List of update sites

Revision as of 07:01, 25 February 2016 by Stelfrich (talk | contribs) (Update links for Biomedgroup site)

Template:UpdateSites


Introduction

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 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/ Base update site for ImageJ2 and Fiji components (e.g., ImageJ Ops and the 3D Viewer) which have migrated to Java 7 or Java 8. Will not work with Java 6 or 7. 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! Mark Hiner
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
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, Image Segmentation and Bitmap Morphometry. Tiago Ferreira
Bio-Formats http://sites.imagej.net/Bio-Formats/ A version of Bio-Formats with the latest bugfixes from the 5.1.x development branch. The last successful build is automatically uploaded daily. Curtis Rueden, ImageJ Jenkins
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
CellMotility http://sites.imagej.net/CellMotility/ Plugins from the Cellular Signalling and Cytoskeletal Function Lab at The Francis Crick Institute, including ADAPT. David Barry
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
CMTK Registration http://sites.imagej.net/Jefferis/ CMTK Registration GUI. Gregory Jefferis
CMP-BIA tools http://sites.imagej.net/CMP-BIA/ The development version of CMP-BIA tools. Jiri Borovec
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
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
FFMPEG http://fiji.sc/~schindelin/ffmpeg-plugins/ Fiji plugins which allow reading and writing to FFmpeg-supported formats via native bindings. Johannes Schindelin
Funimage http://sites.imagej.net/Funimage/ Fiji plugin that provides Clojure wrappings of many commonly used functions from ImageJ and ImgLib2. Works with SciJava scripting for Clojure, and Funimage 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: https://github.com/astartes91/imagej-neural-fuzzy-plugins. Vladimir Nizamutdinov
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
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
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
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
ImageJ Latex http://sites.imagej.net/Yul.liuyu/ Add math equations to an image using Latex. Yu Liu
ImageJ-dev http://sites.imagej.net/ImageJ-dev/ Development version of ImageJ components. Curtis Rueden,Mark Hiner
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. Mark Hiner
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
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
IMCF Uni Basel http://sites.imagej.net/UniBas-IMCF/ Various plugins (most notably the Stitching-Wrapper for FluoView OIF mosaics), macros and Action Bars (they require the IBMP-CNRS update site to be enabled).

Will update your Jython version to 2.7-beta1.

Niko Ehrenfeuchter
LinearDistance http://sites.imagej.net/SimonKlein/ This plugin measures distances between binary inversions of an binary image in x and y direction in pixel or units. Used to measure free mean path in a two phased metal. SimonKlein
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,Mark Hiner
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
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
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
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
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
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
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
PTBIOP http://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
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; density plotting; etc. Sean Parsons at scepticalphysiologist.com
ScientiFig http://sites.imagej.net/Aigouy/ ScientiFig is a tool to build publication-ready scientific figures similar to FigureJ from the IBMP-CNRS site. Benoit Aigouy
SCIFIO-dev http://sites.imagej.net/SCIFIO/ Development version of SCIFIO components. Mark Hiner
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
Slide Set http://cellbio.emory.edu/bnanes/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
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
Vale lab plugins http://sites.imagej.net/Nico/ Utilities useful to our lab members: spot counter plugin, Nico Stuurman
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
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