List of update sites


Update Sites
Introduction
Following an update site
Creating your own update site
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List of update sites
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Introduction

The Updater has a convenient Manage update sites dialog that is populated by a central index.

Available update sites

ImageJ Update Sites
Name Site Description Maintainer
ImageJ https://update.imagej.net/ Base update site for ImageJ2. No need to add this to your list of update sites; it is already included. ImageJ developers
Fiji https://update.fiji.sc/ Base update site for Fiji and core Fiji plugins. If you downloaded Fiji directly, it is already included. Fiji developers
Fiji-Legacy https://sites.imagej.net/Fiji-Legacy/ Restores old Fiji plugins which never made the transition to Maven, as well as obsolete libraries no longer used by current Fiji installations. UNSUPPORTED
Java-8 https://sites.imagej.net/Java-8/ Temporary base update site for ImageJ2 and Fiji components as everything migrates to Java 8. Will not work with Java 6 or 7. See this page for details. ImageJ and Fiji developers
2015-Conference https://sites.imagej.net/2015-Conference/ A collection of plugins highlighting the latest features of ImageJ. As seen in Wayne Rasband's opening talk at the 2015 conference! Curtis Rueden
3D ImageJ Suite https://sites.imagej.net/Tboudier/ A suite of plugins providing enhanced 3D capabilities in ImageJ. Thomas Boudier
ActogramJ https://romulus.oice.uni-erlangen.de/imagej/updatesites/ActogramJ/ ActogramJ is a plugin for analyzing actograms. Benjamin Schmid
AIC Janelia - Course https://sites.imagej.net/AICjanelia-course/ A collection of plugins and macros for students of the Advanced Imaging Center (AIC) Fiji Course. AIC Janelia
Angiogenesis https://sites.imagej.net/Angiogenesis/ A plugin to quantify angiogenic sprout morphology. Jan Eglinger
AngioTool https://sites.imagej.net/AngioTool/ The AngioTool software converted to a Fiji plugin. Jan Eglinger
Archipelago https://sites.imagej.net/Lindsey/ A set of plugins that allow Fiji to be run in parallel on a cluster. Currently, Trainable Weka Segmentation and Elastic Alignment are accelerated in this way. Larry Lindsey
AxoNet https://sites.imagej.net/AxoNet/ An implementation of the AxoNet tool which can be used to count axons in light micrographs of optic nerves. Matthew Ritch
BACMMAN https://sites.imagej.net/Ljp/ BACteria in Mother Machine ANalyzer: a plugin for high-throughput analysis of multichannel mother machine data. See Sources and Wiki Jean Ollion
BAR https://sites.imagej.net/Tiago/ BAR (Broadly Applicable Routines) is a GitHub-curated collection of scripts that simplifies the daily usage of ImageJ. The collection is focused on Data Analysis, Image Annotation and Segmentation. Tiago Ferreira
BaSiC https://sites.imagej.net/BaSiC/ BaSiC is a retrospective image correction method for optical microscopy, available as a Fiji/ImageJ Plugin. It is based on low rank and sparse decomposition, which corrects both shading (uneven illumination) in space and background bleaching in time. Tingying Peng
BIG-EPFL https://sites.imagej.net/BIG-EPFL/ ImageJ plugins from EPFL's Biomedical Imaging Group (BIG). NOT OPEN SOURCE. Curtis Rueden
BigStitcher https://sites.imagej.net/BigStitcher/ Based on the HDF5 multi-resolution datastructures of the BigDataViewer the BigStitcher uses globally optimal registration that is capable of aligning large multi-tile datasets with high precision and automatic error detection within just a few minutes while at the same time allowing for additional user interaction. Stephan Preibisch, David Hörl
BigVolumeViewer Demo https://sites.imagej.net/BigVolumeViewer/ Demo of BDV volume rendering. See this forum post for getting started. Tobias Pietzsch
Bio-Formats https://sites.imagej.net/Bio-Formats/ A version of Bio-Formats with the latest bugfixes from the development branch. The last SNAPSHOTS are automatically uploaded daily. OME development team
Biomat https://sites.imagej.net/Biomat/ Plugins for 3D image preprocessing and detection of fibres in 3D image. Jiri Janacek
Biomedgroup https://sites.imagej.net/Biomedgroup/ A set of plugins developed by the biomedical imaging group of the dortmund university of applied sciences and arts: * Shape Filter (Filter binary images by shape), * Shape Smoothing (Smooth objects via Fourier descriptors), * Non Local Means Denoise (edge preserving noise filter), * NanoTrackJ (Size characterization of freely diffusing nanoparticles by particle tracking), * Ridge Detection (Line / Ridge detection plugin). Thorsten Wagner
BioVoxxel https://sites.imagej.net/BioVoxxel/ A toolset providing a plugins and macros for flat-field background corrections, image filters, color coding of shape descriptors and several tools to process and analyze binary images such as the 'Speckle Inspector', 'Binary Feature Extractor' and an 'Extended Particle Analyzer' and a qualitative and quantitative evaluation tool for Fijis' Auto Threshold methods. More information at the BioVoxxel Toolbox page and the BioVoxxel web site. Jan Brocher
Blind Analysis Tools https://sites.imagej.net/Astja/ Tools to facilitate blind i.e., unbiased analysis of (image) data. For more information visit the documentation page. Astha Jaiswal, Holger Lorenz
BoneJ experimental https://sites.imagej.net/BoneJ/ A collection tools for trabecular geometry and whole bone shape analysis. This update site hosts the new experimental, modernized version of BoneJ that works with the latest Fiji. Enabling the update site creates the menu entries Plugins > BoneJ. The pQCT tools are now hosted on their own update site (see below). Michael Doube, Alessandro Felder
CALM https://sites.imagej.net/CALM/ Plugins from the Crick Advanced Light Microscopy Facility at The Francis Crick Institute. David Barry
CAMDU https://sites.imagej.net/CAMDU/ Plugins from the Computing and Advanced Microscopy Development Unit at the University of Warwick. Erick Martins Ratamero
CellTrackingChallenge https://sites.imagej.net/Ulman/ Implementation of measures and front-end plugins used in and related to the Cell Tracking Challenge. Vladimír Ulman
CIP https://sites.imagej.net/CIP/ An image procesing toolbox focused on scripting. Benoit Lombardot
CircleSkinner https://sites.imagej.net/CircleSkinner/ A Fiji plugin for the automated detection and quantification of circular structures in images. Jean-Yves Tinevez
clij https://sites.imagej.net/clij/ GPU-acceleration for ImageJ. See https://clij.github.io/ Robert Haase
clij2 https://sites.imagej.net/clij2/ Experimental update site / incubator for the future release of clij2. See https://clij.github.io/clij-advanced-filters Robert Haase
ClearVolume https://sites.imagej.net/ClearVolume/ ClearVolume is a fast 3D viewer, for more information see also the ClearVolume wiki. ClearVolume
CMCI-EMBL https://sites.imagej.net/Miura/ A plugin for loading sample images and misc functionality for CMCI ImageJ course. See CMCI course. Eventually more plugins will be added. Kota Miura
CMP-BIA tools https://sites.imagej.net/CMP-BIA/ The development version of CMP-BIA tools. Jiri Borovec
CMTK Registration https://sites.imagej.net/Jefferis/ CMTK Registration GUI. Gregory Jefferis
Cookbook https://sites.imagej.net/Cookbook/ Plugins from the Cookbook. Cookbook Team
CSBDeep https://sites.imagej.net/CSBDeep/ Plugins for executing pretrained CARE networks. Deborah Schmidt
CSIM Laboratory https://sites.imagej.net/Acsenrafilho/ A set of plugins, macros and scripts developed by the CSIM (Computing in Signal and Images in Medicine) research group. One of the methods available are Anomalous Diffusion Filters, Noise Generator, MRI Perfusion and the Sample Entropy for Images. Please, see the CSIM group web page to find out how the methods works and more information about us. Antonio Carlos da S. Senra Filho
CWNS dense nuclei segmenter https://sites.imagej.net/CWNS/ The Fiji implementation of the CWNS dense nuclei segmenter, presented in "Object Segmentation and Ground Truth in 3D Embryonic Imaging", by B. Rajasekaran et al., Plos ONE, 2016. Jean-Yves Tinevez
DeepClas4Bio-plugins https://sites.imagej.net/Adines/ Collection of plugins that use DeepClas4Bio API -- an API that facilitates the interoperability of bioimaging tools with deep learning frameworks. Adrián Inés
DHM Utilities https://sites.imagej.net/Sudgy/ Collection of plugins for use in digital holographic microscopy, such as hologram reconstruction, numerical propagation, and phase unwrapping. David Cohoe
DiameterJ https://sites.imagej.net/DiameterJ/ Macros for quantitative analysis of nanofiber images. DiameterJ is able to analyze any network of connecting lines (validated for SEM micrographs of micro- and nanofibers) and produce metrics such as mean diameter, histograms of fiber diameter, mean pore size, histogram of all pore areas, percent porosity, etc. See soon for more information and the publication describing how DiameterJ works and its limitations. Nathan Hotaling
DiversePathsJ https://sites.imagej.net/Vuhlmann/ DiversePathsJ implements a dynamic programming approach for the general task of finding diverse shortest paths between two end-points. It is not linked to a specific biological problem and can be applied to a large variety of images. See the DiversePathsJ web page for more information. Virginie Uhlmann
EMBL-CBA https://sites.imagej.net/EMBL-CBA/ Collection of image analysis tools. * Image Registration: Plugin for n-dimensional image sequence registration Christian Tischer EMBL-CBA
EpiGraph https://sites.imagej.net/Pedgomgal1/ EpiGraph: an open-source method to quantify epithelial organization. EpiGraph is a Fiji plugin that combines computational geometry and graph theory to measure organization in any computational or natural tessellation image. Pedro J. Gómez Gálvez, Pablo Vicente Munuera
EZFig https://sites.imagej.net/EZF/ EZFig is a tool to build publication-ready scientific figures based on ScientiFig but simpler to use. It must be used in combination with the 'Java-8' update site. Benoit Aigouy
FAST https://sites.imagej.net/FAST/ Fluorescence image AnalysiS Tool automates tasks to process a set of single-channel fluorescence images. C.TURIÈS
FFMPEG https://fiji.sc/~schindelin/ffmpeg-plugins/ Fiji plugins which allow reading and writing to FFmpeg-supported formats via native bindings. Curtis Rueden
FibrilJ https://sites.imagej.net/FibrilJ/ Macros developed to measure the diameters and persistence lengths if amyloids fibrils by AFM, EM, STM etc. iamges. It provides histogram distribution of the average fibril diameter and average fibril persistence length. Was validated for AFM, SEM and TEM images of Sup35NM fibrils on mica, silicon, gold surfaces and formvar film. Petr Sokolov
FilamentDetector https://sites.imagej.net/FilamentDetector/ A Fiji plugin that allows easy, fast and accurate detection and tracking of biological filaments. Hadrien Mary
Filopodyan https://sites.imagej.net/Rb7777/ Filopodia dynamics analysis. See GitHub for the user guide, source code and R scripts for downstream analysis. Richard Butler, Vasja Urbančič
FiloQuant https://sites.imagej.net/FiloQuant/ FiloQuant is a user friendly and modifiable tool for automated detection and quantification of filopodia properties such as length and density. FiloQuant can also track filopodia. Guillaume Jacquemet, Alexandre Carisey
FPBioimage https://sites.imagej.net/Fpbioimage/ A plugin to prepare and upload data for Fpbioimage. FPBioimage
FracLac Suite https://sites.imagej.net/Akarperien/ Fractal Analysis and Modelling tools for neuroscience and other disciplines. Analysis: DB, lacunarity, multifractal spectra, DLC, DMvD, subscanning, and graphical wave analysis for binary and gray scale images, with inline and online theoretical and practical help. Outputs: detailed analyses, raw data, plots, colour-coding, and settings (*.fl) files. Modelling: benchmark fractals, natural structures (e.g., neurons), megadata to graphical wave images. Code in jar. See citations. A. Karperien
FunImageJ https://sites.imagej.net/FunImageJ/ Fiji plugin that provides Clojure wrappings of many commonly used functions from ImageJ and ImgLib2. Works with SciJava scripting for Clojure. FunImageJ scripts can be converted into standalone ImageJ/Fiji-based programs. Code available on GitHub. Kyle Harrington
Fuzzy logic and artificial neural networks image processing toolbox for ImageJ https://sites.imagej.net/Astartes91/ Toolbox includes fuzzy edge detection plugin, fuzzy contrast enhancement plugin and ann edge detection plugin. Source code on GitHub. Vladimir Nizamutdinov
Fuzzy Set https://sites.imagej.net/Rerger/ Fuzzy Set is an ImageJ plugin, to transform the intensity of the image using Fuzzy Sets. Robert Erger
GDSC https://sites.imagej.net/GDSC/ The Genome Damage and Stability Centre (GDSC) plugins are a collection of analysis programs for microscopy images including colocalisation analysis and peak finding (FindFoci). See GDSC Plugins for details. Alex Herbert
GDSC-SMLM https://sites.imagej.net/GDSC-SMLM/ The GDSC Single Molecule Light Microscopy (SMLM) plugins provide various tools for single molecule localisation analysis. This includes PALM, STORM and other single molecule microscopy methods. See SMLM Plugins for details or read the User Manual. Alex Herbert
Hadim https://sites.imagej.net/Hadim/ Contains the ij2-python-lib package. Hadrien Mary
HDF5 https://sites.imagej.net/Ronneber/ The HDF5 plugin allows to load and save data in HDF5 format. For details see HDF5 plugin. Olaf Ronneberger
HistoJ https://sites.imagej.net/Pathomation/ Plugin to interface with Pathomation's digital slide viewer which can open Olympus VSI (.vsi), Ventana / Roche BIF (.bif), Hamamatsu NDPI (.ndpi), 3DHistech MRXS (.mrxs), Aperio / Leica SVS (.svs), Leica SCN (.scn), Carl Zeiss ZVI (.zvi), Carl Zeiss CZI (.czi), Nikon ND2 (.nd2), Sakura SVSlide (.svslide). Pathomation
Hohlbein Lab https://sites.imagej.net/HohlbeinLab/ Plugins created by the Hohlbein Lab (Wageningen University, Laboratory of Biophysics). Includes ThunderSTORM with added phasor-based localization for single-molecule microscopy analysis (pSMLM-3D, Martens et al., JCP, 2018). Koen Martens, Johannes Hohlbein
IamMM https://sites.imagej.net/IamMM/ Image Synthesizer (plugin to generate images from mathematical functions and conditional statements in a coordinate system independent from the aspect ratio or image size), Spheroid RGB (plugin to analyze microscopy RGB images with fluorescent stained cells) Maximilian Maske
IBMP-CNRS https://sites.imagej.net/Mutterer/ FigureJ (easy article figure creation), ActionBar (macro-based buttons bars), Droplet (drag and drop file processor), LSM Reader and LSM Toolbox moved to the main Fiji update site, IJ_Ed (jEdit link). Jerome Mutterer
IJ-OpenCV-plugins https://sites.imagej.net/IJ-OpenCV/ Collection of plugins created using the IJ-OpenCV library -- a library that allows the connection of ImageJ and OpenCV. Jónathan Heras
IJPB-plugins https://sites.imagej.net/IJPB-plugins/ Collection of plugins created at the INRA-IJPB Modeling and Digital Imaging lab to perform 2D/3D image segmentation, fast morphological operations and geometric analysis Modeling and Digital Imaging lab, INRA-Versailles
ilastik https://sites.imagej.net/Ilastik/ Provides interoperability between Fiji and ilastik workflows (pixel/object classification, tracking) as well as HDF5 file export/import. Adrian Wolny
ImageJ Latex https://sites.imagej.net/Yul.liuyu/ Add math equations to an image using Latex. Yu Liu
ImageJ-ITK https://sites.imagej.net/ImageJ-ITK/ Adds ITK integration including conversion between ITK and ImageJ images. See the ITK page for more information. Curtis Rueden
ImageJ-MATLAB https://sites.imagej.net/MATLAB/ Adds support for MATLAB scripting and converting between MATLAB arrays and ImageJ components. See the scripting tutorial for more information. Mark Hiner
ImageScience https://sites.imagej.net/ImageScience/ Base update site for all ImageScience related ImageJ plugins. Erik Meijering
ImagingBook https://sites.imagej.net/ImagingBook/ Common ImageJ/Java source code for the Digital Imaging books by Wilhelm Burger and Mark J. Burge. This update site only provides the common "imagingbook" LIBRARY plus required third-parts JAR files. Specific sets of demo plugins are available for each book edition; choose ONE of the update sites listed below. Find the online documentation and additional materials on the SourceForge page. Wilhelm Burger
ImagingBookEn1 https://sites.imagej.net/ImagingBookEn1/ ImageJ PLUGINS (only) for "Digital Image Processing – An Algorithmic Introduction Using Java" by W. Burger & M. Burge, Springer (2008). Wilhelm Burger
ImagingBookEn2 https://sites.imagej.net/ImagingBookEn2/ ImageJ PLUGINS (only) for "Principles of Digital Image Processing" (Vols. 1–3) by W. Burger & M. Burge, Springer (2009–2013). Wilhelm Burger
ImagingBookEn3 https://sites.imagej.net/ImagingBookEn3/ ImageJ PLUGINS (only) for "Digital Image Processing – An Algorithmic Introduction Using Java" by W. Burger & M. Burge, 2nd ed., Springer (2016). Wilhelm Burger
ImagingBookDe2 https://sites.imagej.net/ImagingBookDe2/ ImageJ PLUGINS (only) for "Digitale Bildverarbeitung – Eine Einführung mit Java und ImageJ" by W. Burger & M. Burge, Springer (2006). Wilhelm Burger
ImagingBookDe3 https://sites.imagej.net/ImagingBookDe3/ ImageJ PLUGINS (only) for "Digitale Bildverarbeitung – Eine algorithmische Einführung mit Java" by W. Burger & M. Burge, Springer (2015). Wilhelm Burger
ImagingFCS https://sites.imagej.net/ImagingFCS/ ImagingFCS 1.491 is a basic ImageJ plugin to calculate and view spatio-temporal correlation functions from 16 bit gray tiff stack files. It was written under FIJI (ImageJ 1.51f; Java 1.8.0102) and requires Imagescience for statistics (simulator) and Apache Poi for file reading and writing. Thorsten Wohland
IMCF Uni Basel https://sites.imagej.net/UniBas-IMCF/ Various plugins (most notably the Stitching-Wrapper for Olympus FluoView OIF / OIB mosaics), macros and Action Bars, including a LUT selection bar that lets you click on a visual representation of the LUT. Also ships the MultiStackRegistration plugin (the version modified by Kota Miura that is usable from scripts). Niko Ehrenfeuchter
IMOD-ZOLA https://sites.imagej.net/IMOD-ZOLA/ Zernike Optimized Localization Algorithm for 3D single molecule localizations ZOLA-3D developed in Institut Pasteur, group IMOD -- a CUDA-enabled localization algorithm for extended PSF single-molecule localization microscopy. Paper is under review. Andrey Aristov, Benoit Lelandais
INCF test site https://sites.imagej.net/Dimiterpp/ Update site for scale space filters and other INCF projects from GSOC 2014, 2015, 2016. Dimiter Prodanov
IsletJ https://sites.imagej.net/IsletJ/ Plugin for evaluation of microscopy images of Langerhans islets. Provides estimate of area and count of islets, and an estimate of purity (endocrine-to-exocrine tissue ratio). Jan Schier, Jan Švihlík
JAX Eye https://sites.imagej.net/MarkKrebs/ Macro for processing brightfield fundus images of the mouse eye and plugin for averaging replicate OCT volume scans. Mark Krebs
JOGL Canvas Deep Color / 3D https://sites.imagej.net/JOGLCanvas/ JOGL Canvas is a plugin for ImageJ1 that uses OpenGL and a graphics card to display images rather than the ImageCanvas class, which is extended from java's canvas. It replaces it with a JOGL OpenGL GLCanvas instead. This allows 10-bit or greater color depth for supported monitors and some modest 3D rendering. Aaron Schain
Kappa https://sites.imagej.net/Kappa/ A Fiji plugin for Curvature Analysis. Hadrien Mary
Lab-utility-plugins https://sites.imagej.net/Georgenm/ A collection of plugins for file blinding, batch image conversion of proprietary formats to tif, and other common helper functions. Source and docs on GitHub. Nick George
Labkit https://sites.imagej.net/Labkit/ An advanced plugin for labeling and automatic segmentaion of Images. Matthias Arzt
LAG SIM https://sites.imagej.net/LagSIM/ A plugin and set of macro tools to help with reconstructing SIM data. This has been specifically developed for the Laser Analytics Group SIM in the University of Cambridge - but please download and/or modify for your own needs. LagSIM
Leiden University https://sites.imagej.net/Willemsejj/ At Leiden University we develop user demanded plugins for general use, which could be applicable in your experiments as well. Most questions arise from experiments done in the Cell Observatory. Joost Willemse
LimeSeg https://sites.imagej.net/LimeSeg/ Revisited active contour method for 3D segmentation. Documentation: LimeSeg. Nicolas Chiaruttini, Sarah Machado
Lineage-Mapper https://sites.imagej.net/NIST-ISG-LineageMapper/ Lineage Mapper is an open-source, overlap-based cell tracking system for time-lapse images of biological cells, colonies, and particles. Lineage Mapper tracks objects independently of the segmentation method, detects mitosis in confluence, separates cell clumps mistakenly segmented as a single cell, provides accuracy and scalability even on terabyte-sized datasets, and creates division and/or fusion lineages. NIST ISG
LLTT https://sites.imagej.net/Alex-krull/ The Low Light Tracking Tool can be used to track low-light sub-resolution objects in microscopy images and other applications. Alexander Krull, Damien Ramunno-Johnson
LOCI https://sites.imagej.net/LOCI/ The LOCI update site for their Fiji plugins, including VisBio Fiji plugins and other miscellany. Curtis Rueden
LSM-W2 https://sites.imagej.net/Bionet.nsc/ Plugin extracts Leaf Surface Morphology from Laser Scanning Microscopy images. The plugin can work with multi-channel multi-frame 3D images in *.lsm format obtained from a laser scanning microscope. Has a wide functionality for working with a similar type of image. For more information see documentation. Source code here. Verman Pavel
LUMoS https://sites.imagej.net/Tmcrae/ Plugin performs blind spectral unmixing on multichannel images, particularly for fluorescence microscopy. For more information see documentation. Source code here. Tristan McRae
MaMuT https://sites.imagej.net/MaMuT/ MaMuT, a plugin for the annotation of massive, multi-view data. Jean-Yves Tinevez
Maskflow https://sites.imagej.net/Maskflow/ A Fiji plugin for Mask RCNN semantic segmentation. Hadrien Mary
Mastodon https://sites.imagej.net/Mastodonpreview/ Mastodon is a plugin for tracking in massive, multi-view data. It is the successor to MaMuT and TrackMate. It is still incomplete and in-development. Tobias Pietzsch
Micro-Magellan https://sites.imagej.net/Hpinkard/ Micro-Magellan is a plugin based on Micro-Manager for high throughput microscopy. This update site is used to enable reading of Micro-Magellan datasets by the BigDataViewer. Henry Pinkard
MIST https://sites.imagej.net/NIST-ISG-MIST/ Microscopy Image Stitching Tool (MIST), is a stitching algorithm for small and large two dimensional image grid collections. We developed a new and novel method for optimizing the translations computed by the phase-correlation method using the Fourier transform approach. This new method estimates the microscope stage repeatability from the computed translations of a gridded image tiles. It then optimizes all translation computation using the Hill Climbing algorithm bounded to four times the stage repeatability. This minimizes the maximum uncertainty related to the translation computation for any pair of images. NIST ISG
MiToBo https://sites.imagej.net/MiToBo/ MiToBo is a collection of basic image processing operators (filtering, morphology, labeling, etc.), advanced analysis algorithms (wavelets, snakes, levelsets, etc.), and special applications mainly dedicated to microscopy image analysis (nuclei detection, scratch assay analysis, neurite image segmentation, etc.). The MiToBo Team, Halle, Germany
Molography https://sites.imagej.net/VolkerGatterdam/ Script for Evaluation of Molographic Data Volker Gatterdam
MoMA https://sites.imagej.net/MoMA/ Mother Machine Analyser Florian Jug
Morphology https://sites.imagej.net/Landini/ The update site for the Mathematical Morphology Collection of plugins and macros. Gabriel Landini
MOSAIC ToolSuite https://mosaic.mpi-cbg.de/Downloads/update/Fiji/MosaicToolsuite An integrated toolbox containing the following image-processing software from the MOSAIC Group: 2D and 3D single-particle tracking, 2D and 3D multi-region image segmentation, 2D and 3D globally optimal two-region image segmentation, point-spread function estimation in 2D and 3D, background subtraction, Poisson noise simulator, microscope optics simulator, chromatic aberration correction. MOSAIC Group, MPI-CBG, Dresden
MPIBPC https://sites.imagej.net/MPIBPC/ MPIBPC stands for Max Planck Institute for Biophysical Chemistry. We provide the Imspector OBF reader for the Bio-Formats plugin. MPIBPC, NanoBiophotonics, Bjoern Thiel
MS-ECS-2D https://sites.imagej.net/MS-ECS-2D/ MembraneStained EpithelialCellSegmentation 2D, for more information see also the update site page. MS-ECS-2D
MTrack https://sites.imagej.net/MicrotubuleTracker/ MTrack is a tool, which detects, tracks, and measures the behavior of fluorescently labeled microtubules imaged by TIRF (total internal reflection fluorescence) microscopy. In such an in vitro reconstitution approach, stabilized, non-dynamic microtubule seeds serve as nucleation points for dynamically growing microtubules. MTrack
Multi-Template-Matching https://sites.imagej.net/Multi-Template-Matching/ Multiple template matching allows to easily localize one or multiple objects in images using one or a set of template images. The template images can be flipped and/or rotated to increase the chance to find the objects. Laurent Thomas
N5 https://sites.imagej.net/N5/ N5 libraries. Stephan Saalfeld
NanoJ-Core https://sites.imagej.net/NanoJ/ The update site providing NanoJ's core functionality. NanoJ is a set of high-performance libraries for GPU enabled super-resolution data analysis. The Henriques Team, UCL, UK
NanoJ-SQUIRREL https://sites.imagej.net/NanoJ-SQUIRREL/ NanoJ-SQUIRREL is an analytical toolbox to measure super-resolution image quality and quantitatively map defects, it also provides methods to aid in improving super-resolution images. The Henriques Team, UCL, UK
NanoJ-SRRF https://sites.imagej.net/NanoJ-SRRF/ NanoJ-SRRF is a high-performance analytical approach for Live-cell Super-Resolution Microscopy, provided as a fast GPU-enabled ImageJ plugin. The Henriques Team, UCL, UK
NanoJ-VirusMapper https://sites.imagej.net/NanoJ-VirusMapper/ NanoJ-VirusMapper is a high-throughput ImageJ plugin for single-particle analysis in fluorescence microscopy, particularly super-resolution microscopy. The Henriques Team, UCL, UK
NEUBIAS https://sites.imagej.net/Neubias/ Plugins and scripts developed in the context of NEUBIAS. NEUBIAS members
Neuroanatomy https://sites.imagej.net/Neuroanatomy/ Image Processing Tools for Neuroanatomy and Tree-like structures (list). Tiago Ferreira
NeuroCyto Lab https://sites.imagej.net/Christopheleterrier/ Various tools from the NeuroCyto Lab in Marseille for image processing and quantification, including SMLM scripts. Centered on the analysis of fluorescence in neuronal cultures. Christophe Leterrier, NeuroCyto Lab, INP, Marseille
NeuroCyto LUTs https://sites.imagej.net/NeuroCyto-LUTs/ A collection of LUTs packaged as an easy to use extra menu. LUTs are from various sources detailled in the About section. Christophe Leterrier, NeuroCyto Lab, INP, Marseille
NoiSee https://sites.imagej.net/NoiSee/ An easy-to-use macro for measuring and analyzing SNR (signal-to-noise ratio) of light microscopes. See the NoiSee page for more details. Niko Ehrenfeuchter
Nuclear-Medicine https://sites.imagej.net/Nuclear-Medicine/ Conventional nuclear medicine applications and additional packages for the PET/CT Viewer. Salim Kanoun, Toulouse, France
NucleusJ https://sites.imagej.net/PouletAxel/ A plugin for quantifying nuclear shape and chromatin organization. Segments nuclear boundaries and nuclear bodies, then automatically measures parameters quantifying shape and size of nuclei as well as intra-nuclear objects and the positioning of the objects within the nuclear volume. Axel Poulet, Genetic Reproduction and Development lab, Clermont-Ferrand, France
OMERO 5.0 https://sites.imagej.net/OMERO-5.0/ The OMERO update site for bidirectional integration between ImageJ and OMERO 5.0.x. Curtis Rueden
OMERO 5.1 https://sites.imagej.net/OMERO-5.1/ The OMERO update site for bidirectional integration between ImageJ and OMERO 5.1.x. Curtis Rueden
OMERO 5.2 https://sites.imagej.net/OMERO-5.2/ The OMERO update site for bidirectional integration between ImageJ and OMERO 5.2.x. Curtis Rueden
OMERO 5.4 https://sites.imagej.net/OMERO-5.4/ The OMERO update site for bidirectional integration between ImageJ and OMERO 5.4.x. Curtis Rueden
OpenMIMS https://sites.imagej.net/OpenMIMS2/ OpenMIMS is an ImageJ plugin to open, process and analyze images captured with NanoSIMS 50 & 50L secondary ion mass spectrometers (Cameca). Matt Steinhauser, Walter Taylor
OpenSPIM https://openspim.org/update/ The drivers and software to operate an OpenSPIM (Open Access selective plane light sheet microscope). UNSUPPORTED
OPTIMISME https://sites.imagej.net/Dbenielli/ Optimism is an ImageJ plugin that implements a deconvolution method based on the Majorization minimization algorithm, devoted to two-photon 3d microscopic images. Dominique Benielli, I2M, Marseille, Caroline Chaux Moulin, I2M, Marseille, Sandrine Anthoine, I2M, Marseille, Labex Archimede, I2M, Marseille
Oxford Oncology https://sites.imagej.net/MicroscopyOncologyOxford/ Description: Some basic tools developed for users of the Microscopy Core in the department of Oncology at the University of Oxford. Rhodri Wilson
P2E-IT4Innovations https://sites.imagej.net/P2E-IT4Innovations/ ImageJ plugins from research group involved in the project Path to Exascale IT4Innovations:
  • SPIM Workflow Manager for HPC.
Jan Kožusznik
ParticleSizer https://sites.imagej.net/Ndef-psizer/ A plugin to derive number based size distributions from TEM images. Thorsten Wagner
Pendent Drop https://sites.imagej.net/Daerr/ A plugin for capillary length measurement through the pendent drop method. Adrian Daerr
PET-CT https://sites.imagej.net/Ilan/ Update site for the Pet-Ct-Viewer and other Nuclear Medicine software in use at Beth Israel Hospital, see Help Ilan Tal
PHANTAST https://sites.imagej.net/Nicjac/ Update site for PHANTAST (phase contrast microscopy segmentation toolbox), a collection of tools for the processing of phase contrast microscopy images Nicolas Jaccard
PhotoBend https://sites.imagej.net/Anotherche/ The PhotoBend is a collection of specialized plugins providing tracking a needle-like crystal shape changing during photoinduced bending process. 1. tracking the curvature of uniformly curved rods changing with time; 2. tracking a laser spot movement used in the laser beam deflection technique. Additionally, two auxiliary plugins for reading and writing compressed video using FFmpeg are included, which can be used standalone. Stanislav Chizhik
PhotonImaging https://sites.imagej.net/PhotonImaging/ The PhotonImaging plug-in for ImageJ is able to process single photon event data, by locating the center point of each photon and create a combined greyscale image with all found photons per pixel mapped to the correct pixel value. Lonneke Scheffer, Wout van Helvoirt
PillarTracker https://sites.imagej.net/PillarTracker/ The PillarTracker plug-in enables user to track the pillars and visualize the tracks and deflections. XU Xiaochun, Felix Martin Margadant
PQCT https://sites.imagej.net/PQCT/ Tools for Stratec pQCT bone and soft tissue images. Timo Rantalainen
PTBIOP https://biop.epfl.ch/Fiji-Update The EPFL - PTBIOP (BioImaging & Optics Platform) Update Site, with Fiji plugins and macros, including Action Bars (not the plugin) and HRM Manager. Olivier Burri
Quantixed https://sites.imagej.net/Quantixed/ ImageJ macros for making figures, blind analysis and more. Maintenance and issues here. Stephen Royle
QuimP https://pilip.lnx.warwick.ac.uk/quimp-update-site/ QuimP is software for tracking cellular shape changes and dynamic distributions of fluorescent reporters at the cell membrane. Piotr Baniukiewicz, Till Bretschneider
Radial Symmetry https://sites.imagej.net/Milkyklim/ A plugin for radial symmetry localization on smFISH (and other) images. Klim Kolyvanov
RadialIntensityProfile https://sites.imagej.net/PTschaikner/ RadialIntensityProfile is a simple macro to analyse the radial distribution of a fluorescent signal of interest in relation to a cell's nucleus. Philipp Tschaikner
ResultsToExcel https://sites.imagej.net/ResultsToExcel/ This plugin extracts data from the Results Table and adds it to a new or existing .xlsx Excel file on the user's desktop. It works well with batching as data is not overwritten. A similar plugin exists by another developer but that one didn't work well for me. I did not consult their source code. YouTube tutorial. Anthony Sinadinos
RT-Multiview-Deconvolution https://sites.imagej.net/RT-Multiview-Deconvolution/ Plugins for plane-wise GPU-accelerated multi-view deconvolution of SPIM data. Benjamin Schmid
Sceptical Physiologist https://sites.imagej.net/Scepticalphysiologist/ FFT (spectra + filtering); ROI class management; Image Linker; Tight Montage; Ca2+ imaging tools; etc. Sean Parsons at scepticalphysiologist.com
SCF MPI CBG https://sites.imagej.net/SCF-MPI-CBG/ Common image processing tools from the Scientific Computing Facility at MPI CBG Dresden Benoit Lombardot, Robert Haase
ScientiFig https://sites.imagej.net/Aigouy/ ScientiFig is a tool to build publication-ready scientific figures similar to FigureJ from the IBMP-CNRS site. It must be used in combination with the 'Java-8' update site. ScientiFig is deprecated please use EZFig instead. Benoit Aigouy
Scientifig-deprecated https://sites.imagej.net/SF-Deprecated-Legacy/ ScientiFig is a tool to build publication-ready scientific figures similar to FigureJ from the IBMP-CNRS site. This version of SF is deprecated. It must be used in combination with the 'Fiji-Legacy' update site (on old FIJI systems still using java 6). Note also that this version of SF is not compatible with 'Tissue Analyser'. Benoit Aigouy
Scijava Jupyter Kernel https://sites.imagej.net/Scijava-jupyter-kernel/ A Java kernel for Jupyter. See source on GitHub. Hadrien Mary
Scijava-parallel https://sites.imagej.net/Scijava-parallel/ Scijava-parallel is a framework that provides an access point for using computational resources such as remote computers or HPC clusters. See documentation on ImageJ Wiki. Jan Kožusznik
SciView https://sites.imagej.net/SciView/ SciView 3D/VR/AR visualization package for ImageJ. See source on GitHub. Kyle Harrington, Ulrik Günther
Server https://sites.imagej.net/Server/ ImageJ-server update site. See source on GitHub. Curtis Rueden
SIMcheck https://downloads.micron.ox.ac.uk/fiji_update/SIMcheck/ SIMcheck: a package of ImageJ tools for assessing the quality and reliability of Structured Illumination Microscopy (SIM) data. Micron Oxford
SiMView https://sites.imagej.net/SiMView/ Tools developed by the Keller Lab at the Janelia Research Campus, most notably the KLB file format. Burkhard Hoeckendorf
SimonKlein https://sites.imagej.net/SimonKlein/ Provides the plugins LinearDistance and PointAnalysis Simon Klein
SlideBook https://sites.imagej.net/SlideBook/ This Bio-Formats plugin enables the import of SlideBook SLD files. 3i Support
Slide Set https://b.nanes.org/slideset/update/ Slide Set: Reproducible image analysis and batch processing. Benjamin Nanes
SLIM Curve https://sites.imagej.net/SLIM-Curve/ SLIM Curve: a plugin for combined spectral-lifetime image analysis. Curtis Rueden
SLIM-Notts https://sites.imagej.net/SLIM-Notts/ Plugins and macros from the School of Life Sciences Imaging (SLIM) at the University of Nottingham Chris Gell
Stereoscopic 3D Projection https://sites.imagej.net/JoeNapoli/ Allows users to create 3-D anaglyph and Google Cardboard compatible projections from image stacks. Joe Napoli, Visikol, Inc.
Stowers https://research.stowers.org/imagejplugins/updates/ The Stowers ImageJ Plugins. Jay Unruh
StuartLab https://sites.imagej.net/StuartLab/ Tools developed and used in the labs of Dr. Stuart and Dr. Necakov at Brock University. Andrew Valente
Tango https://sites.imagej.net/Tango/ Tools for Analysis of Nuclear Genome Organization. Jean Ollion, Julien Cochennec
TDS https://sites.imagej.net/TDS/ Fiji-Tools-for-HCS is a collection of macros useful for high-content screening data developed by TDS members at MPI-CBG Dresden. Wiki Martin Stoeter
TEM suite https://sites.imagej.net/Makoten/ TEM suite is a set of easy to use and useful plugins designed for analyzing and presenting TEM data and images. It includes: calc dSpace, which calculates the d-spacing from manual measurements made by the user in their electron diffraction patterns; get dSpace, a more advanced d-spacing calculator; and pub Montage, an image montaging plugin for journal article figures. Mak Koten
TensorFlow https://sites.imagej.net/TensorFlow/ TensorFlow integration for ImageJ, including a microscope image focus quality classifier and a demo Inception image classifier. Curtis Rueden
Tissue Analyzer https://sites.imagej.net/TA/ Tissue Analyzer is a free tool to segment epithelial tissues. Benoit Aigouy
TomancakLab https://sites.imagej.net/Ulman2/ A couple of Fiji scripts to ease daily evo-devo image analysis life, from Tomancak lab. Vladimír Ulman
TrackMateCSVImporter https://sites.imagej.net/TrackMateCSVImporter/ The TrackMateCSVImporter is a Fiji plugin that can import CSV files into TrackMate. It can create TrackMate files out of a csv file and an image. A script also permits its use in headless mode. Jean-Yves Tinevez
TraJClassifier https://sites.imagej.net/TraJClassifier/ The TraJClassifier loads trajectories from TrackMate, characterize them using TraJ and classificate them into normal diffusion, subdiffusion, confined diffusion and directed/active motion by a random forest approach. Thorsten Wagner
Tr2d https://sites.imagej.net/Tr2d/ Tracking in 2d. Florian Jug
U-Net Segmentation https://sites.imagej.net/Falk/ The U-Net segmentation plugin interfaces caffe on a remote Linux host to segment images using artificial neural networks. The Plugin requires a special extended version of caffe that is available via the U-Net Project Page. This plugin is maintained on GitHub. Thorsten Falk
UCB Vision Sciences https://sites.imagej.net/Llamero/ A suite of tools developed as part of the University of California, Berkeley Vision Sciences core grant NIH P30EY003176, including a Hough Circle Transform and a Quiver Plot tool. Ben Smith
Vale lab plugins https://sites.imagej.net/Nico/ Plugins useful to the Vale lab: Saim, spot intensity analysis, spot counter. Nico Stuurman
Vanderbilt Biophotonics Center https://sites.imagej.net/Wilson.adams/ Customized GUI and image analysis scripts designed for local use by the Vanderbilt Biophotonics Center and collaborators. Avoid following if you have a personally customized StartupMacros.ijm file. Wilson R Adams Vanderbilt Biophotonics Center, Nashville, TN, USA
VersiLab plugins https://sites.imagej.net/Sweeneyian/ VersiLab_Plugin, aiming to do real-time image acquisition and processing for Optical Endo-Microscopy (OEM), development phase, code available on GitHub. Ian Sweeney
Virtual Cell https://sites.imagej.net/VCell/ Plugins for using Virtual Cell with ImageJ. Jim Schaff
Void Whizzard https://sites.imagej.net/VezinaLab/ Void Whizzard is a tool for analyzing void spot assay (VSA) images. Royal Oakes
Volumetric Tissue Exploration and Analysis https://sites.imagej.net/ICBM-IUPUI/ VTEA is an interactive tool for 3D tissue cytometry built on ImageJ. Seth Winfree
WhiskerTracking https://sites.imagej.net/Tarokiritani/ WhisketTracking is a set of tools for tracking rodent whisker. Taro Kiritani
WormSizer https://sites.imagej.net/Bradtmoore/ The update site for WormSizer, a tool for measuring volume, length, and surface area of nematodes off of a dissection microscope. Brad T. Moore
XitoSBML https://sites.imagej.net/XitoSBML/ XitoSBML is an ImageJ plugin which creates a Spatial SBML model from segmented images. XitoSBML is not just a converter, but also a spatial model editor so that users can add molecules(species), reactions and advection/diffusion coefficients to the converted Spatial SBML model. Kaito Ii, Akira Funahashi
Xlib https://sites.imagej.net/Xlib/ Xlib is a set of prospective ImageJ plugins: automated imaging tools for filtering, data reconstruction, quantitative data evaluation and data import, tools for interactive segmentation, visualization and management of image data. Beat Münch
Zoom-in-movie https://sites.imagej.net/ZOOM-in-movie/ Zoom-in-movie is a simple tool for creating zoom-in movies with logarithmic approach and dynamic scalebar. Simply select ROI on your image and select Plugins/Zoom-in movie to run the plugin. Thanks to Eugene Katrukha for the initial implementation. Andrey Aristov
ZedMate Suite http://sites.imagej.net/Ayakimovich/ ZedMate is a TrackMate-based plugin for 3D particles detection and measurement. Artur Yakimovich