8000 UU-cellbiology repositories · GitHub

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Cell Biology, Neurobiology and Biophysics Department of Utrecht University

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20 repositories

bvv-playground
Public
playing with BigVolumeViewer LUTs/gamma/render
fiji volume-rendering fiji-plugin
Java
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BSD 2-Clause "Simplified" License
•1•2•1•0•Updated Jul 9, 2025Jul 9, 2025
bigvolumebrowser
Public
browsing large volumetric data
java imglib2 fiji-plugin 3d-volume utrecht-university bigdataviewer volumetric-rendering 3d-microscopy bigvolumeviewer
Java
•
BSD 2-Clause "Simplified" License
•0•5•1•0•Updated Jul 9, 2025Jul 9, 2025
UU_SmartMicroscopy
Public
Python-based modular platform to automate microscopes and design smart microscopy experiments.
Python
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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)
java imagej-plugins fiji-plugin utrecht-university detection particles microscopy dots vesicles
Java
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GNU General Public License v3.0
•4•19•0•0•Updated Jun 16, 2025Jun 16, 2025
PTU_Reader
Public
ImageJ plugin reading PicoQuant ptu/pt3 FLIM image files
converter stack imagej-plugins lifetime fiji-plugin utrecht-university imagej pt3 picoquant
Java
•
GNU General Public License v3.0
•1•7•1•0•Updated Nov 13, 2024Nov 13, 2024
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
java imagej-plugins stacks fiji-plugin utrecht-university kymography
Java
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Other
•1•6•1•0•Updated May 8, 2024May 8, 2024
Correlescence
Public
spatial and temporal cross correlations in 1D and 2D for fluorescent microscopy (ImageJ plugin)
imagej fiji microscopy stacks cross-correlation fiji-plugin utrecht-university imagej-plugin
Java
•
GNU General Public License v3.0
•0•8•0•0•Updated Mar 25, 2024Mar 25, 2024
DoM_Utrecht
Public
Detection of Molecules plugin for ImageJ, Utrecht University
java single-molecule imagej-plugins fiji-plugin imagej utrecht-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
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Other
•1•2•0•0•Updated Jul 29, 2022Jul 29, 2022
radialitymap
Public
Splitting image to radial and non-radial components ImageJ macro
imagej-macro utrecht-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
•2•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
ZstackDepthColorCode
Public
Z-stack Depth Colorcode ImageJ FIJI plugin
imagej fiji microscopy fiji-plugin utrecht-university colorcode imagej-plugin
Java
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GNU General Public License v3.0
•7•24•0•0•Updated Feb 17, 2021Feb 17, 2021
rods-detection-in-noisy-images
Public
Detection of straight line segments (rods) in noisy images
tracking detection matlab-script fluorescence-microscopy-imaging imagej-macro utrecht-university
MATLAB
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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
image imagej fiji contour-lines
Java
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MIT License
•0•3•0•0•Updated Jan 11, 2021Jan 11, 2021
MTA
Public
Multiscale Trend Analysis
MATLAB
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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

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