Repositories list

• Stitching

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

  Java

  •

  GNU General Public License v2.0

  •64•98•34•4•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

• fiji

  Public
  A "batteries-included" distribution of ImageJ 🔋

  Shell

  •

  GNU General Public License v3.0

  •239•786•109•3•Updated Jan 16, 2025Jan 16, 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

  •9•11•8•4•Updated Nov 5, 2024Nov 5, 2024

• 3D_Viewer

  Public
  Java

  •

  GNU General Public License v3.0

  •18•20•20•2•Updated Oct 17, 2024Oct 17, 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

  •61•113•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•5•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•39•1•Updated Aug 29, 2024Aug 29, 2024

• Colocalisation_Analysis

  Public
  Fiji's plugin for colocalization analysis

  Java

  •

  GNU General Public License v3.0

  •17•26•25•0•Updated Aug 27, 2024Aug 27, 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

• simplified-io

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

  Java

  •

  GNU General Public License v3.0

  •4•3•0•0•Updated Apr 25, 2024Apr 25, 2024

• View5D

  Public archive
  Java

  •

  GNU General Public License v2.0

  •1•2•0•0•Updated Mar 15, 2024Mar 15, 2024

• IO

  Public
  Java

  •

  GNU General Public License v3.0

  •24•6•6•2•Updated Feb 21, 2024Feb 21, 2024

• dockerfiles

  Public
  Fiji Dockerfiles for Docker builds.

  Dockerfile

  •9•8•13•0•Updated Jan 9, 2024Jan 9, 2024

• Stochastic_Denoise

  Public
  Java

  •1•1•0•1•Updated Dec 17, 2023Dec 17, 2023

• blockmatching

  Public
  Java

  •

  GNU General Public License v3.0

  •3•0•0•0•Updated Nov 13, 2023Nov 13, 2023

• fiji.github.io

  Public
  Fiji website

  HTML

  •11•35•1•0•Updated Aug 14, 2023Aug 14, 2023

• LocalThickness

  Public
  Java

  •

  GNU General Public License v3.0

  •3•6•0•0•Updated Jul 27, 2023Jul 27, 2023

• learnathon-2017

  Public archive
  Collection of tutorial repositories for 2017 DAIS learnathon

  Shell

  •1•0•0•0•Updated May 4, 2023May 4, 2023

• learnathon-2019

  Public archive
  Collection of material for the 2019 Learnathon

  Java

  •2•3•0•0•Updated May 4, 2023May 4, 2023

• CorrectBleach

  Public
  Java

  •

  GNU General Public License v3.0

  •4•3•1•0•Updated Apr 12, 2023Apr 12, 2023

• Volume_Viewer

  Public
  Java

  •

  GNU General Public License v3.0

  •5•1•3•1•Updated Mar 26, 2023Mar 26, 2023