensuring compatibility across ImageJ1 and ImageJ2 architectures. This facilitates community contributions, allowing users to tailor the software to specific research needs without altering the core codebase.

Distributions and Ecosystem

Fiji Distribution

Fiji, an acronym for "Fiji Is Just ImageJ", serves as the primary "batteries-included" distribution of ImageJ, designed to simplify access to advanced image analysis tools for scientific users. Launched in by Johannes Schindelin and a team of developers at institutions including the , it bundles the core ImageJ2 framework with a curated selection of nearly 1000 additional plugins, enabling immediate use without extensive manual configuration. This distribution emphasizes biological image analysis while remaining compatible with broader scientific applications. Among its key bundled components are Bio-Formats, a library for reading and writing diverse microscopy file formats such as those from confocal and microscopes; TrakEM2, specialized for aligning and tracing features in large-scale microscopy datasets; and BigDataViewer, a tool for interactive visualization and annotation of multi-dimensional, terabyte-scale image volumes. These integrations allow users to handle complex datasets directly upon installation, supporting workflows in fields like and . Fiji offers significant advantages over vanilla ImageJ, including one-click installation across major operating systems, an integrated updater that automatically manages plugin dependencies and security patches, and streamlined setup that minimizes user intervention. This fosters reproducible research by ensuring consistent environments and easy sharing of customized workflows via update sites. Maintenance of is handled through an open-source model on , where the community contributes to ongoing development focused on enhancing compatibility with modern hardware, versions, and emerging formats. As of 2025, regular releases continue to incorporate updates, with stable builds available for various architectures, ensuring long-term viability and integration with the broader ImageJ ecosystem.

Other Variants and Tools

ImageJ2 can be utilized in a standalone configuration, emphasizing its core capabilities for multidimensional image processing without the bundled plugins of distributions like Fiji. This setup leverages ImageJ2's libraries, such as ImageJ Common and ImgLib2, to support N-dimensional data structures and scientific imaging workflows in custom, lightweight environments. Developers integrate it via the SciJava plugin framework for headless operation, scripting in multiple languages, and parameterized commands suitable for automation in tools like or OMERO. Icy serves as an open-source bioimaging platform that incorporates ImageJ plugins to enhance visualization, , quantification, and among researchers. Developed by the BioImage Analysis Laboratory at the Institut Pasteur, Icy provides a graphical programming interface for creating reusable workflows and supports seamless conversion between its native image format and ImageJ-compatible images, enabling near-full compatibility with ImageJ plugins. This integration facilitates collaborative bioimage informatics, allowing users to share protocols via a community-driven repository while extending ImageJ's functionality for multidimensional . The Image Processing extension builds on ImageJ by embedding its operations into a workflow-based platform, using dedicated nodes to execute ImageJ1 macros and ImageJ2 plugins within data pipelines. This allows for modular, high-throughput where ImageJ algorithms are parameterized and chained alongside KNIME's native tools for tasks like filtering, segmentation, and feature extraction. By supporting over 140 image formats via Bio-Formats and enabling GUI-less execution, KNIME extends ImageJ's reach into reproducible, scalable workflows for bioimage analysis. Related projects in the ImageJ ecosystem include CellProfiler, which draws inspiration from ImageJ's modular approach to enable pipeline for high-throughput phenotypic of cellular images. CellProfiler constructs reusable modules for image processing, object identification, and , processing thousands of images without requiring programming expertise, and integrates ImageJ macros via its RunImageJMacro module for hybrid workflows. Similarly, QuPath specializes in whole-slide imaging, offering compatibility with ImageJ through export functions that convert regions of interest or annotations into ImageJ-compatible formats for further processing. Designed for , QuPath handles large-scale tissue images with tools for annotation and , bridging to ImageJ for specialized plugins. Ecosystem tools further enrich ImageJ's capabilities, such as ImageJ Ops, an extensible framework acting as a registry for reusable image processing algorithms across compatible projects. ImageJ Ops unifies operations like filtering and transformations under a "" paradigm, supporting N-dimensional images via ImgLib2 and allowing contributions through the SciJava plugin system for integration in environments like or standalone applications. Another key tool is the Trainable Weka Segmentation plugin, which employs from the library to perform pixel-wise classification for . Users train classifiers on annotated features such as Gaussian derivatives and Hessian responses, enabling automated segmentation of objects in 2D or 3D images with support for saving and reusing models in ImageJ macros.

Applications

Scientific Domains

ImageJ finds extensive application in biomedical , particularly within techniques such as confocal and light-sheet , where it facilitates tasks like , cell tracking, and quantitative analysis of cellular structures. In , researchers leverage ImageJ's plugins for automated segmentation of cellular components and tracking of dynamic processes in live-cell , enabling precise measurements of morphological changes and movement patterns. These capabilities stem from its support for multidimensional data handling and integration with extensible tools, making it a staple for processing complex datasets from and electron in biological research. In , ImageJ is widely employed for analyzing scans and quantifying morphology, including the reconstruction of dendritic arborizations and axonal projections from confocal image stacks. Plugins like Simple Neurite Tracer (SNT) enable semi-automated tracing of neuronal structures, supporting 3D visualization and morphometric analysis such as branch length and soma size quantification. This has facilitated studies on neural connectivity and in tissue images, with tools like NeurphologyJ providing automated extraction of features from 2D fluorescence micrographs of cultured neurons. ImageJ supports through its utility in electron image processing and of surface topographies, where plugins such as FracLac compute dimensions to characterize irregular microstructures like porous materials or surfaces. In scanning and , it aids in post-processing steps including thresholding, particle sizing, and , essential for evaluating material properties such as grain boundaries and defect distributions. For construction materials, extensions like Xlib enable analysis of 3D data from samples, quantifying and aggregate morphology. In astronomy and physics, ImageJ processes images for tasks like alignment, photometric , and particle detection in tracks or events. AstroImageJ, a specialized variant, handles files from astronomical observations, performing aperture photometry and extraction for studies. Its particle analysis tools detect and measure subatomic particles in high-energy physics images, supporting reproducible quantification in experimental data. ImageJ's prevalence across these domains is evidenced by its role as a standard tool for reproducible image analysis in laboratories, with the seminal publication on its development cited over 60,000 times and appearing in more than 5,500 PubMed-indexed articles as of 2025. This widespread adoption underscores its impact on scientific , particularly in biomedical and physical sciences where open-source extensibility ensures consistent methodological application.

Notable Uses and Case Studies

ImageJ's JACoP plugin has been instrumental in analysis for , particularly in research. For instance, in studies of autoreactive B-cell targeting in models, researchers used JACoP within /ImageJ to calculate Mander's coefficients, quantifying the overlap between antigen-labeled B-cell receptors and endosomal (EEA1) or lysosomal (LAMP1) markers in 3F3 cells over time points such as 2 hours and 24 hours. This approach revealed antigen valency effects on receptor internalization and trafficking, with thresholding applied via the Renyi method across at least 100 cells per sample. Similarly, in investigations of immune signal for antigen-presenting cells, JACoP facilitated fraction overlap calculations between signals after manual thresholding in ImageJ, demonstrating enhanced co-delivery to phagosomes. In , ClearVolume, an ImageJ/Fiji-integrated plugin, enables real-time 3D visualization and reconstruction of light-sheet data, supporting in toto of embryos. A key involved live of a 12-cell stage Caenorhabditis elegans embryo during at 6 stacks per second, allowing remote assessment of sample health, drift, and during embryogenesis. ClearVolume's GPU-accelerated rendering was also applied to long-term Drosophila melanogaster embryo development, integrating seamlessly with for multichannel 3D+t analysis and enhancing workflows in light-sheet setups like OpenSPIM. ImageJ has supported visualization in Nobel Prize-related CRISPR research from the 2010s, notably in dynamic RNA imaging protocols using CRISPR-Cas13 systems. For COVID-19 image analysis in the 2020s, a dedicated Fiji macro quantified viral infection and transfection at single-cell resolution in fluorescence microscopy, automating plaque assays and infection rate measurements for SARS-CoV-2 studies. The open-source nature of ImageJ has fostered community-driven tools like ilastik for segmentation, with plugins such as ilastik4ij enabling seamless integration. This allows running ilastik workflows (e.g., pixel classification, object segmentation) directly in ImageJ via HDF5 data transfer, supporting headless execution for automated bioimage analysis in collaborative environments. ImageJ workflows have achieved significant impact, with Fiji distributions and plugins cited extensively in high-profile journals like Nature Methods. For example, the SPIMage Processing plugin for 3D multiview reconstruction from light-sheet data was highlighted for multi-angle registration and fusion. Similarly, colocalization extensions like MosaicIA for spatial interaction analysis have been recognized for advancing pattern quantification in .

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  68. https://github.com/ilastik/ilastik4ij
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