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sites.yml
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sites:
- name: "ImageJ"
id: "ImageJ"
url: "https://update.imagej.net/"
description: >-
Base update site for [ImageJ2](https://imagej.net/software/imagej2). No need
to add this to your list of update sites; it is already included.
maintainers:
- "[ImageJ2 developers](https://imagej.net/people#imagej2)"
- name: "Fiji"
id: "Fiji"
url: "https://update.fiji.sc/"
description: >-
Base update site for [Fiji](https://imagej.net/software/fiji) and
[core Fiji plugins](https://imagej.net/list-of-extensions).
If you downloaded Fiji directly, it is already included.
maintainers:
- "[Fiji developers](https://imagej.net/people#fiji)"
- name: "Fiji-Legacy"
id: "Fiji-Legacy"
url: "https://sites.imagej.net/Fiji-Legacy/"
description: >-
Restores old Fiji plugins which never made the transition to Maven, as
well as obsolete libraries no longer used by current Fiji installations.
maintainers:
- "UNSUPPORTED"
- name: "Java-8"
id: "Java-8"
url: "https://sites.imagej.net/Java-8/"
description: >-
Temporary base update site for [ImageJ2](https://imagej.net/software/imagej2) and
[Fiji](https://imagej.net/software/fiji) components as everything migrates to Java
8. __Will not work with Java 6 or 7.__
See [this page](https://imagej.net/news/2016-05-10-imagej-howto-java-8-java-6-java-3d) for details.
maintainers:
- "[ImageJ2 and Fiji developers](https://imagej.net/people)"
- name: "2015-Conference"
id: "2015-Conference"
url: "https://sites.imagej.net/2015-Conference/"
description: >-
A collection of plugins highlighting the latest features of ImageJ. As
seen in [Wayne Rasband](https://imagej.net/people/rasband)'s
[opening talk](https://vimeo.com/140929691) at the
[2015 conference](https://imagej.net/events/conference-2015)!
maintainers:
- "[Curtis Rueden](https://imagej.net/people/ctrueden)"
- name: "3D ImageJ Suite"
id: "Tboudier"
url: "https://sites.imagej.net/Tboudier/"
description: >-
A [suite of plugins](https://imagejdocu.tudor.lu/doku.php?id=plugin:stacks:3d_ij_suite:start)
providing enhanced 3D capabilities in ImageJ.
maintainers:
- "[Thomas Boudier](https://imagej.net/people/mcib3d)"
- name: "3Dscript"
id: "3Dscript"
url: "https://romulus.oice.uni-erlangen.de/updatesite/"
description: >-
[3Dscript](https://imagej.net/plugins/3dscript) is a plugin animating 3D/4D microscopy data using a natural-language-based syntax.
maintainers:
- "[Benjamin Schmid](https://imagej.net/people/bene51)"
- name: "ActogramJ"
id: "ActogramJ"
url: "https://romulus.oice.uni-erlangen.de/imagej/updatesites/ActogramJ/"
description: >-
[ActogramJ](https://bene51.github.io/ActogramJ) is a plugin for analyzing actograms.
maintainers:
- "[Benjamin Schmid](https://imagej.net/people/bene51)"
- name: "AdipoQ"
id: "AdipoQ"
url: "https://sites.imagej.net/AdipoQ/"
description: >-
ImageJ plugins for quantifying adipocyte morphology and function in tissues and in vitro.
For more details, a link to the corresponding publication, and information on how
to cite the plugins visit the AdipoQ github page https://github.com/hansenjn/AdipoQ/
maintainers:
- "[Jan Hansen](https://github.com/hansenjn/)"
- name: "AIC Janelia - Course"
id: "AICjanelia-course"
url: "https://sites.imagej.net/AICjanelia-course/"
description: >-
A collection of plugins and macros for students of the Advanced Imaging
Center (AIC) Fiji Course.
maintainers:
- "[AIC Janelia](https://imagej.net/orgs/janelia#advanced-imaging-center)"
- name: "ALPACA"
id: "ALPACA"
url: "https://sites.imagej.net/ALPACA/"
description: >-
A collection of macros to study cilia.
maintainers:
- "[Torsten Schmenger](https://github.com/tschmenger/)"
- name: "AMPT"
id: "AMPT"
url: "https://sites.imagej.net/AMPT/"
description: >-
The [Aquatic Mammal Photogrammetry Tool](https://allenmli.github.io/AMPT/)
(AMPT) is an ImageJ plug-in that simplifies the process of measuring
aquatic mammals from aerial imagery. The tool may be configured to support
different guided measurements.
maintainers:
- "[AMPT Developers](mailto:ampt-dev@allenai.org)"
- name: "Angiogenesis"
id: "Angiogenesis"
url: "https://sites.imagej.net/Angiogenesis/"
description: >-
A plugin to quantify angiogenic sprout morphology.
maintainers:
- "[Jan Eglinger](https://imagej.net/people/imagejan)"
- name: "AngioTool"
id: "AngioTool"
url: "https://sites.imagej.net/AngioTool/"
description: >-
The [AngioTool](https://ccrod.cancer.gov/confluence/display/ROB2/Home)
software converted to a Fiji plugin.
maintainers:
- "[Jan Eglinger](https://imagej.net/people/imagejan)"
- name: "apoc"
id: "apoc"
url: "https://sites.imagej.net/apoc/"
description: >-
Accelerated pixel and object classifiers (APOC).
See [clijx-accelerated-pixel-and-object-classification](https://github.com/clij/clijx-accelerated-pixel-and-object-classification).
maintainers:
- "[Robert Haase](https://imagej.net/people/haesleinhuepf)"
- name: "Archipelago"
id: "Lindsey"
url: "https://sites.imagej.net/Lindsey/"
description: >-
A set of plugins that allow Fiji to be run in parallel on a cluster.
Currently,
[Trainable Weka Segmentation](https://imagej.net/plugins/tws)
and [Elastic Alignment](https://imagej.net/plugins/elastic-alignment-and-montage)
are accelerated in this way.
maintainers:
- "[Larry Lindsey](https://imagej.net/people/larrylindsey)"
- name: "AxoNet"
id: "AxoNet"
url: "https://sites.imagej.net/AxoNet/"
description: >-
An implementation of the AxoNet tool which can be used to count axons in
light micrographs of optic nerves.
maintainers:
- "[Matthew Ritch](https://imagej.net/User:Mritch3)"
- name: "BACMMAN"
id: "BACMMAN"
url: "https://sites.imagej.net/BACMMAN/"
description: >-
BACteria in Mother Machine ANalyzer: a plugin for high-throughput
analysis of multichannel mother machine data.
See [Sources](https://github.com/jeanollion/bacmman): https://github.com/jeanollion/bacmman
and [Wiki](https://github.com/jeanollion/bacmman/wiki): https://github.com/jeanollion/bacmman/wiki
maintainers:
- "[Jean Ollion](https://www.sabilab.fr/)"
- name: "BACMMAN-DL"
id: "BACMMAN-DL"
url: "https://sites.imagej.net/BACMMAN-DL/"
description: >-
Enables deep learning for BACMMAN (CPU).
Currently using Tensorflow 2x
maintainers:
- "[Jean Ollion](https://www.sabilab.fr/)"
- name: "BACMMAN-DL-GPU"
id: "BACMMAN-DL-GPU"
url: "https://sites.imagej.net/BACMMAN-DL-GPU/"
description: >-
Enables deep learning for BACMMAN (GPU).
Currently using Tensorflow 2x
maintainers:
- "[Jean Ollion](https://www.sabilab.fr/)"
- name: "BAR"
id: "Tiago"
url: "https://sites.imagej.net/Tiago/"
description: >-
[BAR](https://imagej.net/plugins/bar) (_Broadly Applicable Routines_) is a
[GitHub-curated](https://github.com/tferr/Scripts) collection of scripts
that simplifies the daily usage of ImageJ. The collection is focused on
Data Analysis, Image Annotation and Segmentation.
maintainers:
- "[Tiago Ferreira](https://imagej.net/people/tferr)"
- name: "BaSiC"
id: "BaSiC"
url: "https://sites.imagej.net/BaSiC/"
description: >-
[BaSiC](https://www.helmholtz-muenchen.de/icb/research/groups/quantitative-single-cell-dynamics/software/basic/index.html)
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.
maintainers:
- "[Tingying Peng](mailto:tingying.peng@tum.de)"
- name: "Batch Composite"
id: "BatchComposite"
url: "https://sites.imagej.net/BatchComposite/"
description: >-
[Batch Composite](https://imagej.net/plugins/batch-composite) is a small
plugin that runs the Composite operation on a folder of openable files.
It supports Bio-Formats, recursion, and color customization.
maintainers:
- "[Kevin Fisher](mailto:kfish610@gmail.com)"
- name: "Batch Tools"
id: "BatchTools"
url: "https://sites.imagej.net/BatchTools/"
description: >-
[Batch Tools](https://imagej.net/plugins/batch-tools) provides a toolbar
to support batch image processing and analysis, including batch extract,
merge channels, composite conversion, Z-projection, channel B&C and colour
adjustment, file export, and cell count, gray value & area measurement.
maintainers:
- "[Neville S Ng](https://github.com/neville-s-ng)"
- name: "BD-CellView"
id: "BD-CellView"
url: "https://sites.imagej.net/BD-CellView/"
description: >-
[BD-CellView](https://github.com/embl-cba/ICS)
enables inspection and batch processing of images generated with the BD-CellView imaging flow cytometer.
maintainers:
- "[Christian Tischer](mailto:christian.tischer@embl.de)"
- name: "BIG-EPFL"
id: "BIG-EPFL"
url: "https://sites.imagej.net/BIG-EPFL/"
description: >-
ImageJ plugins from
[EPFL's Biomedical Imaging Group (BIG)](https://imagej.net/licensing/big).
NOT OPEN SOURCE.
maintainers:
- "[Curtis Rueden](https://imagej.net/people/ctrueden)"
- name: "BigDataProcessor"
id: "BigDataProcessor"
url: "https://sites.imagej.net/BigDataProcessor/"
description: >-
[BigDataProcessor2](https://github.com/embl-cba/bigDataProcessor2#bigdataprocessor2)
is an Imglib2 and BigDataViewer based tool for inspection and processing of big (TB-sized) image data.
maintainers:
- "[Christian Tischer](mailto:christian.tischer@embl.de)"
- name: "BigStitcher"
id: "BigStitcher"
url: "https://sites.imagej.net/BigStitcher/"
description: >-
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.
maintainers:
- "[Stephan Preibisch](https://imagej.net/people/StephanPreibisch)"
- "[David Hörl](https://imagej.net/people/hoerldavid)"
- name: "BigVolumeViewer Demo"
id: "BigVolumeViewer"
url: "https://sites.imagej.net/BigVolumeViewer/"
description: >-
Demo of BDV volume rendering. See
[this forum post](https://forum.image.sc/t/bigvolumeviewer-tech-demo)
for getting started.
maintainers:
- "[Tobias Pietzsch](https://imagej.net/people/tpietzsch)"
- name: "Bio-Formats"
id: "Bio-Formats"
url: "https://sites.imagej.net/Bio-Formats/"
description: >-
A version of [Bio-Formats](https://imagej.net/formats/bio-formats) with the
latest bugfixes from the
[development branch](https://github.com/openmicroscopy/bioformats/tree/develop).
The last SNAPSHOTS are automatically uploaded daily.
maintainers:
- "[OME development team](https://www.openmicroscopy.org)"
- name: "Biomat"
id: "Biomat"
url: "https://sites.imagej.net/Biomat/"
description: >-
Plugins for 3D image preprocessing and detection of fibres in 3D image.
maintainers:
- "[Jiri Janacek](https://imagej.net/people/jiri-janacek)"
- name: "Biomedgroup"
id: "Biomedgroup"
url: "https://sites.imagej.net/Biomedgroup/"
description: >-
A set of plugins developed by the biomedical imaging group of the
dortmund university of applied sciences and arts:
* [Shape Filter](https://imagej.net/plugins/shape-filter) (Filter binary images by shape),
* [Shape Smoothing](https://imagej.net/plugins/shape-smoothing) (Smooth objects via Fourier descriptors),
* [Non Local Means Denoise](https://imagej.net/plugins/non-local-means-denoise) (edge preserving noise filter),
* [NanoTrackJ](https://imagej.net/plugins/nanotrackj) (Size characterization of freely diffusing nanoparticles by particle tracking),
* [Ridge Detection](https://imagej.net/plugins/ridge-detection) (Line / Ridge detection plugin).
maintainers:
- "[Thorsten Wagner](https://imagej.net/people/thorstenwagner)"
- name: "BioVoxxel"
id: "BioVoxxel"
url: "https://sites.imagej.net/BioVoxxel/"
description: >-
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](https://imagej.net/plugins/biovoxxel-toolbox) page and the
[BioVoxxel web site](https://www.biovoxxel.de).
maintainers:
- "[Jan Brocher](https://imagej.net/people/biovoxxel)"
- name: "BioVoxxel 3D Box"
id: "bv3dbox"
url: "https://sites.imagej.net/bv3dbox/"
description: >-
Image processing and analysis tools for 2D and 3D images in one place.
Based on GPU accelerated computing via CLIJ2.
[BioVoxxel 3D box](https://biovoxxel.github.io/bv3dbox/)
[BioVoxxel web site](https://www.biovoxxel.de).
maintainers:
- "[Jan Brocher](https://imagej.net/people/biovoxxel)"
- name: "BioVoxxel Figure Tools"
id: "bvft"
url: "https://sites.imagej.net/bvft/"
description: >-
The figure tools are meant to connect Fiji with Inkscape to flexibly prepare images for and create
publication figures with the highest possible data quality.
An introduction video to version 2.2.0 can be found [here](https://youtu.be/F6ll37NOgXc?si=SOICjiqGzw4RCUDR)
maintainers:
- "[Jan Brocher](https://imagej.net/people/biovoxxel)"
- name: "Blind Analysis Tools"
id: "Astja"
url: "https://sites.imagej.net/Astja/"
description: >-
Tools to facilitate blind i.e., unbiased analysis of (image) data.
For more information visit the
[documentation page](https://imagej.net/plugins/blind-analysis-tools).
maintainers:
- "[Astha Jaiswal](https://imagej.net/people/ahtsaJ), Holger Lorenz"
- name: "BoneJ"
id: "BoneJ"
url: "https://sites.imagej.net/BoneJ/"
description: >-
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).
maintainers:
- "[Michael Doube](https://imagej.net/people/mdoube)"
- "[Alessandro Felder](https://imagej.net/people/alessandrofelder)"
- name: "BTrack"
id: "BTrack"
url: "https://sites.imagej.net/BTrack/"
description: >-
[BTrack](https://imagej.net/plugins/btrack) uses the skeletonization
implementation of [ImgLib2](https://imagej.net/libs/imglib2) to track
growing ends of tissue branches. It is suitable for any form of imaging
modality as it requires a segmentation image as an input for performing
the tracking operations.
maintainers:
- "[Varun Kapoor](https://imagej.net/people/kapoorlab)"
- name: "CALM"
id: "CALM"
url: "https://sites.imagej.net/CALM/"
description: >-
Plugins from the Crick Advanced Light Microscopy Facility at
[The Francis Crick Institute](https://www.crick.ac.uk).
maintainers:
- "[David Barry](mailto:david.barry@crick.ac.uk)"
- name: "CAMDU"
id: "CAMDU"
url: "https://sites.imagej.net/CAMDU/"
description: >-
Plugins from the
[Computing and Advanced Microscopy Development Unit](https://www.warwick.ac.uk/camdu)
at the [University of Warwick](https://www.warwick.ac.uk).
maintainers:
- "[Erick Martins Ratamero](mailto:e.martins-ratamero.1@warwick.ac.uk)"
- name: "CATS"
id: "CATS"
url: "https://sites.imagej.net/CATS/"
description: >-
Context Aware Trainable Segmentation [CATS](https://github.com/embl-cba/cats)
maintainers:
- "[Christian Tischer](mailto:tischitischer@gmail.com)"
- name: "CellTrackingChallenge"
id: "Ulman"
url: "https://sites.imagej.net/Ulman/"
description: >-
Implementation of measures and front-end plugins used in and related to
the [Cell Tracking Challenge](http://www.celltrackingchallenge.net).
maintainers:
- "[Vladimír Ulman](mailto:ulman@mpi-cbg.de)"
- name: "Cellular Imaging"
id: "CellularImaging"
url: "https://sites.imagej.net/Cellular-Imaging/"
description: >-
Fiji plugins developed in the Cellular Imaging - Lehmann Group of the FMP-Berlin.
maintainers:
- "[Christopher Schmied](mailto:christopher.schmied@fht.org)"
- name: "CiliaQ"
id: "CiliaQ"
url: "https://sites.imagej.net/CiliaQ/"
description: >-
An set of three ImageJ plugins to quantify ciliary shape, length, and fluorescence in 2D, 3D, and 4D images.
For more details, a link to the corresponding publication, and information on how
to cite the plugin visit the CiliaQ github pages (including manual and wiki) at https://github.com/hansenjn/CiliaQ
maintainers:
- "[Jan Hansen](https://github.com/hansenjn/)"
- name: "CIP"
id: "CIP"
url: "https://sites.imagej.net/CIP/"
description: >-
[An image processing toolbox focused on scripting](https://imagej.net/plugins/cip).
maintainers:
- "[Benoit Lombardot](https://imagej.net/people/benoalo)"
- name: "CircleSkinner"
id: "CircleSkinner"
url: "https://sites.imagej.net/CircleSkinner/"
description: >-
A Fiji plugin for the automated detection and quantification of circular
structures in images.
maintainers:
- "[Jean-Yves Tinevez](https://imagej.net/people/tinevez)"
- name: "ClearVolume"
id: "ClearVolume"
url: "https://sites.imagej.net/ClearVolume/"
description: >-
ClearVolume is a fast 3D viewer, for more information see also the
[ClearVolume wiki](https://github.com/ClearVolume/ClearVolume/wiki).
maintainers:
- "[ClearVolume](https://imagej.net/User:ClearVolume)"
- name: "clij"
id: "clij"
url: "https://sites.imagej.net/clij/"
description: >-
GPU-acceleration for ImageJ.
See [https://clij.github.io/](https://clij.github.io/)
maintainers:
- "[Robert Haase](https://imagej.net/people/haesleinhuepf)"
- name: "clij2"
id: "clij2"
url: "https://sites.imagej.net/clij2/"
description: >-
GPU-acceleration for ImageJ. Please also activate "clij" if you want to use "clij2".
See [https://clij.github.io/](https://clij.github.io/)
maintainers:
- "[Robert Haase](https://imagej.net/people/haesleinhuepf)"
- name: "clijx-assistant"
id: "clijx-assistant"
url: "https://sites.imagej.net/clijx-assistant/"
description: >-
Experimental update site for the future release of clij2.
See [https://clij.github.io/assistant](https://clij.github.io/assistant)
maintainers:
- "[Robert Haase](https://imagej.net/people/haesleinhuepf)"
- name: "clijx-assistant-extensions"
id: "clijx-assistant-extensions"
url: "https://sites.imagej.net/clijx-assistant-extensions/"
description: >-
Experimental update site for the future release of clij2.
See [https://clij.github.io/assistant](https://clij.github.io/assistant)
maintainers:
- "[Robert Haase](https://imagej.net/people/haesleinhuepf)"
- name: "CMCI-EMBL"
id: "Miura"
url: "https://sites.imagej.net/Miura/"
description: >-
A plugin for loading sample images and misc functionality for CMCI ImageJ
course. See [CMCI course](https://wiki.cmci.info/mainpages/courses).
Eventually more plugins will be added.
maintainers:
- "[Kota Miura](https://imagej.net/people/miura)"
- name: "CMP-BIA tools"
id: "CMP-BIA"
url: "https://sites.imagej.net/CMP-BIA/"
description: >-
The development version of
[CMP-BIA tools](https://imagej.net/plugins/cmp-bia-tools).
maintainers:
- "[Jiri Borovec](http://cmp.felk.cvut.cz/~borovji3/)"
- name: "CMTK Registration"
id: "Jefferis"
url: "https://sites.imagej.net/Jefferis/"
description: >-
CMTK Registration GUI.
maintainers:
- "[Gregory Jefferis](https://imagej.net/people/jefferis)"
- name: "Colocalization by Cross Correlation"
id: "Amccall"
url: "https://sites.imagej.net/Amccall/"
description: >-
A co-localization plugin that attempts to find non-random spatial correlations
between two images and provide an estimate of their distance and standard deviation.
Conceptually similar to Van Steensel's CCF. For more details see our
[wiki page](https://imagej.net/plugins/colocalization-by-cross-correlation).
maintainers:
- "[Andrew McCall](https://imagej.net/people/andmccall)"
- name: "ColonyArea"
id: "ColonyArea"
url: "https://sites.imagej.net/ColonyArea/"
description: >-
A plugin that is optimized to perform standard analysis of colony formation assays conducted in 6- to 24-well dishes. The plugin processes each well individually and determines not the colony number, but the area of the well covered with cells, also taking the intensity into account.
maintainers:
- "[Turku BioImaging](https://bioimaging.fi)"
- "[Junel Solis](https://github.com/junelsolis)"
- name: "ColorBlindLUTs"
id: "ColorBlindLUTs"
url: "https://sites.imagej.net/ColorBlindLUTs/"
description: >-
[ColorBlindLUTs](https://github.com/bruvellu/color-blind-luts) is a set
of color blind friendly lookup tables for Fiji/ImageJ.
maintainers:
- "[Bruno C. Vellutini](https://brunovellutini.com/)"
- name: "Colour Deconvolution2"
id: "ColourDeconvolution2"
url: "https://sites.imagej.net/ColourDeconvolution2/"
description: >-
Update site for
[Colour Deconvolution2](https://blog.bham.ac.uk/intellimic/g-landini-software/colour-deconvolution-2/)
maintainers:
- "[Gabriel Landini](https://imagej.net/people/landinig)"
- name: "Cookbook"
id: "Cookbook"
url: "https://sites.imagej.net/Cookbook/"
description: >-
Plugins from the [Cookbook](https://imagej.net/imaging).
maintainers:
- "[Cookbook Team](https://imagej.net/imaging#Credits)"
- name: "CSBDeep"
id: "CSBDeep"
url: "https://sites.imagej.net/CSBDeep/"
description: >-
Plugins for executing pretrained CARE networks.
maintainers:
- "[Deborah Schmidt](https://imagej.net/people/frauzufall)"
- name: "CSIM Laboratory"
id: "Acsenrafilho"
url: "https://sites.imagej.net/Acsenrafilho/"
description: >-
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](https://imagej.net/plugins/anomalous-diffusion-filters),
[Noise Generator](https://imagej.net/plugins/noise-generator),
[MRI Perfusion](https://imagej.net/plugins/mri-perfusion) and the
[Sample Entropy for Images](https://imagej.net/plugins/sampen2d).
Please, see the [CSIM group web page](https://imagej.net/plugins/csim-lab)
to find out how the methods works and more information about us.
maintainers:
- "[Antonio Carlos da S. Senra Filho](https://imagej.net/people/acsenrafilho)"
- name: "CWNS dense nuclei segmenter"
id: "CWNS"
url: "https://sites.imagej.net/CWNS/"
description: >-
The Fiji implementation of the CWNS dense nuclei segmenter, presented in
["Object Segmentation and Ground Truth in 3D Embryonic Imaging"](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0150853),
by B. Rajasekaran et al., Plos ONE, 2016.
maintainers:
- "[Jean-Yves Tinevez](https://imagej.net/people/tinevez)"
- name: "DeepClas4Bio-plugins"
id: "Adines"
url: "https://sites.imagej.net/Adines/"
description: >-
Collection of plugins that use
[DeepClas4Bio API](https://github.com/adines/DeepClas4Bio) --
an API that facilitates the interoperability of bioimaging tools with
deep learning frameworks.
maintainers:
- "[Adrián Inés](mailto:adines@unirioja.es)"
- name: "DeepImageJ"
id: "DeepImageJ"
url: "https://sites.imagej.net/DeepImageJ/"
description: >-
Bioimage processing using (pre-)trained deep learning models from TensorFlow
or PyTorch. The collection of deepImageJ plugins enables the interaction
with the BioImage Model Zoo. Further details are available in the
[deepImageJ web page](https://deepimagej.github.io/deepimagej/).
maintainers:
- "[Estibaliz Gómez de Mariscal](https://github.com/esgomezm)"
- "[Daniel Sage](mailto:daniel.sage@epfl.ch)"
- "[Arrate Muñoz-Barrutia](mailto:mamunozb@ing.uc3m.es)"
- name: "Dendrite Dynamics Tracker"
id: "DendriteDynamicsTracker"
url: "https://sites.imagej.net/DendriteDynamicsTracker/"
description: >-
Dendrite-Dynamics-Tracker is a plugin based on [TrackMate](https://imagej.net/plugins/trackmate/)
and [AnalyzeSkeleton](https://imagej.net/plugins/analyze-skeleton/index) that can measure
the dynamics of dendrites by tracking their tip over time.
maintainers:
- "[Jean-Yves Tinevez](https://imagej.net/people/tinevez)"
- name: "DHM Utilities"
id: "Sudgy"
url: "https://sites.imagej.net/Sudgy/"
description: >-
Collection of plugins for use in digital holographic microscopy, such as
hologram reconstruction, numerical propagation, and phase unwrapping.
maintainers:
- "[David Cohoe](mailto:dcohoe@pdx.edu)"
- name: "DiameterJ"
id: "DiameterJ"
url: "https://sites.imagej.net/DiameterJ/"
description: >-
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](coming) for more information
and the publication describing how DiameterJ works and its limitations.
maintainers:
- "[Nathan Hotaling](https://imagej.net/people/NHotaling)"
- name: "DiversePathsJ"
id: "Vuhlmann"
url: "https://sites.imagej.net/Vuhlmann/"
description: >-
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](http://bigwww.epfl.ch/algorithms/diversepathsj/) for more
information.
maintainers:
- "[Virginie Uhlmann](https://imagej.net/people/vuhlmann)"
- name: "DNA FISH"
id: "DNA-FISH"
url: "https://sites.imagej.net/DNA-FISH/"
description: >-
Plugin for semi-automated [analysis of DNA FISH spots](https://github.com/embl-cba/DNA-FISH#analyse-fish-spots---fiji-plugin).
maintainers:
- "Christian Tischer"
- name: "ElastixWrapper"
id: "ElastixWrapper"
url: "https://sites.imagej.net/ElastixWrapper/"
description: >-
Image registration using [elastix](http://elastix.isi.uu.nl/)
maintainers:
- "[Christian Tischer](mailto:christian.tischer@embl.de)"
- name: "ELEPHANT"
id: "KoSugawara"
url: "https://sites.imagej.net/ELEPHANT/"
description: >-
[ELEPHANT](https://elephant-track.github.io) is a platform for 3D cell tracking,
based on incremental and interactive deep learning. ELEPHANT is implemented as a
plugin for [Mastodon](https://github.com/mastodon-sc/mastodon). Please not that
users need to set up the ELEPHANT server in addition to this plugin.
The detailed instructions can be found [here](https://elephant-track.github.io).
maintainers:
- "[Ko Sugawara](https://github.com/ksugar)"
- name: "EM Tool"
id: "IMBalENce"
url: "https://sites.imagej.net/IMBalENce/"
description: >-
[EM tool](https://imagej.net/plugins/imbalence) is a suite of simple tools for electron microscopist
maintainers:
- "[Zhou Xu](mailto:zhou.xu@monash.edu)"
- name: "EpiGraph"
id: "Pedgomgal1"
url: "https://sites.imagej.net/Pedgomgal1/"
description: >-
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.
maintainers:
- "[Pedro J. Gómez Gálvez](mailto:pgomez-ibis@us.es)"
- "[Pablo Vicente Munuera](https://github.com/Pablo1990)"
- name: "EVAnalyzer"
id: "evanalyzer"
url: "https://sites.imagej.net/evanalyzer/"
description: >-
[EVAnalyzer](https://github.com/joda01/evanalyzer)
EVAnalyzer is a Fiji ImageJ plugin designed for analyzing microscope pictures of EVs.
This plugin can be used for: Counting the number of EVs; Calculating the colocalization
of evs and other particles; Detect biological cells and counting EVs updatekn from cells;
Analysis of a large amount of images automatically;Generating XLSX (Excel) reports with
automatic statistics generation.
maintainers:
- "[Joachim Danmayr](mailto:joachim.danmayr@mailbox.org)"
- name: "Excel Functions"
id: "ExcelMacroExtensions"
url: "https://sites.imagej.net/ExcelMacroExtensions/"
description: >-
The Excel Functions and Excel Macro Extensions are meant to build an interface beween
ImageJ and Excel (.xlsx). It serves as a library which can be used via the ImageJ macro language,
Java and Jython to facilitate data transfer
[Excel Macro Extensions](https://gitlab.com/biovoxxel/excel-table-macro-extensions).
maintainers:
- "[Jan Brocher](https://imagej.net/people/biovoxxel)"
- name: "EZFig"
id: "EZF"
url: "https://sites.imagej.net/EZF/"
description: >-
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.
maintainers:
- "[Benoit Aigouy](mailto:scientifig@gmail.com)"
- name: "FAST"
id: "FAST"
url: "https://sites.imagej.net/FAST/"
description: >-
Fluorescence image AnalysiS Tool automates tasks to process a set of
single-channel fluorescence images.
maintainers:
- "[C.TURIÈS](https://imagej.net/people/cyrilturies)"
- name: "Fast4DReg"
id: "Fast4DReg"
url: "https://sites.imagej.net/Fast4DReg/"
description: >-
[Fast4DReg](https://imagej.net/plugins/fast4dreg) is a Fiji macro for
drift correction of 3D videos or channel alignment in 3D multichannel
image stacks. Drift or misalignment can be corrected in all x-, y- and/or
z-directions.
maintainers:
- "[Joanna Pylvänäinen](https://imagej.net/people/jpylvanainen)"
- name: "FFMPEG"
id: "FFMPEG"
url: "https://fiji.sc/~schindelin/ffmpeg-plugins/"
description: >-
Fiji plugins which allow reading and writing to
[FFmpeg](https://www.ffmpeg.org/)-supported formats via native bindings.
maintainers:
- "[Curtis Rueden](https://imagej.net/people/ctrueden)"
- name: "FibrilJ"
id: "FibrilJ"
url: "https://sites.imagej.net/FibrilJ/"
description: >-
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.
maintainers:
- "Petr Sokolov"
- name: "Filopodyan"
id: "Rb7777"
url: "https://sites.imagej.net/Rb7777/"
description: >-
Filopodia dynamics analysis. See
[GitHub](https://github.com/gurdon-institute/Filopodyan) for the user
guide, source code and R scripts for downstream analysis.
maintainers:
- "Richard Butler"
- "Vasja Urbančič"
- name: "FiloQuant"
id: "FiloQuant"
url: "https://sites.imagej.net/FiloQuant/"
description: >-
[FiloQuant](https://imagej.net/people/guijacquemet) 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.
maintainers:
- "Guillaume Jacquemet"
- "Alexandre Carisey"
- name: "FiubaMate"
id: "FiubaMate"
url: "https://sites.imagej.net/FiubaMate/"
description: >-
[FiubaMate](https://github.com/franco-giordano/fiuba-taller3-final) is a detection and tracking system for bodies in channels, built for 'Medios Porosos' lab, FIUBA.
maintainers:
- "[Julian Ferres](mailto:jferres@fi.uba.ar)"
- "[Franco Giordano](mailto:fgiordano@fi.uba.ar)"
- name: "FLIMJ"
id: "FLIMJ"
url: "https://sites.imagej.net/FLIMJ/"
description: >-
[FLIMJ](https://imagej.net/plugins/flimj) is a plugin for analyzing FLIM
data in ImageJ, using the [FLIMLib](https://flimlib.github.io/)
library.
maintainers:
- "Dasong Gao"
- "Curtis Rueden"
- name: "FlyReg"
id: "FlyReg"
url: "https://sites.imagej.net/FlyReg/"
description: >-
[FlyReg](https://github.com/tischi/fly-reg) is a plugin for the 3D registration of fly (drosophila) embryos.
maintainers:
- "Christian Tischer"
- name: "FPBioimage"
id: "Fpbioimage"
url: "https://sites.imagej.net/Fpbioimage/"
description: >-
A plugin to prepare and upload data for
[Fpbioimage](https://imagej.net/plugins/fpbioimage).
maintainers:
- "[FPBioimage](https://imagej.net/User:Fpbioimage)"
- name: "FracLac Suite"
id: "Akarperien"
url: "https://sites.imagej.net/Akarperien/"
description: >-
Fractal Analysis and Modelling tools for neuroscience and other
disciplines. __Analysis:__ <abbr title=\"Box Counting Fractal
Dimension\">D<sub>B</sub></abbr>, <abbr title=\"Fixed Grid and Sliding
Box\">lacunarity</abbr>, multifractal spectra, <abbr title=\"Local
Connected Fractal Dimension\">D<sub>LC</sub></abbr>, <abbr title=\"Mass
vs Distance Dimension\">D<sub>MvD</sub></abbr>, subscanning, and
graphical wave analysis for binary and gray scale images, with inline and
[online](https://imagej.net/plugins/fraclac/FLHelp/Introduction.htm)
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](https://imagej.net/plugins/fraclac/FLHelp/FLCitations.htm).
maintainers:
- "[A. Karperien](https://imagej.net/User:Akarperien)"
- name: "FreQ"
id: "FreQ"
url: "https://sites.imagej.net/FreQ/"
description: >-
An ImageJ plugin to analyze pixel intensity oscillations in time-lapse 2D images.
For example, this allows to characterize the ciliary beat of multi-ciliated cells
in time-lapse images acquired with a bright-field or phase-contrast microscope.
For more details, a link to the corresponding publication, and information on how
to cite the plugin visit the FreQ github pages at https://github.com/hansenjn/FreQ
maintainers:
- "[Jan Hansen](https://github.com/hansenjn/)"
- name: "FRET Imaging"
id: "FRET-Imaging"
url: "https://sites.imagej.net/FRET-Imaging/"
description: >-
ImageJ plugins for 3-cube FRET ([RiFRET](https://imagej.net/plugins/rifret)) and
acceptor photobleaching FRET ([AccPbFRET](https://imagej.net/plugins/accpbfret))
from [CellMoTher](https://github.com/CellMoTher).
maintainers:
- "[Cameron Lloyd](https://imagej.net/people/camlloyd)"
- name: "FunImageJ"
id: "FunImageJ"
url: "https://sites.imagej.net/FunImageJ/"
description: >-
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](https://github.com/kephale/fun.imagej).
maintainers:
- "[Kyle Harrington](https://imagej.net/people/kephale)"
- name: "Fuzzy logic and artificial neural networks image processing toolbox for ImageJ"
id: "Astartes91"
url: "https://sites.imagej.net/Astartes91/"
description: >-
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).
maintainers:
- "[Vladimir Nizamutdinov](mailto:astartes91@gmail.com)"
- name: "Fuzzy Set"
id: "Rerger"
url: "https://sites.imagej.net/Rerger/"
description: >-
[Fuzzy Set](https://imagej.net/plugins/fuzzy-set) is an ImageJ plugin, to
transform the intensity of the image using Fuzzy Sets.
maintainers:
- "[Robert Erger](mailto:rerger@leomail.tamuc.edu)"
- name: "GDSC"
id: "GDSC"
url: "https://sites.imagej.net/GDSC/"
description: >-
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](http://www.sussex.ac.uk/gdsc/intranet/microscopy/UserSupport/AnalysisProtocol/imagej/gdsc_plugins/)
for details.
maintainers:
- "[Alex Herbert](mailto:a.herbert@sussex.ac.uk)"
- name: "GDSC-SMLM2"
id: "GDSC-SMLM2"
url: "https://sites.imagej.net/GDSC-SMLM2/"
description: >-
Tools for Single Molecule Light Microscopy (SMLM) including PALM,
STORM and other single molecule microscopy methods.
See the latest documentation on [ReadTheDocs](https://gdsc-smlm.readthedocs.io/).
maintainers:
- "[Alex Herbert](mailto:a.herbert@sussex.ac.uk)"
- name: "Gut Analysis Toolbox"
id: "GAT"
url: "https://sites.imagej.net/GutAnalysisToolbox/"
description: >-
[Gut Analysis Toolbox](https://imagej.net/plugins/gut-analysis-toolbox) enables semi-automated analysis of
the neuronal and glial distribution within the gut wall in 2D. It uses a combination of FIJI macros, StarDist
and deepImageJ for automated segmentation. The primary focus is on characterising the enteric nervous system.
The aim is to expand the analysis to other celltypes within the gut and enable 3D analysis.
maintainers:
- "[Pradeep Rajasekhar](https://imagej.net/people/pr4deepr)"
- name: "Hadim"
id: "Hadim"
url: "https://sites.imagej.net/Hadim/"
description: >-
Contains the ij2-python-lib package.
maintainers:
- "[Hadrien Mary](https://imagej.net/people/hadim)"
- name: "HDF5"
id: "Ronneber"
url: "https://sites.imagej.net/Ronneber/"
description: >-
The HDF5 plugin allows to load and save data in HDF5 format.
For details see
[HDF5 plugin](https://lmb.informatik.uni-freiburg.de/resources/opensource/imagej_plugins/hdf5.html).
maintainers:
- "[Olaf Ronneberger](mailto:ronneber@informatik.uni-freiburg.de)"
- name: "HistoJ"
id: "Pathomation"
url: "https://sites.imagej.net/Pathomation/"
description: >-
Plugin to interface with
[Pathomation's digital slide viewer](https://www.pathomation.com/)
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).
maintainers: