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    153 repositories

    • fiji-builds

      Public
      Downloadable Fiji bundles
      Shell
      •3•5•0•1•Updated Mar 2, 2026Mar 2, 2026

    • fiji-links

      Public
      Standard fiji:// URL handlers
      Java
      •
      BSD 2-Clause "Simplified" License
      •0•0•0•0•Updated Feb 3, 2026Feb 3, 2026

    • fiji

      Public
      A "batteries-included" distribution of ImageJ :battery:
      Shell
      •
      GNU General Public License v3.0
      •252•932•130•2•Updated Dec 26, 2025Dec 26, 2025

    • fiji-llm

      Public
      LLM chatbot integration in Fiji
      Java
      •
      GNU General Public License v3.0
      •1•1•3•0•Updated Dec 9, 2025Dec 9, 2025

    • i2k-2025-appose

      Public
      Appose workshop for "Halfway to I2K" 2025
      Shell
      •0•0•0•0•Updated Nov 19, 2025Nov 19, 2025

    • fiji.github.io

      Public
      Fiji website
      HTML
      •11•38•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•7•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•8•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
      •70•114•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
      •64•121•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
      •3•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