ImageJ
The gold standard in open-source scientific image analysis and multidimensional processing.

The batteries-included, open-source distribution of ImageJ2 for multidimensional scientific image analysis.
Fiji is a high-performance distribution of ImageJ2, a Java-based image processing framework designed specifically for scientific multidimensional data. As of 2026, Fiji remains the gold standard in the global research community, serving as a robust middleware that bridges hardware-specific microscopy formats with advanced computational workflows. Its architecture is built on the SciJava software stack, enabling seamless interoperability between different programming languages and tools. Fiji integrates a sophisticated 'Update Site' system, allowing users to subscribe to specialized plugin repositories from leading research institutes. Its core capability lies in handling 'Big Data' via the BigDataViewer, which supports terabyte-scale imagery through lazy loading and multi-resolution pyramids. By incorporating deep learning plugins such as StarDist, Cellpose, and DeepImageJ, Fiji has transitioned from a traditional pixel-manipulation tool into an AI-orchestration platform for bioimage informatics. The distribution includes the Bio-Formats library, enabling it to read over 150 proprietary file formats, ensuring data longevity and reproducibility across heterogeneous laboratory environments. Its headless mode and scripting capabilities (Groovy, Jython, Clojure) facilitate large-scale deployments on High-Performance Computing (HPC) clusters for high-throughput screening applications.
Combines a collection of machine learning algorithms with a set of selected image features to produce pixel-based classifications.
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A re-slicing browser for multi-view, multi-channel, time-lapse datasets that handles terabyte-scale images via an HDF5-based data backend.
A software tool for reading and writing over 150 proprietary life sciences image file formats.
A polyglot scripting environment that allows users to write scripts in Groovy, Python, JavaScript, Clojure, and Scala.
A plugin that allows the execution of pre-trained deep learning models (TensorFlow/Keras) directly within Fiji.
A modular framework for automated and semi-automated manual curation of single-particle tracking.
Global optimization algorithms for 2D/3D tile stitching and elastic image registration (BigWarp).
Manual counting of thousands of cells is error-prone and time-consuming.
Registry Updated:2/7/2026
Visualizing complex branching structures in 3D brain scans.
Quantifying the velocity and trajectory of vesicles in time-lapse videos.