|ImageJ Update Sites
||Base update site for ImageJ2. No need to add this to your list of update sites; it is already included.
||Base update site for Fiji and core Fiji plugins. If you downloaded Fiji directly, it is already included.
||Restores old Fiji plugins which never made the transition to Maven, as well as obsolete libraries no longer used by current Fiji installations.
||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.
||ImageJ2 and Fiji developers
||A collection of plugins highlighting the latest features of ImageJ. As seen in Wayne Rasband's opening talk at the 2015 conference!
|3D ImageJ Suite
||A suite of plugins providing enhanced 3D capabilities in ImageJ.
||3Dscript is a plugin animating 3D/4D microscopy data using a natural-language-based syntax.
||ActogramJ is a plugin for analyzing actograms.
||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/
|AIC Janelia - Course
||A collection of plugins and macros for students of the Advanced Imaging Center (AIC) Fiji Course.
||The Aquatic Mammal Photogrammetry Tool (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.
||A plugin to quantify angiogenic sprout morphology.
||The AngioTool software converted to a Fiji plugin.
||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.
||Accelerated pixel and object classifiers (APOC). See clijx-accelerated-pixel-and-object-classification.
||An implementation of the AxoNet tool which can be used to count axons in light micrographs of optic nerves.
||BACteria in Mother Machine ANalyzer: a plugin for high-throughput analysis of multichannel mother machine data. See Sources: https://github.com/jeanollion/bacmman and Wiki: https://github.com/jeanollion/bacmman/wiki
||Enables deep learning for BACMMAN (CPU). Currently using Tensorflow 2x
||Enables deep learning for BACMMAN (GPU). Currently using Tensorflow 2x
||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.
||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.
||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.
||Batch Tools provides a toolbar to support batch image processing and analysis, including batch merge channels, composite conversion, Z-projection, channel B&C and colour adjustment, file export, and cell count, gray value & area.
||Neville S Ng
||BD-CellView enables inspection and batch processing of images generated with the BD-CellView imaging flow cytometer.
||BigDataProcessor2 is an Imglib2 and BigDataViewer based tool for inspection and processing of big (TB-sized) image data.
||ImageJ plugins from EPFL's Biomedical Imaging Group (BIG). NOT OPEN SOURCE.
||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
||Demo of BDV volume rendering. See this forum post for getting started.
||A version of Bio-Formats with the latest bugfixes from the development branch. The last SNAPSHOTS are automatically uploaded daily.
||OME development team
||Plugins for 3D image preprocessing and detection of fibres in 3D image.
||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).
||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.
|BioVoxxel 3D Box
||Image processing and analysis tools for 2D and 3D images in one place. Based on GPU accelerated computing via CLIJ2. BioVoxxel 3D box BioVoxxel web site.
|Blind Analysis Tools
||Tools to facilitate blind i.e., unbiased analysis of (image) data. For more information visit the documentation page.
||Astha Jaiswal, Holger Lorenz
||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
||BTrack uses the skeletonization implementation of 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.
||Plugins from the Crick Advanced Light Microscopy Facility at The Francis Crick Institute.
||Plugins from the Computing and Advanced Microscopy Development Unit at the University of Warwick.
||Erick Martins Ratamero
||Context Aware Trainable Segmentation CATS
||Implementation of measures and front-end plugins used in and related to the Cell Tracking Challenge.
||Fiji plugins developed in the Cellular Imaging - Lehmann Group of the FMP-Berlin.
||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
||An image processing toolbox focused on scripting.
||A Fiji plugin for the automated detection and quantification of circular structures in images.
||GPU-acceleration for ImageJ. See https://clij.github.io/
||GPU-acceleration for ImageJ. Please also activate "clij" if you want to use "clij2". See https://clij.github.io/
||Experimental update site for the future release of clij2. See https://clij.github.io/assistant
||Experimental update site for the future release of clij2. See https://clij.github.io/assistant
||ClearVolume is a fast 3D viewer, for more information see also the ClearVolume wiki.
||A plugin for loading sample images and misc functionality for CMCI ImageJ course. See CMCI course. Eventually more plugins will be added.
||The development version of CMP-BIA tools.
||CMTK Registration GUI.
|Colocalization by Cross Correlation
||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.
||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.
||Turku BioImaging, Junel Solis
||ColorBlindLUTs is a set of color blind friendly lookup tables for Fiji/ImageJ.
||Bruno C. Vellutini
||Update site for Colour Deconvolution2
||Plugins from the Cookbook.
||Plugins for executing pretrained CARE networks.
||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
||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.
||Collection of plugins that use DeepClas4Bio API -- an API that facilitates the interoperability of bioimaging tools with deep learning frameworks.
||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.
||Estibaliz Gómez de Mariscal, Daniel Sage, Arrate Muñoz-Barrutia
||Collection of plugins for use in digital holographic microscopy, such as hologram reconstruction, numerical propagation, and phase unwrapping.
||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.
||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.
||Plugin for semi-automated analysis of DNA FISH spots.
||ELEPHANT is a platform for 3D cell tracking, based on incremental and interactive deep learning. ELEPHANT is implemented as a plugin for Mastodon. Please not that users need to set up the ELEPHANT server in addition to this plugin. The detailed instructions can be found here.
||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
||Image registration using elastix
||EM tool is a suite of simple tools for electron microscopist
||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.
||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.
||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.
||Fluorescence image AnalysiS Tool automates tasks to process a set of single-channel fluorescence images.
||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.
||Fiji plugins which allow reading and writing to FFmpeg-supported formats via native bindings.
||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.
||Filopodia dynamics analysis. See GitHub for the user guide, source code and R scripts for downstream analysis.
||Richard Butler, Vasja Urbančič
||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
||FiubaMate is a detection and tracking system for bodies in channels, built for 'Medios Porosos' lab, FIUBA.
||Julian Ferres, Franco Giordano
||FLIMJ is a plugin for analyzing FLIM data in ImageJ, using the FLIMLib library.
||Dasong Gao, Curtis Rueden
||FlyReg is a plugin for the 3D registration of fly (drosophila) embryos.
||A plugin to prepare and upload data for Fpbioimage.
||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.
||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
||ImageJ plugins for 3-cube FRET (RiFRET) and acceptor photobleaching FRET (AccPbFRET) from CellMoTher.
||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.
|Fuzzy logic and artificial neural networks image processing toolbox for ImageJ
||Toolbox includes fuzzy edge detection plugin, fuzzy contrast enhancement plugin and ann edge detection plugin. Source code on GitHub.
||Fuzzy Set is an ImageJ plugin, to transform the intensity of the image using Fuzzy Sets.
|Gut Analysis Toolbox
||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.
||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.
||Tools for Single Molecule Light Microscopy (SMLM) including PALM, STORM and other single molecule microscopy methods. See the latest documentation on ReadTheDocs.
||Contains the ij2-python-lib package.
||The HDF5 plugin allows to load and save data in HDF5 format. For details see HDF5 plugin.
||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).
||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
||Plugins using parallelization and HPC.
||Plugins using HPC Datastore.
||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)
||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).
||Collection of plugins created using the IJ-OpenCV library -- a library that allows the connection of ImageJ and OpenCV.
||Plugins from IJ-Plugins bundle project, include color calibration and conversions, segmentation algorithms, various anisotropic diffucion filters, raw image processing, additional 2D and 3D file formats support, and more.
||ImageJ Macro Markdown scripting language interpreter to create notebook-like pages using ImageJ Macro and Markdown.
||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
||Provides interoperability between Fiji and ilastik workflows (pixel/object classification, tracking) as well as HDF5 file export/import.
||Add math equations to an image using Latex.
||Adds ITK integration including conversion between ITK and ImageJ images. See the ITK page for more information.
||Adds support for MATLAB scripting and converting between MATLAB arrays and ImageJ components. See the scripting tutorial for more information.
||Base update site for all ImageScience related ImageJ plugins.
||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.
|IMCF Uni Basel
||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).
||ImgLib2-Imaris-Bridge provides sharing arbitrarily large images between Imaris and Fiji/ImageJ2 without duplicating memory requirements. Imaris datasets are represented as cached images in ImgLib2, lazily loaded via Imaris XT, and exposed through an ImageJ2 service.
||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
||Update site for scale space filters and other INCF projects from GSOC 2014, 2015, 2016.
|Intensity Profile tools
||Provides a macro-toolset for interactive inspection of images using intensity profile plots. Including an interactive mouse tool (line profiles) and an action tool for the generation of horizontal/vertical average intensity panels.
||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
||Macro for processing brightfield fundus images of the mouse eye and plugin for averaging replicate OCT volume scans.
||A collection of lookup tables, including some designed for high dynamic range data.
||JIPipe is a visual programming language based on ImageJ.
||Ruman Gerst, Zoltán Cseresnyés, Marc Thilo Figge
|JOGL Canvas Deep Color / 3D
||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.
||A Fiji plugin for Curvature Analysis.
||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.
||An advanced plugin for labeling and automatic segmentaion of Images.
||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.
||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.
||Revisited active contour method for 3D segmentation. Documentation: LimeSeg.
||Nicolas Chiaruttini, Sarah Machado
||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.
||Generate kymographs with a live preview.
||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
||Plugins developed for work at LMCF IMG, including Wavelet Denoise.
|Local Z Projector
||Local Z Projector is an ImageJ2 plugin to perform local-Z projection of a 3D stack, possibly over time, possibly very large.
||The LOCI update site for their Fiji plugins, including VisBio Fiji plugins and other miscellany.
||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.
||Plugin performs blind spectral unmixing on multichannel images, particularly for fluorescence microscopy. For more information see documentation. Source code here.
||LysoQuant is a deep learning approach for the automatic segmentation and classification of fluorescence images capturing cargo delivery within endolysosomes. For more information see documentation. Source code here.
||Mars, a platform for storage, exploration, and processing of image-derived properties of biomolecules together with enhanced OME metadata.
||MaMuT, a plugin for the annotation of massive, multi-view data.
||A Fiji plugin for Mask RCNN semantic segmentation.
|Masks from ROIs
||Add the command Mask(s) from Roi(s) to Edit > Selection. Generate mask images (0/255) from Rois in the RoiManager. Compatible with image-stacks too. Ideal for the generation of ground-truth segmentation masks.
||Mastodon is a software for automatic, semi-automatic and manual cell tracking in very large images. It is meant to be an interactive tool able to harness a large amount of annotations. You can see it as the successor of MaMuT and TrackMate on steroids.
||Tobias Pietzsch, Jean-Yves Tinevez
||The MSOT cluster analysis toolkit Mcat is a software for objective and quantitative analysis of multispectral optoacoustic tomography (MSOT) image data. It is based on a signal-oriented analysis approach, i.e. the entire sample is analysed regarding the signal kinetics of the molecule of interest and pixel-wise kinetic clustering is performed to extract quantitative information about the pharmacokinetics of the investigated molecule and its biodistribution in the sample.
||Research Group Applied Systems Biology, HKI, Jena
|MiC mask comparator
||MiC is a plugin to compare segmentation mask to a reference one. the comparison is available at pixel or object's level. It computes the number of true positives, false positives and false negatives and provides metrics for quantitative estimation of segmentation quality. It displays several result tables containing all information, plots and superposition of masks for visual inspection. The plugins works on stacks (only 2D comparison) and is macro recordable.
||[MIC-MAQ] (https://github.com/MultimodalImagingCenter/MIC-MAQ) is a plugin for automatic segmentation of nuclei and/or cells for quantifications in other channels including foci detection. MIC-MAQ automatically segments cells and/or nuclei on 2D microscopy images using thresholding or deep-learning approaches. It takes Z-stack but works only on 2D projection. It provides intensity based and/or morphological measurements in nuclei and/or cells in multi channels experiment. The plugin propose the foci/spots detection inside nuclei/cells. the plugins works on all images present in working directory (any image format that can be read by bioformat).
||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.
||Microglia-Morphometry is a tool for the semi-automated segmentation, tracking and morphometric analysis of 2D microglia time-lapse images.
|Mighty Data, Inc.
||Dendritic Spine Counter creates a modular wizard dialog to assist with the task of counting dendritic spines in microscope images using open-source statistical image processing techniques.
||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.
||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
||Multimodal Big Image Data Exploration and Sharing MoBIE
||MIA is a plugin which provides a modular framework for assembling image and object analysis workflows. Detected objects can be transformed, filtered, measured and related. Analysis workflows are batch-enabled by default, allowing easy processing of high-content datasets. For more information please see the documentation at mianalysis.github.io or on imagej.net.
||Script for Evaluation of Molographic Data
||Mother Machine Analyser
||The update site for the Mathematical Morphology Collection of plugins and macros.
||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
||An set of ImageJ plugins to quantify dynamics, morphology, and fluorescence of microglial (or other) cells in 2D and 3D (also time-lapse) images. For more details, a link to the corresponding publication, and information on how to cite the plugins visit the MotiQ github pages at https://github.com/hansenjn/MotiQ
||MPIBPC stands for Max Planck Institute for Biophysical Chemistry. We provide the Imspector OBF reader for the Bio-Formats plugin.
||MPIBPC, NanoBiophotonics, Bjoern Thiel
||MembraneStained EpithelialCellSegmentation 2D, for more information see also the update site page.
||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.
||Multifrac is a tool for multifractal and scaling analysis of 2D and 3D stack images, including lacunarity, configuration entropy, characteristic lenght and multifractal spectrum of gray and black and white images. This is particularly desginated and tested for addressing analysis on soil pore structre.
||Ivan G Torre
||MultiStackReg does registration of a stack based on the registration results of another stack. It uses Turboreg as the backend.
||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.
||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 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 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 is a high-throughput ImageJ plugin for single-particle analysis in fluorescence microscopy, particularly super-resolution microscopy.
||The Henriques Team, UCL, UK
||Plugins and scripts developed in the context of NEUBIAS.
||Image Processing Tools for Neuroanatomy and Tree-like structures (list).
||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
||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
||An easy-to-use macro for measuring and analyzing SNR (signal-to-noise ratio) of light microscopes. See the NoiSee page for more details.
||Conventional nuclear medicine applications and additional packages for the PET/CT Viewer.
||Salim Kanoun, Toulouse, France
||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
||The OMERO update site for bidirectional integration between ImageJ and OMERO 5.0.x.
||The OMERO update site for bidirectional integration between ImageJ and OMERO 5.1.x.
||The OMERO update site for bidirectional integration between ImageJ and OMERO 5.2.x.
||The OMERO update site for bidirectional integration between ImageJ and OMERO 5.4.x.
||The OMERO update site for bidirectional integration between ImageJ and OMERO 5.5.x and 5.6.x.
||Mark Hiner, Curtis Rueden
||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
||The drivers and software to operate an OpenSPIM (Open Access selective plane light sheet microscope).
||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
||Description: Some basic tools developed for users of the Microscopy Core in the department of Oncology at the University of Oxford.
||A plugin to derive number based size distributions from TEM images.
||A plugin for capillary length measurement through the pendent drop method.
||Update site for the Pet-Ct-Viewer and other Nuclear Medicine software in use at Beth Israel Hospital, see Help
||Update site for PHANTAST (phase contrast microscopy segmentation toolbox), a collection of tools for the processing of phase contrast microscopy images
||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.
||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
||The PillarTracker plug-in enables user to track the pillars and visualize the tracks and deflections.
||XU Xiaochun, Felix Martin Margadant
||PixFRET - an ImageJ plug-in for FRET calculation which can accommodate variations in spectral bleed-throughs
||PlateViewer - an ImageJ plug-in for visualisation of high-throughput microscopy multi-well plate image data.
||Tools for Stratec pQCT bone and soft tissue images.
||The EPFL - PTBIOP (BioImaging & Optics Platform) Update Site, with Fiji plugins, macros and ActionBars. We recommend that you also activate the IBMP-CNRS, ImageScience and 3D ImageJ Suite update sites. Update site contents at https://wiki-biop.epfl.ch/en/ipa/fiji/update-site#ptbiop-update-site-contents
||Plugins to describe images or rois with qualitative keywords (ground-truth classes, categories...) Selected keywords are reported in a result table and stored as roi properties.
||ImageJ macros for making figures, blind analysis and more. Maintenance and issues here.
||ImageJ PlugIn for making publication quality figures from multichannel images. User friendly, fast, efficient and versatile. Automates dozens of steps. Comparable to ScientiFig, FigureJ and omero.figure. See youtube tutorial here. Also see publication for more details.
||QuimP is software for tracking cellular shape changes and dynamic distributions of fluorescent reporters at the cell membrane.
||Piotr Baniukiewicz, Till Bretschneider
||A plugin for radial symmetry localization on smFISH (and other) images.
||RadialIntensityProfile is a simple macro to analyse the radial distribution of a fluorescent signal of interest in relation to a cell's nucleus.
||This macro measures absorbance values from an image of a multi-well plate. ReadPlate 3.0 version incorporates the capability of reading multi-well plates of 6 (3x2), 12 (4x3), 24 (6x4), 48 (8x6) and 96 (12x8) wells. An new user-friendly interface facilitates image analysis. This version allows new user-defined features to optimize blank correction. Multiple readings of the same plate has also considerably been facilitated, appending the full parameter file to the results and log file.
||José María Delfino (firstname.lastname@example.org)
||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.
|ROI 1-click Tools
||This update sites provides ROI tools similar to the built-in ImageJ ROI, but with additional functionalities. A single cick generates a predefined ROI, adds it to the RoiManager, run "Measure" for the outlined region, and go to the next slice for stacks. These options can be modified by double-clicking the ROI icon.
||This update sites provides a single helper plugin to set the category names associated to the ROI-group integer indexes via an intuitive table. The plugin also allows importing/exporting the category names mappings from/to a text file, for exchange between ImageJ/Fiji installations.
||Plugins for plane-wise GPU-accelerated multi-view deconvolution of SPIM data.
||FFT (spectra + filtering); ROI class management; Image Linker; Tight Montage; Ca2+ imaging tools; etc.
||Sean Parsons at scepticalphysiologist.com
|SCF MPI CBG
||Common image processing tools from the Scientific Computing Facility at MPI CBG Dresden
||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.
||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'.
|Scijava Jupyter Kernel
||A Java kernel for Jupyter. See source on GitHub.
||sciview 3D/VR/AR visualization package for ImageJ. See the documentation here and source on GitHub.
||Kyle Harrington, Ulrik Günther
||ImageJ-server update site. See source on GitHub.
a package of ImageJ tools for assessing the quality and reliability of
Structured Illumination Microscopy (SIM) data.
||Tools developed by the Keller Lab at the Janelia Research Campus, most notably the KLB file format.
||Provides the plugins LinearDistance and PointAnalysis
||This Bio-Formats plugin enables the import of SlideBook SLD files.
||Slide Set: Reproducible image analysis and batch processing.
||SLIM Curve: a plugin for combined spectral-lifetime image analysis.
||Plugins and macros from the School of Life Sciences Imaging (SLIM) at the University of Nottingham
||ImageJ plugins to analyze the flagellar beat and the swimming path of sperm from time-lapse 2D bright-field, dark-field, phase contrast, or fluorescence microscopy images. SpermQ can analyze images from head-tethered or free swimming sperm of different species. SpermQ can also analyze the beat of motile cilia if the analyzed cilium is clearly distinguishable from / not close to neighboring cilia. For more details, a link to the corresponding publication, and information on how to cite the plugins, visit the SpermQ github page https://github.com/hansenjn/SpermQ/
||3D segmentation and morphometry of mitotic spindles
||Object Detection with Star-convex Shapes
||Uwe Schmidt, Martin Weigert
|Stereoscopic 3D Projection
||Allows users to create 3-D anaglyph and Google Cardboard compatible projections from image stacks.
||Joe Napoli, Visikol, Inc.
||The Stowers ImageJ Plugins.
||Tools developed and used in the labs of Dr. Stuart and Dr. Necakov at Brock University.
||Tools for Analysis of Nuclear Genome Organization.
||Jean Ollion, Julien Cochennec
||Fiji-Tools-for-HCS is a collection of macros useful for high-content screening data developed by TDS members at MPI-CBG Dresden. Wiki
||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.
||TensorFlow integration for ImageJ, including a microscope image focus quality classifier and a demo Inception image classifier.
||The Timebar plugin is intended for stacks with a temporal dimension (2D+T, 3D+T, etc.). Frames in the time series will be decorated with a timestamp and, optionally, a progressing bar.
||Tissue Analyzer is a free tool to segment epithelial tissues.
||A couple of Fiji scripts to ease daily evo-devo image analysis life, from Tomancak lab.
||Vladimír Ulman, Matthias Arzt
||This update site provides TrackMate-Cellpose, a detector module for TrackMate that relies on cellpose.
||This update site provides TrackMate-ExTrack, a track analysis module for TrackMate, that is a port of the ExTrack analysis tool written in Python. ExTrack can reveal diffusion and binding kinetics in live cells and beyond. It is made to be robust against noise, notably if displacements are small and state transitions are fast.
||The TrackMate-Helper is a plugin made to run parameter sweeps on an image to track. It allows a user to configure a very large batch of tracking parameters to test with TrackMate, and will run them. The Cell-Tracking-Challenge metrics are calculated for each parameter set tested, which allows to find the best tracking configuration for a dataset with respect to a specific tracking metric. Check here for documentation.
||This update site provides TrackMate-Ilastik, a detector module for TrackMate that relies on Ilastik to segment objects in 2D or 3D.
||This update site provides TrackMate-MorphoLibJ, a detector module for TrackMate that relies on the Morphological Segmentation plugin shipped with the MorphoLibJ library.
||This update site provides TrackMate-Oneat, a track corrector module for TrackMate that relies on oneat.
||This update site provides TrackMate-StarDist, a detector module for TrackMate that relies on StarDist to segment objects in 2D.
||This update site provides TrackMate-Weka, a detector module for TrackMate that relies on the Trainable Weka Segmentation plugin to segment objects in 2D or 3D.
||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.
||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.
||Tracking in 2d.
||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.
|UCB Vision Sciences
||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.
|Vale lab plugins
||Plugins useful to the Vale lab: Saim, spot intensity analysis, spot counter.
|Vanderbilt Biophotonics Center
||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
||A set of ImageJ scripts for analysis of VerCINI (Vertical Cell Imaging by Nanostructured Immobilization) microscopy data of vertically oriented bacteria. See https://github.com/HoldenLab/VerciniAnalysisJ for documentation.
||Seamus Holden Newcastle University, UK
||VersiLab_Plugin, aiming to do real-time image acquisition and processing for Optical Endo-Microscopy (OEM), development phase, code available on GitHub.
||Plugins for using Virtual Cell with ImageJ.
||Michael Blinov, Frank Morgan, Ion Moraru
||A macro Toolset helping daily handling and visualization of multichannel images and stacks.
||Void Whizzard is a tool for analyzing void spot assay (VSA) images.
|Volumetric Tissue Exploration and Analysis
||VTEA is an interactive tool for 3D tissue cytometry built on ImageJ.
||WhisketTracking is a set of tools for tracking rodent whisker.
||WormBox is a plugin for measuring linear distances and counting structures based on landmarks.
||Bruno C. Vellutini, Fernando P. L. Marques
||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 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 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.
||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.
||ZedMate is a TrackMate-based plugin for 3D particles detection and measurement.
|Zeiss Quick Start Reader
||An alternative Bio-Formats Zeiss reader for big files. Documentation: Zeiss Quick Start Reader.
||Zellige is a software tool allowing the automated extraction of a non-prescribed number of various surfaces from a 3D image acquired by fluorescence microscopy. The program is available through a Fiji plugin.
||Céline Trébeau, Jean-Yves Tinevez
||ZFBONE is a toolset that provides tools needed for a rapid, reliable and semi-automatized morphometric analysis of zebrafish bone structures such as operculum, caudal fin and scales.
||liveim-tools Macros and plugins of the MPIBPC live-cell imaging facility to process data generated by facility microscopes (e.g. Abberior, Zeiss, Visitron).