Difference between revisions of "List of update sites"

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|At [https://www.universiteitleiden.nl/ 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 [https://www.universiteitleiden.nl/en/research/research-facilities/science/cell-observatory#tab-1 Cell Observatory].  
|At [https://www.universiteitleiden.nl/ 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 [https://www.universiteitleiden.nl/en/research/research-facilities/science/cell-observatory#tab-1 Cell Observatory].  
|[mailto:jwillemse@biology.leidenuniv.nl Joost Willemse]
|[mailto:jwillemse@biology.leidenuniv.nl Joost Willemse]
|- valign="top"
|Revisited active contour method for 3D segmentation. Preprint and [http://imagej.net/LimeSeg/ documentation] expected Jan 2018.
|[mailto:nicolas.chiaruttini@unige.ch Nicolas Chiaruttini] & Sarah Machado
|- valign="top"
|- valign="top"

Revision as of 08:42, 12 December 2017

Update Sites
Following an update site
Creating your own update site
Terms of Service for personal update sites
Automatically upload your site
Uploading to core update sites
List of update sites
Update site FAQ


The Updater has a convenient Manage update sites dialog that is populated by this wiki page.

  • Users: You can enable an update site using the Help  ▶ Update... command and clicking the "Manage update sites" button.
  • Developers: You can add your own update site to this list by registering a wiki account and editing the table below yourself. Please maintain alphabetical order, but please do not change the format of the table—you will most likely break the updater if you do this.

Available update sites

ImageJ Update Sites
Name Site Description Maintainer
Default Update Sites
ImageJ http://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 http://update.fiji.sc/ Base update site for Fiji and core Fiji plugins. If you downloaded Fiji directly, it is already included. Fiji developers
Java-8 http://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
Optional Update Sites
2015-Conference http://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 http://sites.imagej.net/Tboudier/ A suite of plugins providing enhanced 3D capabilities in ImageJ. Thomas Boudier
Angiogenesis http://sites.imagej.net/Angiogenesis/ A plugin to quantify angiogenic sprout morphology. Jan Eglinger
AngioTool http://sites.imagej.net/AngioTool/ The AngioTool software converted to a Fiji plugin. Jan Eglinger
Archipelago http://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
BAR http://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 http://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 http://sites.imagej.net/BIG-EPFL/ ImageJ plugins from EPFL's Biomedical Imaging Group (BIG). Curtis Rueden
BigStitcher http://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 and David Hörl
Bio-Formats http://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
Biomedgroup http://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 http://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
CALM http://sites.imagej.net/CALM/ Plugins from the Crick Advanced Light Microscopy Facility at The Francis Crick Institute. David Barry
CellMotility http://sites.imagej.net/CellMotility/ Plugins from the Cellular Signalling and Cytoskeletal Function Lab at The Francis Crick Institute, including ADAPT. David Barry
CellTrackingChallenge http://sites.imagej.net/Ulman/ Implementation of measures and front-end plugins used in and related to the Cell Tracking Challenge. Vladimír Ulman
CircleSkinner http://sites.imagej.net/CircleSkinner/ A Fiji plugin for the automated detection and quantification of circular structures in images. Jean-Yves Tinevez
Cookbook http://sites.imagej.net/Cookbook/ Plugins from the Cookbook. Cookbook Team
ClearVolume http://sites.imagej.net/ClearVolume/ ClearVolume is a fast 3D viewer, for more information see also ClearVolumeWiki. ClearVolume
CMCI-EMBL http://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 http://sites.imagej.net/CMP-BIA/ The development version of CMP-BIA tools. Jiri Borovec
CMTK Registration http://sites.imagej.net/Jefferis/ CMTK Registration GUI. Gregory Jefferis
CSIM Laboratory http://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 http://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
DiameterJ http://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 [coming soon] for more information and the publication describing how DiameterJ works and its limitations. Nathan Hotaling
EpiGraph http://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 and Pablo Vicente Munuera
FFMPEG http://fiji.sc/~schindelin/ffmpeg-plugins/ Fiji plugins which allow reading and writing to FFmpeg-supported formats via native bindings. Johannes Schindelin
FibrilJ http://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
Fiji-Legacy http://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
FilamentDetector http://sites.imagej.net/FilamentDetector/ A Fiji plugin that allows easy, fast and accurate detection and tracking of biological filaments. Hadrien Mary
FiloQuant http://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
FracLac Suite http://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 http://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 http://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 http://sites.imagej.net/Rerger/ Fuzzy Set is an ImageJ plugin, to transform the intensity of the image using Fuzzy Sets. Robert Erger
GDSC http://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 http://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 http://sites.imagej.net/Hadim/ Contains the ij2-python-lib package. For details see the GitHub page. Hadrien Mary
HDF5 http://sites.imagej.net/Ronneber/ The HDF5 plugin allows to load and save data in HDF5 format. For details see HDF5 plugin. Olaf Ronneberger
HistoJ http://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
HistoJ Lite http://sites.imagej.net/Pathomation/ Plugin to interface with Pathomation's free 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
IBMP-CNRS http://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 http://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 http://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 Import Export http://sites.imagej.net/Ilastik/ Plugin for importing/exporting the hdf5 fileformat from ilastik Jonas Massa
ImageJ Latex http://sites.imagej.net/Yul.liuyu/ Add math equations to an image using Latex. Yu Liu
ImageJ-ITK http://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 http://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 http://sites.imagej.net/ImageScience/ Base update site for all ImageScience related ImageJ plugins. Erik Meijering
ImagingBook http://sites.imagej.net/ImagingBook/ Common ImageJ/Java source code for the Digital Imaging books by Wilhelm Burger and Mark J. Burge (see http://www.imagingbook.com). 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 at http://sourceforge.net/projects/imagingbook/ Wilhelm Burger
ImagingBookEn1 http://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 http://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 http://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 http://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 http://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 http://sites.imagej.net/ImagingFCS/ Imaging_FCS 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 1.8.0_102) and requires Imagescience for statistics (simulator) and Apache Poi for file reading and writing. Thorsten Wohland
IMCF Uni Basel http://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
INCF test site http://sites.imagej.net/Dimiterpp/ Update site for scale space filters and other INCF projects from GSOC 2014, 2015, 2016. Dimiter Prodanov
JAX Eye http://sites.imagej.net/MarkKrebs/ Macro for processing brightfield fundus images of the mouse eye and plugin for averaging replicate OCT volume scans. Mark Krebs
Kappa http://sites.imagej.net/Kappa/ A Fiji plugin for Curvature Analysis. Hadrien Mary
Leiden University http://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 http://sites.imagej.net/LimeSeg/ Revisited active contour method for 3D segmentation. Preprint and documentation expected Jan 2018. Nicolas Chiaruttini & Sarah Machado
Lineage-Mapper http://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 http://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 and Damien Ramunno-Johnson
LOCI http://sites.imagej.net/LOCI/ The LOCI update site for their Fiji plugins, including VisBio Fiji plugins and other miscellany. Curtis Rueden
MaMuT http://sites.imagej.net/MaMuT/ MaMuT, a plugin for the annotation of massive, multi-view data. Jean-Yves Tinevez
Micro-Magellan http://sites.imagej.net/Hpinkard/ Micro-Magellan (https://micro-manager.org/wiki/MicroMagellan) 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 (http://fiji.sc/BigDataViewer). Henry Pinkard
MIST http://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 http://sites.imagej.net/MiToBo/ MiToBo (http://www.informatik.uni-halle.de/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 http://sites.imagej.net/VolkerGatterdam/ Script for Evaluation of Molographic Data Volker Gatterdam
MoMA http://sites.imagej.net/MoMA/ Mother Machine Analyser [1] Florian Jug
Morphology http://sites.imagej.net/Landini/ The update site for the Mathematical Morphology Collection of plugins and macros. Gabriel Landini
MOSAIC ToolSuite http://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
MS-ECS-2D http://sites.imagej.net/MS-ECS-2D/ MembraneStained EpithelialCellSegmentation 2D, for more information see also the update site page. MS-ECS-2D
MTrack http://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
NanoJ-Core http://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 http://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 http://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 http://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 http://sites.imagej.net/Neubias/ Plugins and scripts developed in the context of NEUBIAS. NEUBIAS members
Neuroanatomy http://sites.imagej.net/Neuroanatomy/ Image Processing Tools for Neuroanatomy and Tree-like structures (list). Tiago Ferreira
NeuroCyto Lab http://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. http://www.neurocytolab.org Christophe Leterrier, NeuroCyto Lab, NICN, Marseille
NucleusJ http://sites.imagej.net/PouletAxel/ This plugin is dedicated to researchers interested in nuclear shape and chromatin organization. Starting from image stacks, the nuclear boundary as well as nuclear bodies are segmented. As output, NucleusJ automatically measures 15 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 http://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 http://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 http://sites.imagej.net/OMERO-5.2/ The OMERO update site for bidirectional integration between ImageJ and OMERO 5.2.x. Curtis Rueden
OpenSPIM http://openspim.org/update/ The drivers and software to operate an OpenSPIM (Open Access selective plane light sheet microscope). Luke Stuyvenberg and Johannes Schindelin
OPTIMISME http://sites.imagej.net/Dbenielli/ Description: Optimism is an ImageJ plugin that implements a deconvolution method based on the Majorization minimization algorithm, devoted to two-photon 3d microscopic images. https://www.i2m.univ-amu.fr/ Dominique Benielli, Caroline Chaux Moulin, Sandrine Anthoine, Labex Archimede , I2M, Marseille
Oxford Oncology http://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
ParticleSizer http://sites.imagej.net/Ndef-psizer/ A plugin to derive number based size distributions from TEM images. Thorsten Wagner
Pendent Drop http://sites.imagej.net/Daerr/ A plugin for capillary length measurement through the pendent drop method. Adrian Daerr
PET-CT http://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 http://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
PhotonImaging http://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 http://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
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 http://sites.imagej.net/Quantixed/ ImageJ macros for making figures, blind analysis and more. Maintenance and issues here. Stephen Royle
QuimP http://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 (CellDynamics)
Radial Symmetry http://sites.imagej.net/Milkyklim/ A plugin for radial symmetry localization on smFISH (and other) images. Klim Kolyvanov
RadialIntensityProfile http://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. PTschaikner
ResultsToExcel http://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 ResultsToExcel
RT-Multiview-Deconvolution http://sites.imagej.net/RT-Multiview-Deconvolution/ Plugins for plane-wise GPU-accelerated multi-view deconvolution of SPIM data. Benjamin Schmid
Sceptical Physiologist http://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 http://sites.imagej.net/SCF-MPI-CBG/ Common image processing tools from the Scientific Computing Facility at MPI CBG Dresden Benoit Lombardot and Robert Haase
ScientiFig http://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. Benoit Aigouy
Scientifig-deprecated http://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 http://sites.imagej.net/Scijava-jupyter-kernel/ A Java kernel for Jupyter. See source on GitHub Hadrien Mary
SIMcheck http://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 http://sites.imagej.net/SiMView/ Tools developed by the Keller Lab at the Janelia Research Campus, most notably the KLB file format. Burkhard Hoeckendorf
SimonKlein http://sites.imagej.net/SimonKlein/ Provides the plugins LinearDistance and PointAnalysis SimonKlein
SlideBook http://sites.imagej.net/SlideBook/ This Bio-Formats plugin enables the import of SlideBook SLD files. 3i Support
Slide Set http://b.nanes.org/slideset/update/ Slide Set: Reproducible image analysis and batch processing. Benjamin Nanes
SLIM Curve http://sites.imagej.net/SLIM-Curve/ SLIM Curve: a plugin for combined spectral-lifetime image analysis. Curtis Rueden
Stereoscopic 3D Projection http://sites.imagej.net/JoeNapoli/ Allows users to create 3-D anaglyph and Google Cardboard compatible projections from image stacks. Joe Napoli and Visikol, Inc.
Stowers http://research.stowers.org/imagejplugins/updates/ The Stowers ImageJ Plugins. Jay Unruh
Tango http://sites.imagej.net/Tango/ Tools for Analysis of Nuclear Genome Organization. Jean Ollion, Julien Cochennec
TDS http://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
TensorFlow http://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 http://sites.imagej.net/TA/ Tissue Analyzer is a free tool to segment epithelial tissues. Benoit Aigouy
TraJClassifier http://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 http://sites.imagej.net/Tr2d/ Tracking in 2d. Florian Jug
U-Net Segmentation http://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 will be available soon. It does not work with currently available versions of caffe with U-Net extensions. Thorsten Falk
UCB Vision Sciences http://sites.imagej.net/Llamero/ This is a suite of tools that were developed as part of the University of California, Berkeley Vision Sciences core grant NIH P30EY003176. These tools include a Hough Circle Transform and a Quiver Plot tool. Ben Smith
Vale lab plugins http://sites.imagej.net/Nico/ Utilities useful to our lab members: spot counter plugin, Nico Stuurman
VersiLab plugins http://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, Sweeneyian
Virtual Cell http://sites.imagej.net/VCell/ Plugins for using Virtual Cell with ImageJ. Jim Schaff
Volumetric Tissue Exploration and Analysis http://sites.imagej.net/ICBM-IUPUI/ VTEA is an interactive tool for 3D tissue cytometry built on ImageJ. Seth Winfree
WhiskerTracking http://sites.imagej.net/Tarokiritani/ WhisketTracking is a set of tools for tracking rodent whisker. Taro Kiritani
WormSizer http://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 http://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 and Akira Funahashi
Xlib http://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