Repositories list

• BoneJ2

  Public
  Plugins for bone image analysis

  imagejtravis-ciimage-processing+ 7

  imagejtravis-ciimage-processingscientific-computingjava-8image-analysisimagej-pluginsmaven-multimodulefiji-pluginskeletal-biology

  Java

  •

  BSD 2-Clause "Simplified" License

  •1212 forks•2525 stars•3434 issues•11 pull request•Updated Mar 17, 2026Mar 17, 2026

• pom-scijava

  Public
  Friendly base POM for all SciJava-based software

  Shell

  •

  The Unlicense

  •3535 forks•00 stars•00 issues•00 pull requests•Updated Nov 26, 2025Nov 26, 2025

• BoneJ_Headless

  Public template
  Scripts for executing Fiji plugin BoneJ in headless mode in Python to compute bone microstructure metrics

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •55 forks•00 stars•00 issues•00 pull requests•Updated Oct 20, 2025Oct 20, 2025

• LocalThickness

  Public
  Java

  •

  GNU General Public License v3.0

  •44 forks•00 stars•00 issues•00 pull requests•Updated Sep 21, 2025Sep 21, 2025

• clinfo

  Public
  Print all known information about all available OpenCL platforms and devices in the system

  C

  •

  Other

  •8484 forks•00 stars•00 issues•00 pull requests•Updated Jun 24, 2025Jun 24, 2025

• clij-parent-pom

  Public
  BSD 3-Clause "New" or "Revised" License

  •33 forks•00 stars•00 issues•00 pull requests•Updated Jun 3, 2023Jun 3, 2023

• bonej-scripts

  Public
  Helper scripts and macros using BoneJ

  jythonimagej-macroimagej-macros+ 1

  jythonimagej-macroimagej-macrosimagej-macro-scripts

  ImageJ Macro

  •11 fork•11 star•00 issues•00 pull requests•Updated Jul 18, 2022Jul 18, 2022

• imagej-ops

  Public
  ImageJ Ops: "Write once, run anywhere" image processing

  Java

  •

  BSD 2-Clause "Simplified" License

  •4343 forks•00 stars•00 issues•00 pull requests•Updated Aug 27, 2021Aug 27, 2021

• clij

  Public
  CLIJ is deprecated. Visit CLIJ2

  Java

  •

  Other

  •99 forks•00 stars•00 issues•00 pull requests•Updated Jun 12, 2021Jun 12, 2021

• clij-clearcl

  Public
  Multi-backend Java Object Oriented Facade API for OpenCL.

  Java

  •

  GNU Lesser General Public License v3.0

  •88 forks•00 stars•00 issues•00 pull requests•Updated Jun 12, 2021Jun 12, 2021

• bonej

  Public
  BoneJ 1.x releases. For up-to-date code see https://github.com/bonej-org/BoneJ2

  Java

  •77 forks•66 stars•11 issue•00 pull requests•Updated Mar 10, 2021Mar 10, 2021

• imagej.github.io

  Public
  GitHub Pages for ImageJ

  JavaScript

  •

  Other

  •178178 forks•00 stars•00 issues•00 pull requests•Updated Nov 14, 2020Nov 14, 2020

• list-of-update-sites

  Public
  The update sites ImageJ knows about automatically

  Python

  •105105 forks•00 stars•00 issues•00 pull requests•Updated Mar 25, 2020Mar 25, 2020

• javadoc.scijava.org

  Public
  Javadocs for SciJava projects

  HTML

  •00 forks•00 stars•00 issues•00 pull requests•Updated Aug 13, 2018Aug 13, 2018

• imagej-common

  Public
  ImageJ core data model

  Java

  •

  Other

  •1515 forks•00 stars•00 issues•00 pull requests•Updated Jul 4, 2018Jul 4, 2018

• AnalyzeSkeleton

  Public
  ImageJ/Fiji plugin to analyze 2D and 3D skeleton images

  Java

  •

  GNU General Public License v3.0

  •2121 forks•00 stars•00 issues•00 pull requests•Updated Jul 4, 2018Jul 4, 2018

• BoneJ2Wiki

  Public
  Files for the wiki of the BoneJ2 repo

  00 forks•00 stars•00 issues•00 pull requests•Updated Jun 28, 2018Jun 28, 2018

• scifio

  Public
  SCientific Image Format Input & Output: a flexible, extensible framework for image I/O. *EXPERIMENTAL* All API is subject to change, so depend at your own risk!…

  Java

  •

  Other

  •4040 forks•00 stars•00 issues•00 pull requests•Updated Nov 9, 2017Nov 9, 2017

• imagej-legacy

  Public
  Backwards compatibility with ImageJ 1.x

  Java

  •

  Other

  •2727 forks•00 stars•00 issues•00 pull requests•Updated May 25, 2017May 25, 2017

• scijava-common

  Public
  A plugin framework and application container with built-in extensibility mechanism

  Java

  •

  Other

  •5353 forks•00 stars•00 issues•00 pull requests•Updated May 15, 2017May 15, 2017

• ImageJFractalDimension

  Public
  Estimates fractal dimension of 2D and 3D images, including topographic surface maps

  Java

  •77 forks•00 stars•00 issues•00 pull requests•Updated Apr 13, 2017Apr 13, 2017

• scifio-tutorials

  Public
  Tutorials for use of SCIFIO and its plugins.

  Java

  •

  Creative Commons Zero v1.0 Universal

  •44 forks•00 stars•00 issues•00 pull requests•Updated Mar 7, 2017Mar 7, 2017

• imglib2-ij

  Public
  Translation between ImgLib & ImageJ data structures (both 1.x and 2)

  Java

  •

  Other

  •88 forks•00 stars•00 issues•00 pull requests•Updated May 11, 2016May 11, 2016

• Skeletonize3D

  Public
  ImageJ/Fiji plugin to skeletonize binary images

  Java

  •1212 forks•00 stars•00 issues•00 pull requests•Updated May 6, 2016May 6, 2016

• VIB

  Public
  Java

  •3333 forks•00 stars•00 issues•00 pull requests•Updated Apr 27, 2016Apr 27, 2016

• imagej-tutorials

  Public
  ImageJ2 programming examples

  Java

  •116116 forks•00 stars•00 issues•00 pull requests•Updated Feb 1, 2016Feb 1, 2016