Repositories list

• bigvolumebrowser

  Public
  browsing large volumetric data and shapes

  javaimglib2point-cloud+ 8meshesfiji-plugin3d-volumeutrecht-universitybigdataviewervolumetric-rendering3d-microscopy+ 1

  Java

  •

  BSD 2-Clause "Simplified" License

  •0•12•0•0•Updated Dec 22, 2025Dec 22, 2025

• bvv-playground

  Public
  playing with BigVolumeViewer LUTs/gamma/render

  fijivolume-renderingfiji-plugin

  Java

  •

  BSD 2-Clause "Simplified" License

  •1•4•0•0•Updated Dec 22, 2025Dec 22, 2025

• BigTrace

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

  javaimglib2volume-rendering+ 6fiji-plugin3d-volumeutrecht-universitybigdataviewercurve-tracing3d-microscopy

  Java

  •

  BSD 2-Clause "Simplified" License

  •4•29•1•1•Updated Nov 27, 2025Nov 27, 2025

• Correlescence

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

  imagejfijimicroscopy+ 5stackscross-correlationfiji-pluginutrecht-universityimagej-plugin

  Java

  •

  GNU General Public License v3.0

  •0•8•0•0•Updated Nov 6, 2025Nov 6, 2025

• ZstackDepthColorCode

  Public
  Z-stack Depth Colorcode ImageJ FIJI plugin

  imagejfijimicroscopy+ 4fiji-pluginutrecht-universitycolorcodeimagej-plugin

  Java

  •

  GNU General Public License v3.0

  •7•25•0•0•Updated Nov 6, 2025Nov 6, 2025

• Signed16bit_to_Unsigned16bit

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

  ImageJ Macro

  •

  BSD 2-Clause "Simplified" License

  •0•0•0•0•Updated Sep 19, 2025Sep 19, 2025

• averageBasalBodies

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

  ImageJ Macro

  •

  BSD 2-Clause "Simplified" License

  •0•0•0•0•Updated Sep 1, 2025Sep 1, 2025

• PTU_Reader

  Public
  ImageJ plugin reading PicoQuant ptu/pt3 FLIM image files

  converterstackimagej+ 8imagej-pluginslifetimefiji-pluginflimutrecht-universitypt3picoquant+ 1

  Java

  •

  GNU General Public License v3.0

  •1•9•0•0•Updated Aug 25, 2025Aug 25, 2025

• AveragingND

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

  javaimglib2microscopy+ 4fiji-pluginutrecht-universityaveraging3d-microscopy

  Java

  •

  BSD 2-Clause "Simplified" License

  •1•0•1•0•Updated Jul 29, 2025Jul 29, 2025

• UU_SmartMicroscopy

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

  Python

  •

  MIT License

  •2•1•0•0•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+ 6microscopyimagej-pluginsdotsfiji-pluginutrecht-universityvesicles

  Java

  •

  GNU General Public License v3.0

  •5•19•0•0•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

  •1•0•0•0•Updated May 15, 2024May 15, 2024

• KymoResliceWide

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

  javaimagej-pluginsstacks+ 3fiji-pluginutrecht-universitykymography

  Java

  •

  Other

  •2•6•1•0•Updated May 8, 2024May 8, 2024

• DoM_Utrecht

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

  javasingle-moleculeimagej+ 3imagej-pluginsfiji-pluginutrecht-university

  Java

  •

  GNU General Public License v3.0

  •4•15•11•0•Updated Nov 16, 2022Nov 16, 2022

• TrackMate2MTrackJ

  Public
  converter of Trackmate XML files to MTrackJ MDF

  Java

  •

  Other

  •1•2•0•0•Updated Jul 29, 2022Jul 29, 2022

• radialitymap

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

  imagej-macroutrecht-university

  ImageJ Macro

  •

  GNU General Public License v2.0

  •2•6•0•0•Updated Jul 11, 2022Jul 11, 2022

• REALM

  Public
  Adaptive Optics plugin for MicroManager

  Java

  •

  GNU General Public License v2.0

  •3•0•0•0•Updated May 23, 2022May 23, 2022

• MIRAO_DeviceAdapter

  Public
  Device adapter for MIRAO52E for Micro-Manager

  C++

  •

  GNU General Public License v2.0

  •1•0•0•0•Updated May 23, 2022May 23, 2022

• CurveTrace

  Public
  Curve tracing ImageJ plugin

  microscopyimagej-pluginsfiji-plugin+ 2utrecht-universitycurve-tracing

  Java

  •

  MIT License

  •4•20•0•0•Updated Feb 11, 2021Feb 11, 2021

• rods-detection-in-noisy-images

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

  trackingdetectionmatlab-script+ 3fluorescence-microscopy-imagingimagej-macroutrecht-university

  MATLAB

  •

  GNU General Public License v3.0

  •3•4•0•0•Updated Jan 22, 2021Jan 22, 2021

• ContourLines

  Public
  imagej plugin generating contour lines with equal spacing

  imageimagejfiji+ 1contour-lines

  Java

  •

  MIT License

  •0•3•0•0•Updated Jan 11, 2021Jan 11, 2021

• MTA

  Public
  Multiscale Trend Analysis

  MATLAB

  •

  GNU General Public License v2.0

  •0•1•0•0•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

  •1•1•0•0•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

  •1•0•0•0•Updated May 8, 2014May 8, 2014

• AIS

  Public
  axon initial segment characterization/alignment

  MATLAB

  •0•1•0•0•Updated Apr 14, 2014Apr 14, 2014