Repositories list

• hackathonJuly2026

  Public
  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jul 27, 2026Jul 27, 2026

• LiveFoci

  Public
  LiFT: Live foci tracking for quantitative analysis of DNA damage dynamics

  Jupyter Notebook

  •

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

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jul 17, 2026Jul 17, 2026

• bigvolumebrowser

  Public
  browsing large volumetric data and shapes

  javaimglib2point-cloud+ 8

  javaimglib2point-cloudmeshesfiji-plugin3d-volumeutrecht-universitybigdataviewervolumetric-rendering3d-microscopy+ 1

  Java

  •

  BSD 2-Clause "Simplified" License

  •11 fork•2121 stars•00 issues•00 pull requests•Updated Jul 10, 2026Jul 10, 2026

• bvv-playground

  Public
  playing with BigVolumeViewer LUTs/gamma/render

  fijivolume-renderingfiji-plugin

  fijivolume-renderingfiji-plugin

  Java

  •

  BSD 2-Clause "Simplified" License

  •11 fork•44 stars•00 issues•00 pull requests•Updated Jul 7, 2026Jul 7, 2026

• Intestinal-ExM-Analysis

  Public
  Code for publication "Multiscale three-dimensional ultrastructural mapping of intestinal tissues and organoids".

  Jupyter Notebook

  •

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

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jul 2, 2026Jul 2, 2026

• CurveMorph

  Public
  Fiji plugin to morph 2D curve/line ROIs and generate kymographs along them

  Java

  •

  BSD 2-Clause "Simplified" License

  •00 forks•44 stars•00 issues•00 pull requests•Updated Jun 18, 2026Jun 18, 2026

• KymoResliceWide

  Public
  ImageJ plugin making kymographs of maximum or average intensity with wide lines, polylines, curves

  javaimagej-pluginsstacks+ 3

  javaimagej-pluginsstacksfiji-pluginutrecht-universitykymography

  Java

  •

  Other

  •22 forks•66 stars•00 issues•00 pull requests•Updated Jun 3, 2026Jun 3, 2026

• BigTrace

  Public
  FIJI plugin for tracing of curvilinear structures in volumetric microscopy datasets

  javaimglib2volume-rendering+ 6

  javaimglib2volume-renderingfiji-plugin3d-volumeutrecht-universitybigdataviewercurve-tracing3d-microscopy

  Java

  •

  BSD 2-Clause "Simplified" License

  •44 forks•3131 stars•22 issues•00 pull requests•Updated May 28, 2026May 28, 2026

• Signed16bit_to_Unsigned16bit

  Public
  FIJI macro to convert signed 16 bit TIFF files to unsigned 16 bit.

  ImageJ Macro

  •

  BSD 2-Clause "Simplified" License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 8, 2026Apr 8, 2026

• PTU_Reader

  Public
  ImageJ plugin reading PicoQuant ptu/pt3 FLIM image files

  converterstackimagej+ 8

  converterstackimagejimagej-pluginslifetimefiji-pluginflimutrecht-universitypt3picoquant+ 1

  Java

  •

  GNU General Public License v3.0

  •11 fork•99 stars•00 issues•00 pull requests•Updated Mar 16, 2026Mar 16, 2026

• averageBasalBodies

  Public
  a set of ImageJ macros for extraction and averaging of basal bodies from ExM images

  ImageJ Macro

  •

  BSD 2-Clause "Simplified" License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Feb 5, 2026Feb 5, 2026

• Correlescence

  Public
  spatial and temporal cross correlations in 1D and 2D for fluorescent microscopy (ImageJ plugin)

  imagejfijimicroscopy+ 5

  imagejfijimicroscopystackscross-correlationfiji-pluginutrecht-universityimagej-plugin

  Java

  •

  GNU General Public License v3.0

  •00 forks•88 stars•00 issues•00 pull requests•Updated Nov 6, 2025Nov 6, 2025

• ZstackDepthColorCode

  Public
  Z-stack Depth Colorcode ImageJ FIJI plugin

  imagejfijimicroscopy+ 4

  imagejfijimicroscopyfiji-pluginutrecht-universitycolorcodeimagej-plugin

  Java

  •

  GNU General Public License v3.0

  •77 forks•2525 stars•00 issues•00 pull requests•Updated Nov 6, 2025Nov 6, 2025

• AveragingND

  Public
  FIJI plugin for the averaging of ND (2/3/4D) images

  javaimglib2microscopy+ 4

  javaimglib2microscopyfiji-pluginutrecht-universityaveraging3d-microscopy

  Java

  •

  BSD 2-Clause "Simplified" License

  •11 fork•00 stars•11 issue•00 pull requests•Updated Jul 29, 2025Jul 29, 2025

• UU_SmartMicroscopy

  Public
  Python-based modular platform to automate microscopes and design smart microscopy experiments.

  Python

  •

  MIT License

  •22 forks•22 stars•00 issues•00 pull requests•Updated Jul 3, 2025Jul 3, 2025

• ComDet

  Public
  ImageJ plugin detecting and colocalizing particles of given size (vesicles, dots, etc on biological microscopy images)

  javadetectionparticles+ 6

  javadetectionparticlesmicroscopyimagej-pluginsdotsfiji-pluginutrecht-universityvesicles

  Java

  •

  GNU General Public License v3.0

  •55 forks•2020 stars•00 issues•00 pull requests•Updated Jun 16, 2025Jun 16, 2025

• neuron_motorPAINT

  Public
  Analysis codes for neuronal motor-PAINT assays to process raw movies, make reconstructions, and perform analysis.

  Jupyter Notebook

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

• DoM_Utrecht

  Public
  Detection of Molecules plugin for ImageJ: SMLM 2D/3D localizations, drift and chromatic aberration correction, etc

  javasingle-moleculeimagej+ 3

  javasingle-moleculeimagejimagej-pluginsfiji-pluginutrecht-university

  Java

  •

  GNU General Public License v3.0

  •33 forks•1515 stars•1111 issues•00 pull requests•Updated Nov 16, 2022Nov 16, 2022

• TrackMate2MTrackJ

  Public
  converter of Trackmate XML files to MTrackJ MDF

  Java

  •

  Other

  •11 fork•22 stars•00 issues•00 pull requests•Updated Jul 29, 2022Jul 29, 2022

• radialitymap

  Public
  Splitting image to radial and non-radial components ImageJ macro

  imagej-macroutrecht-university

  imagej-macroutrecht-university

  ImageJ Macro

  •

  GNU General Public License v2.0

  •22 forks•66 stars•00 issues•00 pull requests•Updated Jul 11, 2022Jul 11, 2022

• REALM

  Public
  Adaptive Optics plugin for MicroManager

  Java

  •

  GNU General Public License v2.0

  •33 forks•00 stars•00 issues•00 pull requests•Updated May 23, 2022May 23, 2022

• MIRAO_DeviceAdapter

  Public
  Device adapter for MIRAO52E for Micro-Manager

  C++

  •

  GNU General Public License v2.0

  •11 fork•00 stars•00 issues•00 pull requests•Updated May 23, 2022May 23, 2022

• CurveTrace

  Public
  Curve tracing ImageJ plugin

  microscopyimagej-pluginsfiji-plugin+ 2

  microscopyimagej-pluginsfiji-pluginutrecht-universitycurve-tracing

  Java

  •

  MIT License

  •44 forks•2020 stars•00 issues•00 pull requests•Updated Feb 11, 2021Feb 11, 2021

• rods-detection-in-noisy-images

  Public
  Detection of straight line segments (rods) in noisy images

  trackingdetectionmatlab-script+ 3

  trackingdetectionmatlab-scriptfluorescence-microscopy-imagingimagej-macroutrecht-university

  MATLAB

  •

  GNU General Public License v3.0

  •33 forks•44 stars•00 issues•00 pull requests•Updated Jan 22, 2021Jan 22, 2021

• ContourLines

  Public
  imagej plugin generating contour lines with equal spacing

  imageimagejfiji+ 1

  imageimagejfijicontour-lines

  Java

  •

  MIT License

  •00 forks•33 stars•00 issues•00 pull requests•Updated Jan 11, 2021Jan 11, 2021

• MTA

  Public
  Multiscale Trend Analysis

  MATLAB

  •

  GNU General Public License v2.0

  •00 forks•11 star•00 issues•00 pull requests•Updated Apr 15, 2020Apr 15, 2020

• Axonal_transport_model

  Public
  Simple mathematical model of bidirectional active transport in axons (written in Mathematica)

  Mathematica

  •

  GNU General Public License v3.0

  •11 fork•11 star•00 issues•00 pull requests•Updated Nov 20, 2016Nov 20, 2016

• rods_bending

  Public
  Mathematica package to calculate the shape of thin flexible elastic rod under load.

  GNU General Public License v2.0

  •11 fork•00 stars•00 issues•00 pull requests•Updated May 8, 2014May 8, 2014

• AIS

  Public
  axon initial segment characterization/alignment

  MATLAB

  •00 forks•11 star•00 issues•00 pull requests•Updated Apr 14, 2014Apr 14, 2014