Repositories list

• fiji-llm

  Public
  LLM chatbot integration in Fiji

  Java

  •

  BSD 2-Clause "Simplified" License

  •22 forks•1111 stars•3333 issues•00 pull requests•Updated Oct 5, 2026Oct 5, 2026

• HDF5_Vibez

  Public
  HDF5 plugin for ImageJ and Fiji.

  Java

  •

  GNU General Public License v2.0

  •1111 forks•1212 stars•99 issues•44 pull requests•Updated Oct 1, 2026Oct 1, 2026

• H5J_Loader_Plugin

  Public
  H5J Reader Plugin for Fiji project.

  Java

  •

  Other

  •33 forks•44 stars•00 issues•00 pull requests•Updated Oct 1, 2026Oct 1, 2026

• fiji-updater

  Public
  Keep your Fiji up-to-date

  Java

  •

  BSD 2-Clause "Simplified" License

  •00 forks•11 star•00 issues•00 pull requests•Updated Sep 20, 2026Sep 20, 2026

• Descriptor_based_registration

  Public
  Java

  •

  GNU General Public License v3.0

  •66 forks•44 stars•00 issues•00 pull requests•Updated Jul 3, 2026Jul 3, 2026

• Stitching

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

  Java

  •

  GNU General Public License v2.0

  •6666 forks•120120 stars•3838 issues•55 pull requests•Updated Jun 21, 2026Jun 21, 2026

• OMEVisual

  Public
  A Fiji plugin to easily visualize OME metadata.

  Java

  •

  MIT License

  •11 fork•55 stars•22 issues•00 pull requests•Updated May 29, 2026May 29, 2026

• FilamentDetector

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

  Java

  •

  MIT License

  •22 forks•88 stars•88 issues•00 pull requests•Updated May 29, 2026May 29, 2026

• fiji-links

  Public
  Standard fiji:// URL handlers

  Java

  •

  BSD 2-Clause "Simplified" License

  •00 forks•11 star•22 issues•00 pull requests•Updated Apr 23, 2026Apr 23, 2026

• KymographBuilder

  Public
  KymographBuilder is Yet Another Kymograph Fiji plugin.

  Java

  •

  MIT License

  •44 forks•44 stars•22 issues•00 pull requests•Updated Apr 21, 2026Apr 21, 2026

• appose-fiji-plugin

  Public
  A template to get started creating Fiji plugin based on appose-java.

  Java

  •22 forks•33 stars•00 issues•00 pull requests•Updated Mar 2, 2026Mar 2, 2026

• 3D_Viewer

  Public
  Java

  •

  GNU General Public License v3.0

  •1818 forks•2222 stars•2020 issues•11 pull request•Updated Oct 6, 2025Oct 6, 2025

• Fiji_Plugins

  Public
  Java

  •

  GNU General Public License v2.0

  •1010 forks•1212 stars•11 issue•00 pull requests•Updated Jul 17, 2025Jul 17, 2025

• 3D_Objects_Counter

  Public
  Java

  •55 forks•33 stars•11 issue•11 pull request•Updated Apr 8, 2025Apr 8, 2025

• IO

  Public
  Java

  •

  GNU General Public License v3.0

  •2323 forks•77 stars•66 issues•11 pull request•Updated Mar 13, 2025Mar 13, 2025

• Graph_Cut

  Public
  Java

  •99 forks•99 stars•11 issue•00 pull requests•Updated Feb 24, 2025Feb 24, 2025

• Colocalisation_Analysis

  Public
  Fiji's plugin for colocalization analysis

  Java

  •

  GNU General Public License v3.0

  •1717 forks•2828 stars•2525 issues•00 pull requests•Updated Feb 24, 2025Feb 24, 2025

• Fiji_Archipelago

  Public
  Java

  •11 fork•00 stars•00 issues•11 pull request•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

  •11 fork•22 stars•11 issue•22 pull requests•Updated Jan 22, 2025Jan 22, 2025

• LSM_Toolbox

  Public
  Java

  •11 fork•00 stars•11 issue•11 pull request•Updated Jan 22, 2025Jan 22, 2025

• Volume_Calculator

  Public
  Java

  •

  GNU General Public License v3.0

  •44 forks•22 stars•00 issues•00 pull requests•Updated Sep 28, 2024Sep 28, 2024

• VIB

  Public
  Java

  •

  GNU General Public License v3.0

  •3333 forks•1515 stars•55 issues•00 pull requests•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

  •6363 forks•126126 stars•2828 issues•11 pull request•Updated Sep 28, 2024Sep 28, 2024

• legacy-imglib1

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

  Java

  •11 fork•11 star•00 issues•00 pull requests•Updated Sep 28, 2024Sep 28, 2024

• 3D_Blob_Segmentation

  Public
  Java

  •

  GNU General Public License v3.0

  •11 fork•22 stars•00 issues•00 pull requests•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

  •2222 forks•2323 stars•4040 issues•11 pull request•Updated Aug 29, 2024Aug 29, 2024

• old-school-repls

  Public
  Fiji's original script interpreter plugins

  Java

  •

  GNU General Public License v3.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 30, 2024Apr 30, 2024

• simplified-io

  Public
  Read, write, type convert images using simple methods.

  Java

  •

  GNU General Public License v3.0

  •44 forks•33 stars•00 issues•00 pull requests•Updated Apr 25, 2024Apr 25, 2024

• View5D

  Public archive
  Java

  •

  GNU General Public License v2.0

  •11 fork•22 stars•00 issues•00 pull requests•Updated Mar 15, 2024Mar 15, 2024

• Stochastic_Denoise

  Public
  Java

  •11 fork•11 star•00 issues•11 pull request•Updated Dec 17, 2023Dec 17, 2023