Repositories list

• fiji-llm

  Public

  fiji/fiji-llm’s past year of commit activity
  LLM chatbot integration in Fiji

  Java

  •

  GNU General Public License v3.0

  •1•0•3•0•Updated Nov 25, 2025Nov 25, 2025

• fiji-builds

  Public

  fiji/fiji-builds’s past year of commit activity
  Downloadable Fiji bundles

  Shell

  •3•5•0•1•Updated Nov 24, 2025Nov 24, 2025

• i2k-2025-appose

  Public

  fiji/i2k-2025-appose’s past year of commit activity
  Appose workshop for "Halfway to I2K" 2025

  Shell

  •0•0•0•0•Updated Nov 19, 2025Nov 19, 2025

• fiji

  Public
  A "batteries-included" distribution of ImageJ 🔋

  Shell

  •

  GNU General Public License v3.0

  •249•891•127•2•Updated Nov 13, 2025Nov 13, 2025

• fiji-links

  Public

  fiji/fiji-links’s past year of commit activity
  Standard fiji:// URL handlers

  Java

  •

  BSD 2-Clause "Simplified" License

  •0•0•0•0•Updated Nov 6, 2025Nov 6, 2025

• fiji.github.io

  Public

  fiji/fiji.github.io’s past year of commit activity
  Fiji website

  HTML

  •11•37•1•0•Updated Nov 1, 2025Nov 1, 2025

• 3D_Viewer

  Public
  Java

  •

  GNU General Public License v3.0

  •18•22•20•1•Updated Oct 6, 2025Oct 6, 2025

• fiji-learn

  Public
  An extensible image analysis workshop in Fiji

  0•0•2•0•Updated Aug 27, 2025Aug 27, 2025

• Fiji_Plugins

  Public
  Java

  •

  GNU General Public License v2.0

  •10•12•1•0•Updated Jul 17, 2025Jul 17, 2025

• 3D_Objects_Counter

  Public
  Java

  •5•2•1•1•Updated Apr 8, 2025Apr 8, 2025

• IO

  Public
  Java

  •

  GNU General Public License v3.0

  •24•6•6•2•Updated Mar 13, 2025Mar 13, 2025

• Graph_Cut

  Public
  Java

  •9•9•1•0•Updated Feb 24, 2025Feb 24, 2025

• Colocalisation_Analysis

  Public
  Fiji's plugin for colocalization analysis

  Java

  •

  GNU General Public License v3.0

  •17•28•25•0•Updated Feb 24, 2025Feb 24, 2025

• FilamentDetector

  Public
  A Fiji plugin that allows easy, fast and accurate detection and tracking of biological filaments.

  Java

  •

  MIT License

  •2•7•8•0•Updated Jan 29, 2025Jan 29, 2025

• OMEVisual

  Public
  A Fiji plugin to easily visualize OME metadata.

  Java

  •

  MIT License

  •1•4•2•0•Updated Jan 29, 2025Jan 29, 2025

• Stitching

  Public
  Fiji's Stitching plugins reconstruct big images from tiled input images.

  Java

  •

  GNU General Public License v2.0

  •69•109•38•5•Updated Jan 22, 2025Jan 22, 2025

• Fiji_Archipelago

  Public
  Java

  •1•0•0•1•Updated Jan 22, 2025Jan 22, 2025

• Image_5D

  Public
  A plugin to extend image stacks to 5 dimensions: x, y, channel (color), slice (z), frame (t).

  Java

  •

  Other

  •1•2•1•2•Updated Jan 22, 2025Jan 22, 2025

• LSM_Toolbox

  Public
  Java

  •1•0•1•1•Updated Jan 22, 2025Jan 22, 2025

• dotfiles

  Public
  Configuration files for Fiji resources

  0•0•0•0•Updated Nov 13, 2024Nov 13, 2024

• HDF5_Vibez

  Public
  HDF5 plugin for ImageJ and Fiji.

  Java

  •

  GNU General Public License v2.0

  •11•12•9•4•Updated Nov 5, 2024Nov 5, 2024

• Volume_Calculator

  Public
  Java

  •

  GNU General Public License v3.0

  •4•2•0•0•Updated Sep 28, 2024Sep 28, 2024

• VIB

  Public
  Java

  •

  GNU General Public License v3.0

  •33•14•5•0•Updated Sep 28, 2024Sep 28, 2024

• Trainable_Segmentation

  Public
  Fiji library to perform image segmentation based on the Weka learning schemes

  Java

  •

  GNU General Public License v3.0

  •63•120•28•1•Updated Sep 28, 2024Sep 28, 2024

• legacy-imglib1

  Public
  OBSOLETE; see https://github.com/imglib/imglib2

  Java

  •1•1•0•0•Updated Sep 28, 2024Sep 28, 2024

• Correct_3D_Drift

  Public
  Python

  •

  GNU General Public License v3.0

  •2•6•3•0•Updated Sep 28, 2024Sep 28, 2024

• 3D_Blob_Segmentation

  Public
  Java

  •

  GNU General Public License v3.0

  •1•2•0•0•Updated Sep 28, 2024Sep 28, 2024

• SPIM_Registration

  Public
  Deprecated, instead check out: https://github.com/preibischLab/multiview-reconstruction & https://github.com/PreibischLab/BigStitcher

  Java

  •

  GNU General Public License v2.0

  •22•23•40•1•Updated Aug 29, 2024Aug 29, 2024

• Descriptor_based_registration

  Public
  Java

  •

  GNU General Public License v3.0

  •6•4•0•0•Updated Aug 14, 2024Aug 14, 2024

• old-school-repls

  Public
  Fiji's original script interpreter plugins

  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Apr 30, 2024Apr 30, 2024