ImageJ plugin that uses automated Sholl to perform neuronal morphometry directly from segmented images and traces from ...

Implementation of the SLF4J API for Logback, a reliable, generic, fast and flexible logging framework.

Core implementation of Logback, a reliable, generic, fast and flexible logging framework.

HDF5 is an efficient, well-documented, non-proprietary binary data format

RSyntaxTextArea is the syntax highlighting text editor for Swing applications. Features include syntax highlighting for ...

AutoComplete is a library allowing you to add IDE-like auto-completion (aka "code completion" or "Intellisense") to any ...

A library adding code completion and other advanced features for Java, JavaScript, Perl, and other languages to ...

Gson is a Java library that can be used to convert Java Objects into their JSON representation. It can also be used to ...

Guava is a suite of core and expanded libraries that include

A Free Java-PDF library

JSch is a pure Java implementation of SSH2

JZlib is a re-implementation of zlib in pure Java

MiGLayout - Java Layout Manager for Swing

A simple library for reading and writing CSV in Java

Java Advanced Imaging Codecs supporting support BMP, GIF (read only),

The Apache Commons Codec component contains encoders and decoders for

The Apache Commons IO library contains utility classes, stream implementations, file filters,

POM was created by Sonatype Nexus

Mathematical morphology library and plugins for ImageJ/Fiji.

JAMA is a basic linear algebra package for Java. It provides

SCIFIO is a library for scientific N-dimensional image I/O.

Compatibility layer for using un-converted Bio-Formats readers in SCIFIO applications.

Pluggable command-line tools for performing SCIFIO-based image IO operations.

SCIFIO plugins for HDF5-based formats.

Java API to handle JPEG and JPEG2000 files. Used by Bio-Formats to read images compressed with JPEG2000 and lossless ...

Provides SCIFIO support for proprietary life science formats.

SCIFIO support for the OME data model, including OME-XML and OME-TIFF.

POM was created by Sonatype Nexus

A java port of the ITK thin plate spline implementation.

Joda-Time provides a quality replacement for the Java date and time classes. Note that from Java SE 8 onwards, users ...

JUnit Jupiter is the API for writing tests using JUnit 5.

MPICBG Core Library.

MPICBG plugin for Fiji.

ImageJ2 is a rewrite of ImageJ for multidimensional image data, with a focus on scientific imaging.

ImageJ is an open source Java image processing program inspired by NIH Image for the Macintosh.

A runtime patcher to introduce extension points into the original ImageJ (1.x). This project offers extension points for ...

This library contains ImageJ's core image data model, based on ImgLib2. It is the primary mechanism by which image data ...

Deprecated ImageJ packages.

The executable which runs ImageJ. Its purpose is also to make sure that updates downloaded by the ImageJ Updater will be ...

The legacy component enables backward compatibility with the original version of ImageJ (1.x). It contains the code ...

3D mesh structures for ImageJ.

Functions for working with ImageJ in scientific notebook software.

Server- and client-side communication between ImageJ and OMERO.

ImageJ Operations: a framework for reusable algorithms.

Core commands for ImageJ.

Core tool plugins for ImageJ.

ImageJ Updater support for uploading via SSH.

ImageJ Updater support for uploading via WebDAV.

ImageJ applications and examples for SciJava script languages.

ImageJ/TensorFlow integration.

ImageJ UI for Java AWT.

ImageJ UI for Java Swing.

Keeps components of ImageJ up-to-date.

Keeps components of ImageJ up-to-date.

Anonymous usage statistics plugin for ImageJ.

Interactive UI component for browsing and running available Ops.

A multidimensional, type-agnostic image processing library.

Useful image processing algorithms.

Image processing algorithms related to Fast Fourier Transforms.

Useful image processing algorithms, licensed under the GPL.

Cache interfaces and java.lang.ref based implementation.

ImgLib2 display logic using ImageJ.

Real space coordinate transformations.

Regions of interest in ImgLib2.

ImgLib2 scripting infrastructure.

Interactive image visualization using ImgLib2.

JNA provides Java programs easy access to native shared libraries without writing anything but Java code - no JNI or ...

Software for the reconstruction of multi-view microscopic acquisitions

Library for simulating a multi-view acquisition including

High performance collections for Java

The Waikato Environment for Knowledge Analysis (WEKA), a machine

A collection of plugins for ImageJ, including the Bio-Formats Importer, Bio-Formats Exporter, Bio-Formats Macro ...

Top-level reader and writer APIs.

Reader and writer implementations that are BSD-licensed.

A library for reading and writing popular microscopy file formats.

Apache Commons Lang, a package of Java utility classes for the classes that are in java.lang's hierarchy, or are ...

Alternate implementations of JDK's "Math" functions.

The Commons Text library provides additions to the standard JDK text handling. It includes algorithms for string ...

Apache POI - Java API To Access Microsoft Format Files

Batik animation engine

Batik AWT utilities

Batik bridge

Batik image codecs

Batik constants library

Batik CSS engine

Batik DOM implementation

Batik external code

Batik Extension Support

Batik GUI utilities

Batik Graphics Vector Tree (GVT)

Batik i18n library

Batik SVG microsyntax parser

Batik SVG Rasterizer Application

Batik SVG Rasterizer Application with Extensions

Batik script language support

Batik SVG Slideshow Application

Batik SVG Browser Application

Batik SVG Browser Application with Extensions

Batik SVG DOM implementation

Batik Java2D SVG generator

Batik SVG Pretty Printer Application

Batik SVG Swing components

Batik SVG transcoder

Batik Truetype Font to SVG Font Converter Application

Batik utility library

Batik XML utilities

XML Graphics Common Support

Jetty Annotations Artifact

Jetty Client is a lightweight HTTP client library for Java.

Asynchronous API

Jetty Deployer Artifact

Jetty module for handling HTTP protocol logic, including requests, responses, and connection management.

Jetty OpenJDK HTTP SPI Artifact

Jetty module that provides I/O utilities and abstractions used by other Jetty components.

Jetty JAAS support

Jetty security infrastructure

Jetty JMX Artifact

Jetty JNDI Artifact

Jetty maven plugins

Performance monitoring artifact for jetty.

Jetty JNDI and Annotation Support Artifact

Jetty Proxy Artifact

Jetty Rewrite Artifact

Jetty Server Security Artifact

Jetty Server Artifact

Jetty Servlet Container

Utility Servlets from Jetty

Jetty Start Artifact

Jetty Utilities Artifact

Jetty JSON Utilities Artifact

Jetty web application support

Jetty XML Artifact

A Maven project implementing an ImageJ plugin

Javassist (JAVA programming ASSISTant) makes Java bytecode manipulation

A complete, Java-based solution for accessing, manipulating,

JFreeChart is a class library, written in Java, for generating charts.

JNI binding generator (runtime)

Java™ Binding for the OpenAL® API

Java™ Binding for the OpenCL® API

Java™ Binding for the OpenGL® API

Mockito mock objects library core API and implementation

Contains common I/O, date parsing, and XML processing classes.

Java API to handle Microsoft OLE 2 Compound Document format (Word, Excel). Based on poi-2.5.1-final-20040804.jar, with ...

A library for working with OME-XML metadata structures.

A minimal build system interpreting Maven-style pom.xml files

A library for loading native libraries.

A general-purpose mathematical expression parser, which converts infix expression strings into postfix queues and/or ...

SciJava cache implementation using Google Guava.

SciJava Common is a shared library for SciJava software. It provides a plugin framework, with an extensible mechanism ...

SciJava Common is a shared library for SciJava software. It provides a plugin framework, with an extensible mechanism ...

SciJava Configuration is a shared collection of files for SciJava software. It provides configuration files for common ...

SciJava library for dynamically grabbing dependencies.

SciJava I/O support for HTTP/HTTPS.

Utility classes for working with Java 3D.

SciJava polyglot kernel for Jupyter.

This adapter package enables the use of SLF4J-based logging within SciJava Common's logging framework. It is kept ...

Core commands for SciJava applications.

Core platform plugins for SciJava applications.

Core text format plugin for Markdown.

Core text format plugin for plain text.

Search framework for SciJava applications.

SciJava user interface components for Java AWT.

SciJava user interface components for Java Swing.

Script Editor and Interpreter for SciJava script languages.

JSR-223-compliant BeanShell scripting language plugin.

JSR-223-compliant Clojure scripting language plugin.

JSR-223-compliant Groovy scripting language plugin.

JSR-223-compliant Java scripting language plugin.

JSR-223-compliant JavaScript scripting language plugin.

JSR-223-compliant JRuby scripting language plugin.

JSR-223-compliant Jython scripting language plugin.

JSR-223-compliant Kotlin scripting language plugin.

MATLAB scripting language plugin.

SciJava wrapper around the Renjin R implementation.

JSR-223-compliant Scala scripting language plugin.

A set of components for use with Swing JTrees that provide support for JCheckBox nodes.

JEP is a Java library for parsing and evaluating mathematical expressions.

3D Graphics API for the Java Platform

Utility functions for the Java 3D Graphics API

Math functions for the Java 3D Graphics API

A framework for writing performance micro-benchmarks using JUnit4 annotations, forked from ...

API for SLF4J (The Simple Logging Facade for Java) which serves as a simple facade or abstraction for various logging ...

Extensions to the SLF4J API

SLF4J JCL Binding

SLF4J JDK14 Provider

Binding/provider for NOP, an implementation that silently discards all logging messages.

Binding/provider for SLF4J, which outputs all events to System.err. Only messages of level INFO and higher are printed.

TensorFlow for Java: A software library for machine intelligence.

Java API for TensorFlow protocol buffers.

JGraphX Swing Component - Java Graph Visualization Library

PostgreSQL JDBC Driver Postgresql

Fiji is a distribution of ImageJ for the life sciences.

Analysis of 2D and 3D skeleton images.

Anisotropic Diffusion 2D plugin for Fiji.

Archipelago Plugins plugin for Fiji.

Arrow plugin for Fiji.

Auto Threshold plugin for Fiji.

Balloon Segmentation plugin for Fiji.

Bug Submitter plugin for Fiji.

CPU Meter plugin for Fiji.

Calculator Plus plugin for Fiji.

Cell Counter plugin for ImageJ.

Fiji's plugin for colocalization analysis.

Color Histogram plugin for Fiji.

Color Inspector 3D plugin for Fiji.

Colour Deconvolution plugin for Fiji.

CorrectBleach plugin for Fiji.

Script to register time frames (stacks) to each other.

Descriptor based registration plugin for Fiji.

Dichromacy plugin for Fiji.

Directionality plugin for Fiji.

FS Align TrakEM2 plugin for Fiji.

Feature Detection plugin for Fiji.

3D Blob Segmentation plugin for Fiji.

Fiji Archipelago plugin for Fiji.

Fiji Developer plugin for Fiji.

Fiji Package Maker plugin for Fiji.

Fiji Plugins plugin for Fiji.

FlowJ plugin for Fiji.

Graph Cut plugin for Fiji.

Gray Morphology plugin for Fiji.

Helmholtz Analysis plugin for Fiji.

IJ Robot plugin for Fiji.

IO plugin for Fiji.

The Image5D plugins extend image stacks to 5 dimensions: x, y, channel (color), slice (z), frame (t).

3D Objects Counter plugin for Fiji.

3D Viewer for visualizing image stacks three-dimensionally.

Image Expression Parser plugin for Fiji.

Interactive 3D Surface Plot plugin for Fiji.

IsoData Classifier plugin for Fiji.

Kuwahara Filter plugin for Fiji.

KymographBuilder: Yet Another Kymograph Fiji plugin.

LSM Reader plugin for Fiji.

LSM Toolbox plugin for Fiji.

Lasso and Blow Tool plugin for Fiji.

Linear Kuwahara plugin for Fiji.

Local Thickness is used to compute the local thickness of a 3D image stack.

MTrack2 plugin for Fiji.

M I P plugin for Fiji.

Manual Tracking plugin for Fiji.

Measure velocities of moving structures in an image time series.

A Fiji plugin to easily visualize OME metadata.

PIV analyser plugin for Fiji.

QuickPALM plugin for Fiji.

RATS plugin for Fiji.

Reconstruct Reader plugin for Fiji.

SPIM Opener plugin for Fiji.

Software for the reconstruction of multi-view microscopic acquisitions like Selective Plane Illumination Microscopy ...

Samples plugin for Fiji.

Series Labeler plugin for Fiji.

The ImageJ framework for semi-automated tracing of neurons and other tube-like structures.

Siox Segmentation plugin for Fiji.

Skeletonize3D plugin for Fiji.

SplineDeformationGenerator plugin for Fiji.

Stack Manipulation plugin for Fiji.

Statistical Region Merging plugin for Fiji.

A plugin for reconstructing big images/stacks from an arbitrary number of tiled input images/stacks.

Sync Win plugin for Fiji.

Thread Killer plugin for Fiji.

Time Lapse tools written in conjunction with the work for "A Doppler effect in embryonic pattern formation", Soroldoni ...

Time Stamper plugin for Fiji.

ToAST plugin for Fiji.

TopoJ plugin for Fiji.

TrackMate plugin for Fiji.

Trainable Segmentation plugin for Fiji.

TrakEM2 Support for Fiji Archipelago

Support library for all the VIB stuff.

VIB plugin for Fiji.

Custom reader for Vaa3D application 3D volume file formats .v3draw and .v3dpbd.

Plugin to write .v3draw files readable by Vaa3d.

Video Editing plugin for Fiji.

View5D plugin for Fiji.

The Volume Calculator plugin is designed to let users measure the volumes of arbitrary segments of blood vessels by ...

Volume Viewer plugin for Fiji.

bUnwarpJ plugin for Fiji.

Biomedical imaging software, manuals, documentation and presentations.

Block Matching plugin for Fiji.

Old compatibility layer for Fiji.

Utility classes for Fiji-based projects.

This project serves purely for phasing out ImgLib1 in favor of ImgLib2.

Level Sets plugin for Fiji.

PAL: Phylogenetic Analysis Library

panorama plugin for Fiji.

Registers image slices from a sequence of image slices stored in a folder.

registration 3d plugin for Fiji.

Jython code weaver for Fiji.

A tool for manual pointwise deformable registration using bigdataviewer.

Thin plate splines in TrakEM2.

Z spacing plugin for Fiji.

BigDataViewer core classes with minimal dependencies.

A web server for BigDataViewer datasets.

Helpers to use BigDataViewer as quick visualization in other projects

Fiji plugins for starting BigDataViewer and exporting data.

representation of multi-angle, multi-channel (etc.) SPIM images and their registration

T2-NIT component of TrakEM2 suite.

T2-TreelineGraph component of TrakEM2 suite.

TrakEM2 plugin for ImageJ.

VectorString component of TrakEM2 suite.

trakem2-transform component of TrakEM2 suite.