| Nuclei Tracking (ImageJ) |
13 |
|
3D, time-series |
ImageJ |
Software |
… Type Workflow Author Bäcker, Volker Requires ImageJ Execution Platform Linux Mac Windows Implementation Type plugin Programming Language ImageJ Macros Supported image dimension 3D time-series … Page Neubias BIAFLOWS workflow of nuclei tracking with ImageJ has comparison BIAFLOWS-PROBLEM: … |
| pyimagej |
11 |
|
2D, 3D, multi-channel, time-series |
Python |
Software |
… a set of wrapper functions for integration between ImageJ and Python. It also provides a high-level entry point for invoking ImageJ server APIs. has function Image processing has topic … Download Page GitHub repo of pyimagej: Python wrapper for ImageJ Documentation Link PyImageJ’s documentation Reference … |
| DeepImageJ |
11 |
|
|
ImageJ, Tensorflow |
Software |
… Type Component Author Estibaliz Gómez de Mariscal Requires ImageJ Tensorflow Execution Platform Linux Mac Windows Implementation Type plugin is compatible with ImageJ Macro License/Openness Free and open source … use of a variety of pre-trained deep learning models in ImageJ and Fiji . The plugin bridges the gap between deep … |
| Semi-automated quantification of three stages of phagocytosi using ImageJ |
11 |
|
2D |
ImageJ |
Software |
… Type Workflow Author Nicholas Ahti Hamilton Requires ImageJ Execution Platform Linux Mac Windows Programming Language ImageJ Macros is compatible with ImageJ Supported image dimension 2D Interaction Level … The authors present an ImageJ-based, semi-automated phagocytosis workflow to rapidly … |
| Spot Detection 3D (ImageJ) |
10 |
|
3D |
ImageJ, FeatureJ Laplacian, Analyze Particles |
Software |
… Workflow Author Tosí, Sébastien Bäcker, Volker Requires ImageJ FeatureJ Laplacian Analyze Particles Execution … Windows Implementation Type plugin Programming Language ImageJ Macros Supported image dimension 3D Interaction Level … spots from a 3D image by using straightforward set of ImageJ components. It receives the Laplacian Radius and the … |
| Counting foci in ImageJ |
9.786 |
|
2D |
ImageJ |
Software |
… Type Workflow Author Peter Bankhead Requires ImageJ Execution Platform Linux Mac Windows Supported image … 18:38 Last modified 06/09/2018 - 02:41 Documentation Link ImageJ documentation: Find Maxima ImageJ user guide documentation: Find Maxima Algorithm of … Counting foci in ImageJ … |
| Adipocyte quantification ImageJ by Baecker |
9 |
|
2D |
ImageJ |
Software |
… Type Workflow Author Volker Baecker Requires ImageJ Execution Platform Linux Mac Windows Programming Language ImageJ Macros is compatible with ImageJ Supported image dimension 2D Interaction Level … Adipocyte quantification ImageJ by Baecker … |
| Creating an ImageJ plugin / command |
9 |
|
2D, 3D, multi-channel, time-series |
ImageJ, Fiji, IntelliJ IDEA, Fiji |
Software |
… Type Workflow Author Curtis Rueden Requires ImageJ Fiji IntelliJ IDEA Fiji Execution Platform Linux Mac … 10/18/2018 - 15:34 Download Page https://github.com/imagej/example-imagej-command Documentation Link Source code Online video … Creating an ImageJ plugin / command … |
| Nuclei Segmentation 3D Watershed (NucleiSegmentation3D-ImageJ) |
9 |
|
3D |
ImageJ |
Software |
… Type Workflow Author Tosí, Sébastien Requires ImageJ Execution Platform Linux Mac Windows Implementation Type plugin Programming Language ImageJ Macros is compatible with ImageJ Macro Supported image dimension 3D Interaction Level … Nuclei Segmentation 3D Watershed (NucleiSegmentation3D-ImageJ) … |
| Nuclei Segmentation 2D watershed (NucSeg3DThr-ImageJ) |
9 |
|
2D, 3D |
ImageJ |
Software |
… Type Workflow Author Tosí, Sébastien Requires ImageJ Execution Platform Linux Mac Windows Programming Language ImageJ Macros Supported image dimension 2D 3D Interaction … Neubias BIAFLOWS workflow of Nuclei Segmentation 3D with ImageJ has comparison BIAFLOWS NUCLEI-SEGMENTATION-3D … |
| ImageJFX |
9 |
|
2D, 3D, multi-channel, time-series |
Fiji |
Software |
… aims to create a new user interface for the software ImageJ in order to ease scientific image analysis. While keeping the core components of ImageJ, ImageJFX brings scientists closer to their goal by … aims to create a new user interface for the software ImageJ in order to ease scientific image analysis. While … |
| Voronoi ImageJ |
8.845 |
|
2D |
ImageJ |
Software |
… Type Component Author Wayne Rasband Michael Schmid Requires ImageJ Execution Platform Linux Mac Windows Implementation … Free and open source Description A resident function in ImageJ, located in the menu as [Process > Binary > Voronoi] . Quote from the ImageJ reference page: Splits the image by lines of points … |
| SciView |
8 |
|
3D |
ImageJ |
Software |
… Günther Ulrik orcid.org/0000-0002-1179-8228 Requires ImageJ Execution Platform Linux Mac Windows Implementation … 2-Clause "Simplified" License Description SciView is an ImageJ/FIJI plugin for 3D visualization of images and meshes. … SciView integrates ImageJ2 functionality, including ImageJ Ops and ImageJ Mesh , to provide the ability to … |
| Nuclei Segmentation 2D (ImageJ) |
8 |
|
2D |
ImageJ |
Software |
… Workflow Author Tosí, Sébastien Bäcker, Volker Requires ImageJ Execution Platform Linux Mac Windows Implementation Type plugin Programming Language ImageJ Macros Supported image dimension 2D Interaction Level … Page Neubias BIAFLOWS workflow of nuclei segmentation with ImageJ has comparison BIAFLOWS Nuclei Segmentation project … |
| Spot detection (ImageJ) |
8 |
|
2D |
ImageJ, FeatureJ Laplacian, Find Maxima, ImageJ Built-in Macro Functions |
Software |
… Workflow Author Tosí, Sébastien Bäcker, Volker Requires ImageJ FeatureJ Laplacian Find Maxima ImageJ Built-in Macro Functions Execution Platform Linux Mac … Windows Implementation Type plugin Programming Language ImageJ Macros Supported image dimension 2D Interaction Level … |
| Neuron Tracing 3D (ImageJ) |
8 |
|
3D |
ImageJ |
Software |
… Workflow Author Tosí, Sébastien Chessel, Anatole Requires ImageJ Execution Platform Linux Mac Windows Implementation Type plugin Programming Language ImageJ Macros Supported image dimension 3D Interaction Level … Page Neubias BIAFLOWS workflow of Neuron Tracing 3D with ImageJ has comparison BIAFLOWS Neuron Tracing 3D project … |
| Spot Detection Dmap (ImageJ) |
8 |
|
2D |
ImageJ, FeatureJ Laplacian, ImageJ Built-in Macro Functions |
Software |
… Type Workflow Author Tosi, Sebastien Requires ImageJ FeatureJ Laplacian ImageJ Built-in Macro Functions Implementation Type plugin Programming Language ImageJ Macros Supported image dimension 2D Interaction Level … Spot Detection Dmap (ImageJ) … |
| Filament Tracing Tubeness (ImageJ) |
8 |
|
3D |
ImageJ, Tubeness |
Software |
… Type Workflow Author Tosí, Sébastien Requires ImageJ Tubeness Execution Platform Linux Mac Windows Programming Language ImageJ Macros Supported image dimension 3D Interaction Level … Page Neubias BIAFLOWS workflow of Filament Tracing with ImageJ has comparison BIAFLOWS-PROBLEM: VESSEL-TRACING-3D … |
| JIPipe: visual batch processing for ImageJ |
8 |
|
2D, 3D, multi-channel, time-series |
Maven |
Software |
… Implementation Type library plugin is compatible with ImageJ Supported image dimension 2D 3D multi-channel … language to realize code-free workflow building for ImageJ-based image analyses. GUI, graphical user … JIPipe unifies the functionality of over 1,000 ImageJ commands into a standardized interface, represented as … |
| Angiogenesis Analyzer for ImageJ |
8 |
|
2D |
ImageJ |
Software |
… Type Workflow Author Gilles Carpentier Requires ImageJ Execution Platform Linux Mac Windows Programming Language ImageJ Macros Supported image dimension 2D Interaction Level … Source code https://imagej.nih.gov/ij/macros/toolsets/Angiogenesis%20Analyzer.txt … Source code https://imagej.nih.gov/ij/macros/toolsets/Angiogenesis%20Analyzer.txt … |
| OligoMacro Toolset |
7.993 |
|
2D, time-series |
StackReg, TurboReg |
Software |
… Execution Platform Linux Mac Windows Programming Language ImageJ Macros Supported image dimension 2D time-series … and open source Description OligoMacro Toolset , is an ImageJ macro-toolset aimed at isolating oligodendrocytes … numerical data and plotting them. It takes benefit of ImageJ built-in functions to process images and extract data, … |
| clij2 |
7.727 |
|
2D, 3D |
Fiji, Icy, MATLAB |
Software |
… Implementation Type library plugin Programming Language ImageJ Macros Java Javascript Jython Matlab is compatible with Icy Protocols ImageJ Fiji Icy MATLAB Supported image dimension 2D 3D … CLIJ2 is a GPU-accelerated image processing library for ImageJ/Fiji , Icy , Matlab and Java. It comes with hundreds … |
| ImageJ Built-in Macro Functions |
7 |
|
|
ImageJ |
Software |
… Type Collection Requires ImageJ Execution Platform Linux Mac Windows Implementation … Free and open source License BSD-2 Description A set of ImageJ Built-in Macro Functions used to perform operations on the ImageJ platform. has topic Bioimage informatics Entry Curator … |
| Spot Detection 3D Hessian (ImageJ) |
7 |
|
3D |
ImageJ, FeatureJ Laplacian, ImageJ Built-in Macro Functions, FeatureJ Hessian |
Software |
… Type Workflow Author Tosi, Sebastien Requires ImageJ FeatureJ Laplacian ImageJ Built-in Macro Functions FeatureJ Hessian Execution Platform Linux Mac Windows Programming Language ImageJ Macros Supported image dimension 3D Interaction Level … Spot Detection 3D Hessian (ImageJ) … |
| Arabidopsis Seedlings Tool |
7 |
|
2D |
ImageJ |
Software |
… Type Workflow Author Volker Baecker Requires ImageJ Execution Platform Linux Mac Windows Programming Language ImageJ Macros Supported image dimension 2D Interaction Level … detected per well. See http://dev.mri.cnrs.fr/projects/imagej-macros/wiki/Arabidopsis_Seedlings_Tool Test images can … |
| ImageJ Threshold |
7 |
|
2D |
ImageJ |
Software |
… Type Component Author ImageJ developers Requires ImageJ Execution Platform Linux Mac Windows Supported image … License/Openness Free and open source Description This ImageJ function automatically or interactively sets lower and … ImageJ developers … This ImageJ function automatically or interactively sets lower and … |
| Measure cell volume over time |
7 |
|
3D, time-series |
ImageJ, Imaris |
Software |
… Workflow Author Imaris Tutorials Christoph Moehl Requires ImageJ Imaris Programming Language ImageJ Macros Supported image dimension 3D time-series … workflow measures the growth of cells in 3D, combining an ImageJ macro for preprocessing and successive tracking using … |
| HDF5 plugin for Fiji and ImageJ |
7 |
|
2D, 3D, multi-channel, time-series |
ImageJ, Fiji |
Software |
… Type Component Author Olaf Ronneberger Requires ImageJ Fiji Execution Platform Linux Mac Windows … extremely large and complex data collections. This Fiji/ImageJ HDF5 plugin saves and loads 2D - 5D datasets with … modified 05/25/2018 - 18:34 Download Page HDF5 Plugin for ImageJ and Fiji Documentation Link … |
| ImageJ |
7 |
|
2D, 3D, multi-channel, time-series |
|
Software |
… Execution Platform Windows Mac Linux Programming Language ImageJ Macros Java Supported image dimension 2D 3D … Last modified 09/13/2017 - 12:12 Download Page http://imagej.net Documentation Link http://imagej.net/User_Guides Reference Publication Link … ImageJ … |
| RunImageJ |
7 |
|
|
CellProfiler, ImageJ |
Software |
… Type Component Requires CellProfiler ImageJ Interaction Level Automated License/Openness Free and … the RunImageJ module, CellProfiler can load images, run an ImageJ macro or plugin on them, and retrieve the results for … the RunImageJ module, CellProfiler can load images, run an ImageJ macro or plugin on them, and retrieve the results for … |
| 3D Nuclei Clustering Tool |
6.971 |
|
3D, multi-channel |
ImageJ |
Software |
… Bäcker Volker orcid.org/0000-0002-9129-6403 Requires ImageJ Execution Platform Linux Mac Windows Implementation Type plugin Programming Language ImageJ Macros Jython is compatible with Fiji Supported image … |
| ImageJ Plugin LineageTracker |
6.961 |
|
2D, time-series |
ImageJ |
Software |
… Tamai TK, Koentges G, Vance KW, Bretschneider T. Requires ImageJ Execution Platform Linux Mac Windows Implementation … Quote from the plugin page: >LineageTracker offers an ImageJ based framework which is easily extendible and has the … in all aspects. The webpage is detailed with usage from ImageJ macro. Rather than being simply a component, the … |
| Gaussian blur in ImageJ |
6.946 |
|
2D |
ImageJ |
Software |
… Type Component Author Wayne Rasband Requires ImageJ Execution Platform Linux Mac Windows Supported image … as in Photoshop, but different from earlier versions of ImageJ, where a value 2.5 times as much had to be entered. Like all ImageJ convolution operations, it assumes that out-of-image … |
| MiNA - Mitochondrial Network Analysis |
6.942 |
|
2D, 3D |
ImageJ |
Software |
… Type Workflow Author Valente Andrew Stuart Jeffrey Requires ImageJ Execution Platform Linux Mac Windows Implementation … images or 3D stacks in Fiji. The workflow makes use of ImageJ Ops , 3D Viewer , Skeletonize (2D/3D) , Analyze … Cite the publication Reference Publication Link A simple ImageJ macro tool for analyzing mitochondrial network … |
| MorphoLibJ |
6.931 |
|
2D, 3D |
ImageJ |
Software |
… Author Legland, David Arganda-Carreras, Ignacio Requires ImageJ Execution Platform Linux Mac Windows Implementation … plugin Programming Language Java is compatible with ImageJ Fiji Supported image dimension 2D 3D Interaction Level … source Description MorphoLibJ is a library of plugin for ImageJ with functionalities for image processing such as … |
| Using ImageJ to Analyze the Size, Shape, and Directionality of Networks of Coupled Astrocytes |
6.7 |
|
3D |
Fiji |
Software |
… Using ImageJ to Analyze the Size, Shape, and Directionality of … |
| Orthogonal Views (ImageJ) |
6 |
|
2D, 3D |
ImageJ |
Software |
… Type Component Requires ImageJ Execution Platform Linux Mac Windows Implementation … Free and open source Description A menu item in ImageJ that allows you to inspect a 3D stack with orthogonal … plugin to save the current orthogonal views as montage. ## ImageJ Macro Usages [Save orthogonal views | OrthoSaver]( … |
| ActionBar (ImageJ) |
6 |
|
|
ImageJ |
Software |
… Type Component Author Jérôme Mutterer Requires ImageJ Execution Platform Linux Mac Windows Implementation … is a simple annotated text document that has snippets of Imagej macros or Beanshell arranged into buttons. This tool … Last modified 04/29/2023 - 11:49 Download Page https://imagej.net/plugins/action-bar Documentation Link … |
| ImageJ Bandpass filter |
6 |
|
2D |
ImageJ |
Software |
… Type Component Author Joachim Walter Requires ImageJ Execution Platform Linux Mac Windows Implementation … Fourier transform to obtain a filtered real-space image. ImageJ's _Process > FFT > Bandpass Filter_ implements two … Fourier transform to obtain a filtered real-space image. ImageJ's _Process > FFT > Bandpass Filter_ implements two … |
| 2D Gaussian fitting macro (Fiji/ImageJ) for multiple signals. |
6 |
|
2D |
ImageJ, Fiji |
Software |
… Waithe dominic orcid.org/0000-0003-2685-4226 Requires ImageJ Fiji Programming Language ImageJ Macros Supported image dimension 2D Interaction Level … within detected regions. This macro is unique because the ImageJ/Fiji curve fitting API only supports 1-D curve. I get … |
| Filament Tracing (ImageJ) |
6 |
|
3D |
ImageJ |
Software |
… Type Workflow Author Tosí, Sébastien Requires ImageJ Execution Platform Linux Mac Windows Implementation … Page Neubias BIAFLOWS workflow of Filament Tracing 3D with ImageJ has comparison BIAFLOWS Vessel Tracing 3D project … Filament Tracing (ImageJ) … |
| Protein Array Analyzer for ImageJ |
6 |
|
2D |
ImageJ |
Software |
… Type Collection Author Carpentier Gilles Requires ImageJ Execution Platform Linux Mac Windows Implementation Type plugin Programming Language ImageJ Macros Supported image dimension 2D Interaction Level … The Protein Array Analyzer, which was programmed in ImageJ’s macro language, is an extention of the Dot Blot … |
| Filament Tracing LocThresh (ImageJ) |
6 |
|
3D |
ImageJ |
Software |
… Type Workflow Author Tosí, Sébastien Requires ImageJ Execution Platform Linux Mac Windows Programming Language ImageJ Macros Supported image dimension 3D Interaction Level … BIAFLOWS workflow of Filament Tracing with LocThresh ImageJ has comparison BIAFLOWS-PROBLEM: VESSEL-TRACING-3D … |
| ROI 1-click tools for ImageJ/Fiji |
6 |
|
2D, multi-channel, time-series |
ImageJ, Fiji |
Software |
… Thomas Laurent orcid.org/0000-0001-7686-3249 Requires ImageJ Fiji Implementation Type plugin Programming Language ImageJ Macros Supported image dimension 2D multi-channel … additional click tools for the rapid annotations of ROI in ImageJ/Fiji. The ROI 1-click tools can be setup with a … |
| EVER-ImageJ-Plugin |
6 |
|
2D |
ImageJ |
Software |
… Type Component Author Hongqiang Ma Requires ImageJ Execution Platform Linux Mac Windows Implementation … of parameters and has been implemented as an easy-to-use ImageJ plugin that can immediately enhance the quality of … - 19:45 Download Page https://github.com/YangLiuLab/EVER-ImageJ-Plugin Reference Publication Link Ma, H., Jiang, W., … |
| Manual Frame Drift Registration |
6 |
|
2D, time-series |
ImageJ, Manual Tracking ImageJ |
Software |
… Type Component Author Kota Miura Requires ImageJ Manual Tracking ImageJ Execution Platform Linux Mac Windows Programming Language ImageJ Macros Supported image dimension 2D time-series … |
| ICY Median filter via ImageJ |
6 |
|
|
|
Software |
… perform a median filter on the active sequence using the ImageJ rank filter plugin. Then, it converts the result back … display. An example showing passing data between ICY and ImageJ using ImagePlus object. has function Image processing … https://icy.bioimageanalysis.org/protocol/Median-filter-via-imageJ/ Backlinks … |
| ImageJ2 |
6 |
|
2D, 3D, multi-channel, time-series |
|
Software |
… Last modified 03/03/2020 - 10:30 Download Page https://imagej.net/Downloads Documentation Link https://imagej.net/ImageJ2#Publications Reference Publication Link … |
| Cell Counter ImageJ |
6 |
|
2D |
ImageJ |
Software |
… Type Component Author Kurt De Vos Requires ImageJ Execution Platform Linux Mac Windows Implementation … 01:10 Download Page Cell Counter Documentation Link http://imagej.net/plugins/cell-counter.html Backlinks … Cell Counter ImageJ … |
| Analyze Complex Roots Tool |
5.409 |
|
2D |
Fiji |
Software |
… Windows Implementation Type plugin Programming Language ImageJ Macros is compatible with Fiji Supported image … |
| Morphological Segmentation (ImageJ) |
5 |
|
2D, 3D |
ImageJ |
Software |
… Author Ignacio Arganda-Carreras David Legland Requires ImageJ Execution Platform Linux Mac Windows Implementation … open source Description Morphological Segmentation is an ImageJ/Fiji plugin that combines morphological operations, … is a stack) in the main canvas as if it were any other ImageJ window. On the left side of the canvas there are three … |
| Neural Circuit Tracer |
5 |
|
3D |
Matlab compiler runtime |
Software |
… Implementation Type standalone Programming Language ImageJ Macros Matlab is compatible with ImageJ MATLAB Supported image dimension 3D Interaction Level … (MathWorks, Inc., Natick MA). It is based on the core of ImageJ ( http://rsbweb.nih.gov/ij ) and the graphic user … |
| JFilament |
5 |
|
2D, 3D, time-series |
ImageJ |
Software |
… Dimitrios Vavylonis Xiaolei Huang Matt Smith Requires ImageJ Execution Platform Linux Mac Windows Programming Language Java is compatible with ImageJ Supported image dimension 2D 3D time-series … Free and open source Description JFilament is an ImageJ plugin for segmentation and tracking of 2D and 3D … |
| Skin Tools |
5 |
|
2D |
ImageJ |
Software |
… Type Workflow Author Volker Baecker Requires ImageJ Execution Platform Linux Mac Windows Programming Language ImageJ Macros Supported image dimension 2D Interaction Level … website Documentation Link http://dev.mri.cnrs.fr/projects/imagej-macros/wiki/Skin_Tools Reference Publication Link … |
| Template Matching and Slice Alignment--- ImageJ Plugins |
5 |
|
2D, time-series |
ImageJ, OpenCV |
Software |
… Type Collection Author Qingzong TSENG Requires ImageJ OpenCV Implementation Type plugin Programming Language … License/Openness Free and open source Description This ImageJ plugin contains two functions. The first one is the … This ImageJ plugin contains two functions. The first one is the … |
| DEFCoN-ImageJ |
5 |
|
2D |
Fiji |
Software |
… Free and open source License GNUv3 Description An ImageJ plugin for DEFCoN, the fluorescence spot counter based … site, add Kmdouglass Documentation Link http://defcon-imagej.readthedocs.io/en/latest/ Backlinks … An ImageJ plugin for DEFCoN, the fluorescence spot counter based … |
| Find Maxima (Python) |
5 |
|
2D |
SciPy, PIL, Python, Jupyter, Jupyter notebook |
Software |
… in Python recreated from implementation in Fiji(ImageJ) This is a re-implementation of the java plugin written by Michael Schmid and Wayne Rasband for ImageJ. The original java code source can be found in: … This script is simply to provide the functionality of the ImageJ find maxima algorithm to individuals writing pure … |
| Gaussian Blur 3D (ImageJ) |
5 |
|
3D |
ImageJ |
Software |
… Type Component Author Rasband, Waine Requires ImageJ Execution Platform Linux Mac Windows Implementation … Type plugin Programming Language Java is compatible with ImageJ Macro Supported image dimension 3D Interaction Level … modified 02/05/2019 - 14:53 Download Page Gaussian Blur 3D ImageJ java code Backlinks … |
| Thresholder (ImageJ) |
5 |
|
2D, 3D, time-series |
ImageJ |
Software |
… Type Collection Requires ImageJ Execution Platform Linux Mac Windows Implementation … package and Thresholder java file Documentation Link ImageJ Documentation Fiji Documentation (Links to ImageJ documentation) Backlinks … Thresholder (ImageJ) … |
| 3D Segmentation & visualization of nanoparticles attached to the surface of red blood cells |
5 |
|
3D |
ImageJ |
Software |
… R. Ward Jean-Baptiste Fleuryd Vladimir A. Baulin Requires ImageJ Execution Platform Linux Mac Windows Programming Language ImageJ Macros Supported image dimension 3D Interaction Level … - 13:59 Last modified 05/24/2023 - 16:47 Download Page ImageJ macro files Reference Publication Link High-throughput … |
| Particle Tracking (ImageJ) |
5 |
|
2D, time-series |
ImageJ, FeatureJ Laplacian |
Software |
… Type Workflow Author Tosí, Sébastien Requires ImageJ FeatureJ Laplacian Execution Platform Linux Mac Windows Programming Language ImageJ Macros Supported image dimension 2D time-series … Page Neubias BIAFLOWS workflow of Particle Tracking with ImageJ has comparison BIAFLOWS-PROBLEM: … |
| Object Tracking (ImageJ) |
5 |
|
2D, time-series |
ImageJ |
Software |
… Type Workflow Author Tosí, Sébastien Requires ImageJ Execution Platform Linux Mac Windows Programming Language ImageJ Macros Supported image dimension 2D time-series … Page Neubias BIAFLOWS workflow of Object Tracking with ImageJ has comparison BIAFLOWS-PROBLEM: … |
| NDPI Export Regions Tool |
5 |
|
2D |
ImageJ |
Software |
… Bäcker Volker orcid.org/0000-0002-9129-6403 Requires ImageJ Execution Platform Linux Mac Windows Implementation Type plugin Programming Language ImageJ Macros Supported image dimension 2D Interaction Level … |
| Counting Clumped Cells |
5 |
|
2D |
ImageJ |
Software |
… Curtis Ruden Requires ImageJ Execution Platform Linux Mac Windows Programming Language ImageJ Macros Supported image dimension 2D Interaction Level … Free and open source Description A workflow combining ImageJ macro and manually using Trainable Weka Segmentation … |
| Analyzing gels and western blots with ImageJ |
5 |
|
2D |
ImageJ |
Software |
… Author Luke Miller (contact@lukemiller.org) Requires ImageJ Execution Platform Linux Mac Windows Supported image … Analyzing gels and western blots with ImageJ … |
| Wound healing assay: analysis in ImageJ |
5 |
|
2D, time-series |
ImageJ |
Software |
… J Ashby Fabrice P Cordelières Lionel Larue Requires ImageJ Programming Language ImageJ Macros Supported image dimension 2D time-series … Wound healing assay: analysis in ImageJ … |
| Multi Kymograph |
5 |
|
2D, time-series |
ImageJ |
Software |
… Type Collection Author Jens Rietdorf Arne Seitz Requires ImageJ Execution Platform Linux Mac Windows Implementation Type plugin Programming Language ImageJ Macros Java Supported image dimension 2D time-series … open source Description This macro and plugins suite for ImageJ (and Fiji) serves to measure the velocity of moving … |
| ImageJ Binary Operations |
5 |
|
2D |
ImageJ |
Software |
… Type Collection Requires ImageJ Execution Platform Linux Mac Windows Implementation … Last modified 05/17/2023 - 19:19 Download Page Download ImageJ Documentation Link ImageJ Documentation Usage Example Link Usage Backlinks … ImageJ Binary Operations … |
| Manual Tracking Components of ImageJ |
5 |
|
2D, time-series |
Fiji |
Software |
… Free and open source Description The Fiji distribution of ImageJ comes with several manual tracking tools, two of which … Correction_ * flat-field correction, and/or bandpass (ImageJ's _Process->FFT->Bandpass filter_) according to the … The Fiji distribution of ImageJ comes with several manual tracking tools, two of which … |
| Magic Montage |
5 |
|
2D |
ImageJ |
Software |
… Type Component Author Jerome Mutterer Requires ImageJ Execution Platform Linux Mac Windows Programming Language ImageJ Macros Supported image dimension 2D Interaction Level … Free and open source Description This tool adds to ImageJ functions to build and organize montages. It comes … |
| Update Fiji |
5 |
|
|
Fiji, ImageJ 2.x |
Software |
… Author Johannes Schindelin Curtis Rueden Requires Fiji ImageJ 2.x Execution Platform Linux Mac Windows … open source License BSD-2 Description The purpose of the ImageJ Updater is to keep you up-to-date with all components of ImageJ (or Fiji), i.e. the macros, scripts, plugins and the … |
| Import ROI from ImageJ |
5 |
|
2D, 3D, multi-channel, time-series |
ImageJ |
Software |
… Dufour Alexandre orcid.org/0000-0002-9417-7389 Requires ImageJ Execution Platform Linux Mac Windows Implementation … Description Import ROI from a zip file produced with ImageJ's ROI manager. Works as a standalone plugin and as a … http://icy.bioimageanalysis.org/plugin/import-roi-from-imagej/ Backlinks … |
| ImageJ 2.x |
5 |
|
2D, 3D, multi-channel, time-series |
|
Software |
… Last modified 05/17/2023 - 10:48 Download Page http://imagej.net Reference Publication Link NIH Image to ImageJ: 25 years of image analysis Backlinks Local Z … ImageJ 2.x … |
| ImageJ Plugin for Non-Local-Means Filtering |
4.993 |
|
2D |
ImageJ |
Software |
… Component Author Thorsten Wagner, Pascal Behnel Requires ImageJ Execution Platform Linux Mac Windows Implementation … Last modified 10/21/2019 - 14:38 Download Page https://imagej.net/Non_Local_Means_Denoise Documentation Link https://imagej.net/Non_Local_Means_Denoise Reference Publication Link … |
| NODeJ |
4.906 |
|
2D, 3D |
ImageJ |
Software |
… Type Component Author Axel Poulet Tristan Dubos Requires ImageJ Execution Platform Linux Mac Windows Implementation … standalone Programming Language Java is compatible with ImageJ Supported image dimension 2D 3D Interaction Level … and open source License GNU AGPLv3 Description NODeJ is an ImageJ plugin for 3D segmentation of nuclear objects. "The … |
| ImageJ Analyze Skeleton |
4.864 |
|
2D, 3D |
ImageJ, Analyze 12.0 |
Software |
… Arganda-Carreras orcid.org/0000-0003-0229-5722 Requires ImageJ Analyze 12.0 Execution Platform Linux Mac Windows … Usage Example Link http://imagej.net/AnalyzeSkeleton Backlinks Strahler Analysis / … ImageJ Analyze Skeleton … |
| 3D ImageJ Suite |
4.803 |
|
2D, 3D |
ImageJ, ImageScience.jar |
Software |
… Collection Author Boudier, Thomas Ollion, Jean Requires ImageJ ImageScience.jar Execution Platform Linux Mac Windows … This suite provides plugins to enhance 3D capabilities of ImageJ. 3D Filters (mean, median, max, min, tophat, max … - 14:55 Last modified 04/27/2023 - 14:27 Download Page 3D ImageJ Suite webpage Reference Publication Link J. Ollion, J. … |
| MIA |
4.742 |
|
2D, 3D, multi-channel, time-series |
Fiji, MorphoLibJ |
Software |
… Type plugin Programming Language Java is compatible with ImageJ Macro Jython for ImageJ Supported image dimension 2D 3D multi-channel … License v3.0 Description ModularImageAnalysis (MIA) is an ImageJ plugin which provides a modular framework for … ModularImageAnalysis (MIA) is an ImageJ plugin which provides a modular framework for … |
| Marker-controlled Watershed (ImageJ) |
4 |
|
2D, 3D |
ImageJ |
Software |
… Author Ignacio Arganda-Carreras David Legland Requires ImageJ Execution Platform Linux Mac Windows Implementation … open source Description Marker-controlled Watershed is an ImageJ/Fiji plugin to segment grayscale images of any type … Marker-controlled Watershed is an ImageJ/Fiji plugin to segment grayscale images of any type … |
| Moment thresholding (ImageJ) |
4 |
|
2D, 3D |
ImageJ |
Software |
… Type Component Author W. Tsai Requires ImageJ Execution Platform Linux Mac Windows Implementation … a threshold that preserves the moments of an image. In ImageJ/Fiji, you can access it in Image->Ajust->Threshold and … a threshold that preserves the moments of an image. In ImageJ/Fiji, you can access it in Image->Ajust->Threshold and … |
| Skeletonize |
4 |
|
2D |
ImageJ |
Software |
… Type Component Author Wayne Rasband Requires ImageJ Execution Platform Linux Mac Windows Implementation … License/Openness Free and open source Description ImageJ native "Skeletonize" implementation. - works only with … Last modified 04/27/2023 - 12:51 Download Page https://imagej.net/ Documentation Link … |
| Analyze Particles |
4 |
|
2D |
ImageJ, Fiji |
Software |
… Type Component Requires ImageJ Fiji Execution Platform Linux Mac Windows … open source Description An object detection function in ImageJ. [Analyze > Analyze Particles...]. It could simply be … Last modified 04/25/2023 - 19:55 Download Page Download ImageJ Documentation Link ImageJ documentation Backlinks Spot … |
| NeuriteTracer |
4 |
|
2D |
ImageJ |
Software |
… Workflow Author Pool Madeleine Thiemann Joachim Requires ImageJ Execution Platform Linux Mac Windows Implementation Type standalone Programming Language ImageJ Macros Supported image dimension 2D Interaction Level … length."[...]" NeuriteTracer is a fast simple-to-use ImageJ plugin for the analysis of outgrowth in … |
| LimeSeg |
4 |
|
3D |
ImageJ |
Software |
… Type Component Author Nicolas Chiaruttini Requires ImageJ Execution Platform Linux Mac Windows Implementation … Type plugin Programming Language Java is compatible with ImageJ Fiji Update Fiji Supported image dimension 3D … is no download but you can easily install this plugin via ImageJ update site. If you really need to download the jar … |
| StarDist - ImageJ |
4 |
|
2D, 3D |
ImageJ |
Software |
… Martin Weigert Coleman Broaddus Gene Myers Requires ImageJ Execution Platform Linux Mac Windows Implementation … Free and open source Description This is the ImageJ/Fiji plugin for StarDist , a cell/nuclei detection … This is the ImageJ/Fiji plugin for StarDist , a cell/nuclei detection … |
| NDPItools |
4 |
|
2D |
ImageJ |
Software |
… Type Component Author Deroulers Christophe Requires ImageJ Execution Platform Linux Mac Windows Implementation … directly open in standard image analysis software such as ImageJ . NDPITools is a collection of software that can … computer's memory. It comes with a bundle of plugins for ImageJ which enable the use of the software directly inside … |
| Microtubules Tool (3D) |
4 |
|
3D, multi-channel |
ImageJ, Fiji, Skeletonize3D, 3D Objects Counter |
Software |
… Type Workflow Author Volker Baecker Requires ImageJ Fiji Skeletonize3D 3D Objects Counter Execution … in a 3D image. See: http://dev.mri.cnrs.fr/projects/imagej-macros/wiki/Microtubules_Tool_(3… You can find a test … in a 3D image. See: http://dev.mri.cnrs.fr/projects/imagej-macros/wiki/Microtubules_Tool_(3… You can find a test … |
| Histo_surfaces |
4 |
|
2D |
ImageJ |
Software |
… Requires ImageJ Execution Platform Linux Mac Windows Programming Language ImageJ Macros Supported image dimension 2D Interaction Level … License/Openness Free and open source Description An ImageJ macro for calculating empty surfaces on histological … An ImageJ macro for calculating empty surfaces on histological … |
| aNMJ-Morph |
4 |
|
2D, multi-channel |
ImageJ |
Software |
… Type Workflow Author Gavin Minty Requires ImageJ Execution Platform Linux Mac Windows Implementation Type standalone Programming Language ImageJ Macros is compatible with ImageJ Supported image dimension 2D multi-channel Interaction … ImageJ macro script to streamline the original NMJ-morph … |
| AutoNeuriteJ |
4 |
|
2D |
ImageJ |
Software |
… Type Workflow Author Benoit Boulan Eric Denarier Requires ImageJ Execution Platform Linux Mac Windows Implementation Type standalone Programming Language ImageJ Macros is compatible with ImageJ Supported image dimension 2D Interaction Level … An imageJ/Fiji plugin that measures and classifies neurites from … |
| Intelligent Imaging |
4 |
|
2D |
ImageJ |
Software |
… Type Collection Author Sébastien Tosi Requires ImageJ Execution Platform Linux Mac Windows Programming Language ImageJ Macros Supported image dimension 2D Interaction Level … Description The linked webpage presents a collection of ImageJ macros for Intelligent Imaging (Feedback to microscope … |
| Zebrafish Embryo Tool |
4 |
|
2D |
ImageJ |
Software |
… Type Workflow Author Volker Baecker Requires ImageJ Execution Platform Linux Mac Windows Programming Language ImageJ Macros Supported image dimension 2D Interaction Level … and measure the distribution of Cy3 stained tumor foci. ImageJ macro implementation of the Workflow described in … |
| InfectionCounter |
4 |
|
2D |
ImageJ, Cell Counter ImageJ |
Software |
… Type Workflow Author Joe Grove Requires ImageJ Cell Counter ImageJ Execution Platform Linux Mac Windows Programming Language ImageJ Macros Supported image dimension 2D Interaction Level … antigen associated immunofluorescence. The core is an ImageJ Macro, so it's easy to modify for one's own needs ( … |
| NeurphologyJ |
4 |
|
|
ImageJ |
Software |
… Type Workflow Author Eric Hwang Requires ImageJ Programming Language ImageJ Macros Interaction Level Automated License/Openness … Free and open source I do not know Description ImageJ macro for the morphometry of neurites. > NeurphologyJ; … ImageJ macro for the morphometry of neurites. > NeurphologyJ; … |
| Nucleus Counter (ImageJ) |
4 |
|
|
ImageJ, Graylevel Watershed for ImageJ |
Software |
… Type Component Requires ImageJ Graylevel Watershed for ImageJ Interaction Level Automated License/Openness I do not … Nucleus Counter (ImageJ) … |
| Color Inspector 3D |
4 |
|
2D |
ImageJ |
Software |
… Type Component Author Kai Uwe Barthel Requires ImageJ Execution Platform Linux Mac Windows Implementation … is available at www.f4.fhtw-berlin.de/~barthel/ImageJ/ColorInspector/help.htm . Color Inspector 3D is also available as a stand-alone program that uses ImageJ as a library. To run it, download … |
| Manual Tracking ImageJ |
4 |
|
2D, 3D, time-series |
Fiji |
Software |
… License/Openness Free and open source Description An ImageJ plugin for manually tracking objects by mouse … An ImageJ plugin for manually tracking objects by mouse … Manual Tracking ImageJ … |
| Angiogenesis / Sprout Analyzer (ImageJ) |
4 |
|
2D, multi-channel |
ImageJ |
Software |
… Type Component Author Jan Ellinger Requires ImageJ Execution Platform Linux Mac Windows Programming Language Java is compatible with ImageJ Supported image dimension 2D multi-channel Interaction … Angiogenesis / Sprout Analyzer (ImageJ) … |
| ImageJ Auto Crop |
4 |
|
2D |
ImageJ |
Software |
… Type Component Requires ImageJ Execution Platform Linux Mac Windows Programming … ImageJ Auto Crop … |
| Dithering |
4 |
|
2D |
ImageJ |
Software |
… Type Component Author Gabriel Landini Requires ImageJ Execution Platform Linux Mac Windows Programming Language ImageJ Macros Supported image dimension 2D Interaction Level … Last modified 01/10/2019 - 15:00 Download Page https://imagej.net/Dithering Documentation Link … |
| Spatial statistics 2D/3D ImageJ plugin |
4 |
|
2D, 3D |
ImageJ |
Software |
… Component Author Philippe Andrey Thomas Boudier Requires ImageJ Execution Platform Linux Mac Windows Implementation … reference structure. This plugin comes together with 3D ImageJ suites plugin. has function Object feature extraction … reference structure. This plugin comes together with 3D ImageJ suites plugin. … |
| Multi Otsu Threshold |
4 |
|
2D, 3D, multi-channel, time-series |
ImageJ, KNIME Multilevel Thresholding, Histogram |
Software |
… Type Component Requires ImageJ KNIME Multilevel Thresholding Histogram Execution … License/Openness Free and open source Description This ImageJ plugin segments the image in classes by thresholding. … Last modified 10/16/2019 - 13:30 Download Page https://imagej.net/Multi_Otsu_Threshold Usage Example Link … |
| hIPNAT |
4 |
|
2D, multi-channel, time-series |
ImageJ |
Software |
… Collection Author orcid.org/0000-0001-6866-1540 Requires ImageJ Execution Platform Linux Mac Windows Implementation … and other tree-like morphologies. It is written for ImageJ, the de facto standard in scientific image processing. It is available through the ImageJ Neuroanatomy update site . has function Filament … |
| ImageJ2 Plugin KNIME |
4 |
|
|
ImageJ2 |
Software |
… Documentation Link https://www.knime.com/community/imagej Backlinks … |
| ImgLib2 |
4 |
|
2D, 3D, multi-channel, time-series |
ImageJ |
Software |
… Christian Dietz, Martin Horn, Mark Hiner, et al Requires ImageJ Execution Platform Linux Mac Windows Implementation … Type library Programming Language Java is compatible with ImageJ Supported image dimension 2D 3D multi-channel … Page http://imglib2.net/ Documentation Link http://imagej.net/ImgLib2_Documentation Reference Publication Link … |
| Maximum Entropy Threshold (ImageJ) |
4 |
|
2D |
ImageJ |
Software |
… Type Component Author Jerek Sacha Requires ImageJ Execution Platform Linux Mac Windows Implementation … with few bright objects on large dark background. In ImageJ/FIJI you can acces this tool in … with few bright objects on large dark background. In ImageJ/FIJI you can acces this tool in … |
| Register Virtual Stack Slices (ImageJ) |
3.993 |
|
2D, 3D |
ImageJ |
Software |
… Ignacio Arganda-Carreras and Stephan Saalfeld Requires ImageJ Execution Platform Linux Mac Windows Implementation … Last modified 03/02/2020 - 21:23 Download Page https://imagej.net/Register_Virtual_Stack_Slices Backlinks … Register Virtual Stack Slices (ImageJ) … |
| HyphaTracker |
3.985 |
|
2D, time-series |
ImageJ |
Software |
… Component Workflow Author Sebastian van de Linde Requires ImageJ Execution Platform Linux Mac Windows Implementation Type plugin Programming Language ImageJ Macros is compatible with ImageJ Fiji Supported image dimension 2D time-series … |
| Multiview Reconstruction |
3.9 |
|
3D, multi-channel, time-series |
BigDataViewer, ImageJ, ImgLib2 |
Software |
… Schinelin Johannes Requires BigDataViewer ImageJ ImgLib2 Execution Platform Linux Mac Windows … Last modified 01/30/2018 - 12:34 Download Page http://imagej.net/Multiview-Reconstruction Documentation Link http://imagej.net/Multiview-Reconstruction#Detailed_Tutorials … |
| Texture Analyzer (ImageJ) |
3 |
|
2D |
ImageJ |
Software |
… Type Component Author Julio E. Cabrera Requires ImageJ Execution Platform Linux Mac Windows Implementation … Texture Analyzer (ImageJ) … |
| Distance Analysis (DiAna) |
3 |
|
2D, 3D, multi-channel |
Fiji |
Software |
… - 01:43 Last modified 05/03/2023 - 17:17 Download Page ImageJ DiAna Documentation Link ImageJ DiAna Reference Publication Link DiAna, an ImageJ tool for object-based 3D co-localization and distance … |
| Directionality |
3 |
|
2D |
ImageJ |
Software |
… Jan Eglinger 0000-0001-7234-1435 Mark Hiner Requires ImageJ Supported image dimension 2D Interaction Level … Link goes to source code; useable as a built-in plugin in ImageJ Documentation Link http://imagej.net/Directionality Backlinks … |
| Tubeness |
3 |
|
2D, 3D |
ImageJ |
Software |
… orcid.org/0000-0002-0276-494X Johannes Schindelin Requires ImageJ Execution Platform Linux Mac Windows Implementation … - 11:10 Download Page https://www.longair.net/edinburgh/imagej/tubeness/ Documentation Link https://www.longair.net/edinburgh/imagej/tubeness/ Reference Publication Link Sato Y, Nakajima … |
| FFmpeg |
3 |
|
|
|
Software |
|
| Wound Healing Tool |
3 |
|
2D, time-series |
ImageJ |
Software |
… Type Workflow Author Volker Baecker Requires ImageJ Execution Platform Linux Mac Windows Supported image … Link Wound Healing Tool Reference Publication Link 2012. ImageJ Macro Tool Sets for Biological Image Analysis. ImageJ User and De… Usage Example Link Accelerated Wound … |
| FracLac |
3 |
|
2D |
ImageJ |
Software |
… University, Australia/Canada, Earth 2007-2012 Requires ImageJ Execution Platform Linux Mac Windows Implementation … describe morphological features . FracLac is a plugin for ImageJ. It is freely available software developed and … basic box counting algorithm was originally modified from ImageJ 's box counting algorithm and H. Jelinek's NIH Image … |
| CEM |
3 |
|
2D, 3D, multi-channel |
ImageJ |
Software |
… Type Collection Requires ImageJ Implementation Type plugin is compatible with ImageJ Supported image dimension 2D 3D multi-channel … are given as pixel counts and percents. CEM runs as an imageJ plugin with an optional Matlab extension to remove … are given as pixel counts and percents. CEM runs as an imageJ plugin with an optional Matlab extension to remove … |
| Fourier Bandpass Filter |
3 |
|
2D |
ImageJ |
Software |
… Type Component Author Joachim Walter Requires ImageJ Execution Platform Linux Mac Implementation Type … modified 06/05/2018 - 03:32 Documentation Link https://imagej.nih.gov/ij/plugins/fft-filter.html Backlinks … |
| ImageJ/FIJI |
3 |
|
2D, 3D, multi-channel, time-series |
|
Software |
… Free and open source Description Please also check out ImageJ and Fiji . has function Analysis Annotation Data … Please also check out ImageJ and Fiji . … ImageJ/FIJI … |
| Interactive watershed |
3 |
|
2D, 3D |
Fiji |
Software |
… to other images in a headless mode, for example via ImageJ macro scripting. has function Cell segmentation … - 11:07 Download Page Interactive Watershed on the ImageJ wiki Documentation Link https://imagej.net/Interactive_Watershed Backlinks … to other images in a headless mode, for example via ImageJ macro scripting. … |
| InspectJ |
3 |
|
2D |
ImageJ |
Software |
… Lorenz Holger Jaiswal Astha Requires ImageJ Execution Platform Linux Mac Windows Implementation Type plugin Programming Language ImageJ Macros Supported image dimension 2D Interaction Level … Free and open source Description InspectJ is a free ImageJ/FIJI tool to inspect digital image integrity. … |
| Labkit |
3 |
|
2D, 3D |
ImageJ |
Software |
… Tobias Jug Florian orcid.org/0000-0002-8499-5812 Requires ImageJ Execution Platform Linux Mac Windows Implementation … Documentation Link https://imagej.net/Labkit Usage Example Link https://imagej.net/Labkit Backlinks … |
| MiToBo |
3 |
|
2D, 3D |
Fiji |
Software |
… for the widely used image processing application ImageJ and its new release ImageJ 2.0 . MiToBo ships with a set of operators ready to be used as plugins in ImageJ. They focus on the analysis of biomedical images … for the widely used image processing application ImageJ and its new release ImageJ 2.0 . MiToBo ships with a … |
| jSLIC |
3 |
|
2D |
ImageJ |
Software |
… Type Component Author Jiri Borovec Requires ImageJ Execution Platform Linux Mac Windows Implementation … Last modified 03/08/2019 - 13:06 Download Page https://imagej.net/CMP-BIA_tools Reference Publication Link jSLIC: superpixels in ImageJ Usage Example Link jSLIC: superpixels Backlinks … |
| Correlia |
3 |
|
2D, multi-channel |
ImageJ |
Software |
… Schmidt Matthias orcid.org/0000-0002-0161-8326 Requires ImageJ Execution Platform Linux Mac Windows Implementation … License GPL 3.0 Description Correlia is an open-source ImageJ/FIJI plug-in for the registration of 2D multi-modal … Link Documentation Reference Publication Link Correlia: an ImageJ plug-in to co-register and visualise multimodal … |
| Tissue Cell Segmentation |
3 |
|
2D |
ImageJ |
Software |
… Type Component Author Sébastien Tosi Requires ImageJ Execution Platform Linux Mac Programming Language ImageJ Macros Supported image dimension 2D Interaction Level … organization is automatically extracted and exported to an ImageJ results table. This includes: Cell area, major, minor … |
| Segmentation and Tracking of Mammary Epithelial Organoids in Brightfield Microscopy |
3 |
|
2D, time-series |
ImageJ |
Software |
… Type Workflow Author Lucia Hradecká Requires ImageJ Execution Platform Linux Implementation Type library Programming Language ImageJ Macros Matlab Python is compatible with ImageJ Supported image dimension 2D time-series Interaction … |
| BioVoxxel Toolbox |
3 |
|
|
ImageJ, Fiji |
Software |
… Author Jan Brocher https://www.biovoxxel.de/ Requires ImageJ Fiji Execution Platform Linux Mac Windows Implementation Type plugin Programming Language ImageJ Macros License/Openness I do not know License 3-Clause … Documentation Link https://imagej.net/plugins/biovoxxel-toolbox … |
| Protein Micro-array Analysis |
3 |
|
2D |
Fiji |
Software |
… Execution Platform Linux Mac Windows Programming Language ImageJ Macros Supported image dimension 2D Interaction Level … be cropped for larger arrays). The macro requires the "ImageJ plugins toolkit". To ensure compatibility with … - 15:04 Last modified 04/28/2023 - 16:12 Download Page ImageJ Macro: Protein MicroArray Analysis Usage Example Link … |
| Colocalization Colormap |
3 |
|
2D |
|
Software |
… Type plugin Programming Language Java is compatible with ImageJ Supported image dimension 2D Interaction Level … License GPL3 Description Colocalization Colormap –an ImageJ Plugin for the Quantification and Visualization of Colocalized Signals This ImageJ plugin implements the Jaskolski's algorithm (Jaskolski … |
| Quantifying staining in tissue sections |
3 |
|
2D |
ImageJ, Colour Deconvolution |
Software |
… Type Component Author Peter Bankhead Requires ImageJ Colour Deconvolution Execution Platform Linux Mac … in tissue sections] The Color Deconvolution plugin for ImageJ can be used to digitally separate up to three stains from brightfield images, after which standard ImageJ commands can be used. The algorithm is described in … |
| (Z,T) Hyperstack Stitcher |
3 |
|
3D, time-series |
ImageJ |
Software |
… Type Component Author Sébastien Tosi Requires ImageJ Execution Platform Linux Mac Windows Programming Language ImageJ Macros Supported image dimension 3D time-series … - 15:28 Last modified 04/28/2023 - 16:32 Download Page ImageJ macro - (Z,T) Hyperstack Stitcher Documentation Link … |
| Interactive Volume of Interest Extractor in Large 3D Stacks |
3 |
|
3D |
ImageJ |
Software |
… Type Component Author Sébastien Tosi Requires ImageJ Execution Platform Linux Mac Windows Programming Language ImageJ Macros Supported image dimension 3D Interaction Level … - 15:34 Last modified 04/28/2023 - 16:48 Download Page ImageJ macro - Interactive Volume of Interest Extractor in … |
| Artemia color analysis |
3 |
|
2D |
ImageJ |
Software |
… Type Workflow Author Volker Baecker Requires ImageJ Execution Platform Linux Mac Windows Supported image … in color images. See: http://dev.mri.cnrs.fr/projects/imagej-macros/wiki/Artemia_Tools Test images: … in color images. See: http://dev.mri.cnrs.fr/projects/imagej-macros/wiki/Artemia_Tools Test images: … |
| Leaf Infection Tools |
3 |
|
2D |
ImageJ, GDSC plugins |
Software |
… Type Collection Author Volker Baecker Requires ImageJ GDSC plugins Execution Platform Linux Mac Windows … the two stainings. See: http://dev.mri.cnrs.fr/projects/imagej-macros/wiki/Leaf_Infection_Tools Test image: … the two stainings. See: http://dev.mri.cnrs.fr/projects/imagej-macros/wiki/Leaf_Infection_Tools Test image: … |
| quickPALM |
3 |
|
|
ImageJ, Micro-Manager |
Software |
… Type Workflow Author Ricardo Henriques, et al Requires ImageJ Micro-Manager Programming Language Java Python … (STORM). QuickPALM features the associated QuickPALM ImageJ plugin, which enables PALM/STORM 2D/3D/4D particle detection and image reconstruction in ImageJ. Entry Curator julien colombelli Post date 12/09/2014 … |
| Measure Rosette Area Tool |
3 |
|
2D |
ImageJ |
Software |
… Type Workflow Author Volker Baecker Requires ImageJ Execution Platform Linux Mac Windows Supported image … arabidopsis plants. See: http://dev.mri.cnrs.fr/projects/imagej-macros/wiki/Measure_Rosette_Area… Example data: … arabidopsis plants. See: http://dev.mri.cnrs.fr/projects/imagej-macros/wiki/Measure_Rosette_Area… Example data: … |
| PixFRET |
3 |
|
2D |
ImageJ |
Software |
… Type Component Author Laurent Gelman Requires ImageJ Programming Language Java Supported image dimension 2D … Automated License/Openness I do not know Description The ImageJ pligin, called PixFRET, allows a simple and rapid … Reference Publication Link PixFRET, an ImageJ plug‐in for FRET calculation that can accommodate … |
| Colony Blob Count Tool |
3 |
|
2D |
ImageJ |
Software |
… Type Workflow Author Volker Baecker Requires ImageJ Execution Platform Linux Mac Windows Programming Language ImageJ Macros Supported image dimension 2D Interaction Level … Documentation Link http://dev.mri.cnrs.fr/projects/imagej-macros/wiki/Colony_Blob_Count_Tool Backlinks … |
| 2D and 3D tracking based on global cost function optimization |
3 |
|
2D, 3D, time-series |
ImageJ, MTrackJ, ImageScience.jar, Jama, Tracking2.0 |
Software |
… Type Workflow Author Perrine Paul-Gilloteaux Requires ImageJ MTrackJ ImageScience.jar Jama Tracking2.0 Execution … Windows Implementation Type plugin Programming Language ImageJ Macros Supported image dimension 2D 3D time-series … |
| FibrilTool |
3 |
|
2D |
ImageJ |
Software |
… Type Component Author Arezki Boudaoud Requires ImageJ Execution Platform Linux Mac Windows Implementation Type plugin Programming Language ImageJ Macros Supported image dimension 2D Interaction Level … Reference Publication Link FibrilTool, an ImageJ plug-in to quantify fibrillar structures in raw … |
| classification of hemp fibers based on morphological features |
3 |
|
2D |
ImageJ, MATLAB, MorphoLibJ |
Software |
… Type Workflow Author David Legland Requires ImageJ MATLAB MorphoLibJ Execution Platform Unsure Implementation Type plugin Programming Language ImageJ Macros Supported image dimension 2D Interaction Level … are more robust than the ones implemented by default in ImageJ Export the result table created to a csv file Then for … |
| ImageJ Macro |
3 |
|
|
ImageJ |
Software |
… Type Component Requires ImageJ Interaction Level Automated License/Openness I do not … ImageJ Macro … |
| Super-Resolution Radial Fluctuations (SRRF) |
3 |
|
2D, time-series |
ImageJ |
Software |
… M. Owen Pedro Matos Pereira Ricardo Henriques Requires ImageJ Execution Platform Linux Mac Windows Implementation … Microscopy, provided as a fast GPU-enabled ImageJ plugin. SRRF is capable of extracting high-fidelity … Page The SRRF algorithm source code and plugin for ImageJ and Fiji Documentation Link User guide zip file … |
| JACoP |
3 |
|
2D, 3D, multi-channel, time-series |
ImageJ |
Software |
… Author Fabrice P. Cordelières Susanne Bolte Requires ImageJ Execution Platform Linux Mac Windows Programming Language ImageJ Macros Supported image dimension 2D 3D multi-channel … License/Openness Free and open source Description This ImageJ plug-in is a compilation of co-localization tools. It … |
| Local Normalization (ImageJ) |
3 |
|
2D |
ImageJ |
Software |
… Type Component Author Daniel Sage Requires ImageJ Execution Platform Linux Mac Windows Implementation … Local Normalization (ImageJ) … |
| Linear Kuwahara (ImageJ) |
3 |
|
2D |
ImageJ |
Software |
… Type Component Requires ImageJ Execution Platform Linux Mac Windows Implementation … Linear Kuwahara (ImageJ) … |
| Sholl Analysis (ImageJ) |
3 |
|
2D, 3D |
ImageJ |
Software |
… Type Component Requires ImageJ Execution Platform Linux Mac Windows Implementation … Sholl Analysis (ImageJ) … |
| ImageJ Align RGB planes |
3 |
|
2D |
ImageJ, EBImage rotate, CellProfiler Align |
Software |
… Type Component Author Gabriel Landini Requires ImageJ EBImage rotate CellProfiler Align Programming Language … ImageJ Align RGB planes … |
| ImageJ Feature Extraction |
3 |
|
2D |
ImageJ |
Software |
… Type Component Author Stephan Saalfeld Requires ImageJ Execution Platform Linux Mac Windows Implementation … ImageJ Feature Extraction … |
| Anisotropic Diffusion 2D |
3 |
|
2D |
Fiji |
Software |
… Last modified 12/18/2018 - 04:30 Download Page https://imagej.net/Anisotropic_Diffusion_2D Documentation Link https://imagej.nih.gov/ij/plugins/anisotropic-diffusion-2d.html … |
| Save as animated gif (ImageJ) |
3 |
|
time-series |
ImageJ |
Software |
… Type Component Author Ryan Raz Requires ImageJ Execution Platform Linux Mac Windows Supported image … Save as animated gif (ImageJ) … |
| Point Picker (ImageJ) |
3 |
|
2D |
ImageJ, ICY Annotation |
Software |
… Type Component Author Philippe Thévenaz Requires ImageJ ICY Annotation Execution Platform Linux Mac Windows … Point Picker (ImageJ) … |
| Arrow |
3 |
|
2D |
ImageJ, ICY Annotation, Arrow |
Software |
… Type Component Author Jean-Yves Tinevez Requires ImageJ ICY Annotation Arrow Execution Platform Linux Mac … floating selection, and to tune its shape. Warning: Since ImageJ version 1.43n , a similar tool, made by Wayne Rasband , does a similar thing from the ImageJ core, see here . has function Annotation has topic … |
| Interactive Stack Rotation (ImageJ) |
3 |
|
3D, multi-channel |
ImageJ |
Software |
… Type Component Author Stephan Saalfeld Requires ImageJ Execution Platform Linux Mac Windows Implementation … Interactive Stack Rotation (ImageJ) … |
| Watershed Algorithm |
3 |
|
|
ImageJ, Graylevel Watershed for ImageJ |
Software |
… Type Component Requires ImageJ Graylevel Watershed for ImageJ Interaction Level Automated License/Openness I do not … - 12:07 Download Page http://fiji.sc/Watershed_Algorithm_(ImageJ_plugin) Backlinks … |
| Kalman Stack Filter (ImageJ) |
3 |
|
2D |
ImageJ |
Software |
… Type Component Author Christopher Philip Mauer Requires ImageJ Execution Platform Linux Mac Windows Implementation … Kalman Stack Filter (ImageJ) … |
| Find Dimension of Raw Image (ImageJ) |
3 |
|
|
ImageJ |
Software |
… Type Component Author Johannes Schindelin Requires ImageJ Execution Platform Linux Mac Windows Implementation … Find Dimension of Raw Image (ImageJ) … |
| MultiThresholder (ImageJ) |
3 |
|
2D, 3D |
ImageJ |
Software |
… Type Component Requires ImageJ Execution Platform Linux Mac Windows Implementation … MultiThresholder (ImageJ) … |
| 3D Objects Counter |
3 |
|
3D |
Fiji, ImageJ |
Software |
… Jonathan Jackson Daniel James White Requires Fiji ImageJ Execution Platform Linux Mac Windows Implementation … Type plugin Programming Language Java is compatible with ImageJ Macro Supported image dimension 3D Interaction Level … voxels' map; Centroids' map; Centres of masses' map. As ImageJ's “Analyze Particles” function, 3D-OC also has a … |
| SPIM Registration Method (ImageJ) |
3 |
|
3D |
ImageJ |
Software |
… Type Component Requires ImageJ Execution Platform Linux Mac Windows Implementation … SPIM Registration Method (ImageJ) … |
| Extract Images From PDF |
3 |
|
2D |
ImageJ |
Software |
… Type Component Author Gregory Jefferis Requires ImageJ Execution Platform Mac Windows Implementation Type … Last modified 10/16/2019 - 15:26 Download Page https://imagej.net/Extract_Images_From_PDF... Documentation Link https://imagej.net/Extract_Images_From_PDF... Backlinks … |
| Local Thickness (ImageJ) |
3 |
|
3D |
ImageJ |
Software |
… Type Component Author Bob Dougherty Requires ImageJ Execution Platform Linux Mac Windows Implementation … Local Thickness (ImageJ) … |
| Fiji |
3 |
|
2D, 3D, multi-channel, time-series |
|
Software |
… http://fiji.sc/Fiji:About) Description Fiji is just ImageJ: a distribution of ImageJ (and ImageJ2) together with Java, Java 3D and a lot of … Fiji is just ImageJ: a distribution of ImageJ (and ImageJ2) together with Java, Java 3D and a lot of … |
| Interactive Rigid (ImageJ) |
3 |
|
2D |
ImageJ |
Software |
… Type Component Author Stephan Saalfeld Requires ImageJ Execution Platform Linux Mac Windows Implementation … Interactive Rigid (ImageJ) … |
| Graylevel Watershed for ImageJ |
3 |
|
2D |
ImageJ |
Software |
… Type Component Author Daniel Sage Requires ImageJ Execution Platform Linux Mac Windows Implementation … Graylevel Watershed for ImageJ … |
| Slice Labeler (ImageJ) |
3 |
|
3D, time-series |
ImageJ |
Software |
… Type Component Author Pedro Ramos-Cabrer Requires ImageJ Execution Platform Linux Mac Windows Implementation … Slice Labeler (ImageJ) … |
| MTrack2 (ImageJ) |
3 |
|
2D, time-series |
ImageJ |
Software |
… Author Nico Stuurman Johannes Schindelin Requires ImageJ Execution Platform Linux Mac Windows Implementation … MTrack2 (ImageJ) … |
| Linear Stack Alignment with SIFT (ImageJ) |
3 |
|
3D |
ImageJ |
Software |
… Type Component Author Stephan Saalfeld Requires ImageJ Execution Platform Linux Mac Windows Implementation … Linear Stack Alignment with SIFT (ImageJ) … |
| Interactive Moving Least Squares (ImageJ) |
3 |
|
2D |
ImageJ |
Software |
… Type Component Requires ImageJ Execution Platform Linux Mac Windows Implementation … Interactive Moving Least Squares (ImageJ) … |
| Granulometric Filtering (ImageJ) |
3 |
|
2D |
ImageJ |
Software |
… Type Component Author Dimiter Prodanov Requires ImageJ Execution Platform Linux Mac Windows Implementation … Granulometric Filtering (ImageJ) … |
| RGB-Gray Merge (ImageJ) |
3 |
|
2D, 3D |
ImageJ |
Software |
… Type Component Requires ImageJ Execution Platform Linux Mac Windows Implementation … RGB-Gray Merge (ImageJ) … |
| LSM Toolbox (ImageJ) |
3 |
|
3D |
ImageJ |
Software |
… Author Patrick Pirrotte Jerome Mutterer Requires ImageJ Execution Platform Linux Mac Windows Implementation … LSM Toolbox (ImageJ) … |
| 3D PSF estimator |
3 |
|
3D |
ImageJ, Fiji, MosaicSuite |
Software |
… Component Author Jannick Cardinale Mosaic group Requires ImageJ Fiji MosaicSuite Execution Platform Linux Mac Windows … License/Openness Free and open source Description This ImageJ plugin creates high resolution PSF images by averaging … 17:00 Download Page http://mosaic.mpi-cbg.de/?q=downloads/imageJ Documentation Link … |
| (Z,T,C) Stitcher |
2.924 |
|
3D, multi-channel, time-series |
ImageJ |
Software |
… Type Component Author Sébastien Tosi Requires ImageJ Execution Platform Linux Mac Windows Programming Language ImageJ Macros Supported image dimension 3D multi-channel … - 15:32 Last modified 04/28/2023 - 16:40 Download Page ImageJ macro - (Z,T,C) Stitcher Documentation Link … |
| BigStitcher |
2.888 |
|
2D, 3D, multi-channel, time-series |
ImageJ, BigDataViewer, ImgLib2 |
Software |
… Preibisch Stephan orcid.org/0000-0002-0276-494X Requires ImageJ BigDataViewer ImgLib2 Execution Platform Linux Mac … Last modified 10/27/2025 - 08:39 Download Page https://imagej.net/BigStitcher Documentation Link https://imagej.net/BigStitcher#Documentation Backlinks … |
| Microtubule Length Analysis |
2.811 |
|
2D, 3D |
Fiji, Tubeness |
Software |
… Execution Platform Linux Mac Windows Programming Language ImageJ Macros Supported image dimension 2D 3D Interaction … length can be estimated. Script Workflow is written as an ImageJ macro (Fiji) with following steps: 1. The enhancement … length can be estimated. Script Workflow is written as an ImageJ macro (Fiji) with following steps: 1. The enhancement … |
| MicrotubuleTracker in FIJI |
2.736 |
|
2D, 3D, time-series |
Fiji |
Software |
… Last modified 05/03/2023 - 10:36 Download Page http://imagej.net/MicrotubuleTracker Documentation Link http://imagej.net/MicrotubuleTracker Usage Example Link http://imagej.net/MicrotubuleTracker Backlinks … |
| Find Focused Slices |
2 |
|
3D |
ImageJ |
Software |
… Type Component Author Qingzong TSENG Requires ImageJ Execution Platform Linux Mac Windows Implementation … License/Openness Free and open source Description An ImageJ plugin for selecting a plane in focus among multiple … An ImageJ plugin for selecting a plane in focus among multiple … |
| ijblob |
2 |
|
2D |
ImageJ |
Software |
… Type Component Author Thorsten Wagner Requires ImageJ Execution Platform Linux Mac Windows Implementation … ##Reference Wagner, T and Lipinski, H 2013. IJBlob: An ImageJ Library for Connected Component Analysis and Shape … ##Reference Wagner, T and Lipinski, H 2013. IJBlob: An ImageJ Library for Connected Component Analysis and Shape … |
| VSI File Extractor (ImageJ) |
2 |
|
2D |
Fiji |
Software |
… VSI File Extractor (ImageJ) … |
| FeatureJ Laplacian |
2 |
|
2D, 3D |
ImageJ |
Software |
… Type Component Author Erik Meijering Requires ImageJ Execution Platform Linux Mac Windows Implementation … XYZ-T-Ch1, XYZT-C1-C2 images. Distributed as a part of ImageJ plugin FeatureJ , and included in Fiji. The second URL … Backlinks Particle Tracking (ImageJ) / Workflow Spot Detection 3D Hessian (ImageJ) / … |
| Adiposoft |
2 |
|
2D |
ImageJ |
Software |
… Martínez Fermín Milagro Carlos Ortiz-de-Solórzano Requires ImageJ Execution Platform Linux Mac Windows Implementation … |
| ImageJ Plugin Ridge Detection |
2 |
|
|
Fiji |
Software |
… ImageJ Plugin Ridge Detection … |
| GDSC Single Molecule Localisation Microscopy |
2 |
|
2D |
ImageJ |
Software |
… Type Component Author Alex Herbert Requires ImageJ Execution Platform Linux Mac Windows Implementation … Last modified 05/02/2023 - 12:19 Download Page GDSC-SMLM ImageJ Plugins DOI link … |
| Hough Circles |
2 |
|
2D |
ImageJ |
Software |
… Author Hemerson Pistori, Eduardo Rocha Costa Requires ImageJ Execution Platform Linux Mac Windows Implementation … Last modified 10/21/2019 - 10:59 Download Page https://imagej.nih.gov/ij/plugins/hough-circles.html Backlinks … |
| Fourier Ring Correlation |
2 |
|
|
ImageJ |
Software |
… Type Component Author Olivier Burri Alex Herbert Requires ImageJ Execution Platform Linux Mac Windows Implementation … Last modified 10/21/2019 - 10:44 Download Page http://imagej.net/Fourier_Ring_Correlation_Plugin Reference … |
| iTrack4U |
2 |
|
2D, time-series |
ImageJ, jMathPlot |
Software |
… Type Component Author Fabrice P. Cordelières Requires ImageJ jMathPlot Execution Platform Linux Mac Windows … Description iTrack4U is a Java-based software using ImageJ and jMathPlot libraries, which aims at … iTrack4U is a Java-based software using ImageJ and jMathPlot libraries, which aims at … |
| SIMcheck |
2 |
|
2D, 3D, multi-channel |
ImageJ |
Software |
… Schermelleh, Lothar orcid.org/0000-0002-1612-9699 Requires ImageJ Execution Platform Linux Mac Windows Implementation … and open source License GPL Description SIMcheck is an ImageJ plugin suite for assessing the quality and reliability … SIMcheck is an ImageJ plugin suite for assessing the quality and reliability … |
| gradient by Philippe Thévenaz |
2 |
|
2D |
ImageJ |
Software |
… Type Component Author Philippe Thévenaz Requires ImageJ Execution Platform Linux Mac Windows Programming Language Java is compatible with ImageJ Macro Supported image dimension 2D Interaction Level … |
| AnaMorf |
2 |
|
2D, multi-channel, time-series |
ImageJ |
Software |
… Type Component Author David J. Barry Requires ImageJ Execution Platform Linux Mac Windows Programming … source Description AnaMorf is a plug-in developed for the ImageJ platform to analyse the microscopic morphology of … AnaMorf is a plug-in developed for the ImageJ platform to analyse the microscopic morphology of … |
| Laplacian by Philippe Thévenaz |
2 |
|
2D |
ImageJ |
Software |
… Type Component Author Philippe Thévenaz Requires ImageJ Execution Platform Linux Mac Windows Programming Language Java is compatible with ImageJ Macro Supported image dimension 2D Interaction Level … |
| Hessian by Philippe Thévenaz |
2 |
|
2D |
ImageJ |
Software |
… Type Component Author Philippe Thévenaz Requires ImageJ Execution Platform Linux Mac Windows Programming Language Java is compatible with ImageJ Macro Supported image dimension 2D Interaction Level … |
| NeuronMetrics |
2 |
|
2D |
|
Software |
… Type plugin Programming Language Java is compatible with ImageJ Supported image dimension 2D Interaction Level … as a set of modules that run in the open-source program ImageJ. NeuronMetrics features a novel method for estimating … as a set of modules that run in the open-source program ImageJ. NeuronMetrics features a novel method for estimating … |
| GDSC plugins |
2 |
|
|
Fiji |
Software |
… 17:08 Last modified 12/16/2018 - 16:47 Download Page GDSC ImageJ Plugins Documentation Link Source code FindFoci manual … |
| intelligent Matrix Screener Remote Control |
2 |
|
2D, 3D, multi-channel, time-series |
|
Software |
… Implementation Type standalone web is compatible with ImageJ Matlab Image Processing Toolbox Supported image … of Leica microscopes (via CAM), image analysis (e.g. via ImageJ, Matlab), and adaptive automatic screening of … of Leica microscopes (via CAM), image analysis (e.g. via ImageJ, Matlab), and adaptive automatic screening of … |
| BigDataViewer |
2 |
|
2D, 3D, multi-channel, time-series |
ImgLib2 |
Software |
… Last modified 01/30/2018 - 12:34 Download Page https://imagej.net/BigDataViewer Documentation Link https://imagej.net/BigDataViewer#Usage Reference Publication Link … |
| 2D brain slice region annotation: SliceMap |
2 |
|
2D |
|
Software |
… by an automated region annotation tool. SliceMap is a FIJI/ImageJ plugin for automated brain region annotation of … the sample. The resulting brain regions are saved as FIJI/ImageJ ROI’s (Regions Of Interest) as a single zip-file for … by an automated region annotation tool. SliceMap is a FIJI/ImageJ plugin for automated brain region annotation of … |
| kymograph generation |
2 |
|
|
ImageJ |
Software |
… Type Component Requires ImageJ Implementation Type plugin Interaction Level … Semi-automated Description Kymograph generation under ImageJ: one simple solution, plot a line (ROI line) on the … Kymograph generation under ImageJ: one simple solution, plot a line (ROI line) on the … |
| bleb dynamics |
2 |
|
2D, multi-channel, time-series |
Gaussian blur in ImageJ, Otsu Thresholding, radial reslice, kymograph generation |
Software |
… Arcos Juan Manuel Maurin Mathieu Requires Gaussian blur in ImageJ Otsu Thresholding radial reslice kymograph generation … Execution Platform Linux Mac Windows Programming Language ImageJ Macros Supported image dimension 2D multi-channel … |
| cvMatch_Template |
2 |
|
2D |
ImageJ, OpenCV |
Software |
… Type Component Requires ImageJ OpenCV Implementation Type plugin Programming Language … Download Page Template Matching and Slice Alignment--- ImageJ Plugins Documentation Link Tutorial for … |
| Align slices in stack |
2 |
|
2D, time-series |
ImageJ |
Software |
… Type Component Requires ImageJ Execution Platform Linux Mac Windows Implementation … Download Page Template Matching and Slice Alignment--- ImageJ Plugins Documentation Link Tutorial for Align slices … |
| Tracking2.0 |
2 |
|
2D, 3D |
ImageJ, Jama |
Software |
… Type Component Author Paul-Gilloteaux Perrine Requires ImageJ Jama Execution Platform Linux Mac Windows … Type plugin Programming Language Java is compatible with ImageJ Macro Supported image dimension 2D 3D Interaction … |
| Quantification of outer ring diameters of centriole or PCM proteins of cycling HeLa cells in interphase |
2 |
|
2D, 3D, multi-channel |
ImageJ, R Project for Statistical Computing, Maximum Entropy Threshold (ImageJ), Analyze Particles, OMERO.insight-ij client |
Software |
… Type Workflow Author Open Microscopy Environment Requires ImageJ R Project for Statistical Computing Maximum Entropy Threshold (ImageJ) Analyze Particles OMERO.insight-ij client Execution … |
| Minimum cost Z surface projection |
2 |
|
3D |
Fiji |
Software |
… Last modified 10/18/2018 - 15:16 Download Page https://imagej.net/Minimum_Cost_Z_surface_Projection Documentation Link https://imagej.net/Minimum_Cost_Z_surface_Projection Backlinks … |
| Jython for ImageJ |
2 |
|
|
|
Software |
… Jython for ImageJ … |
| SpotDetectionIJ |
2 |
|
2D |
ImageJ, FeatureJ Laplacian, Find Maxima |
Software |
… Type Workflow Author Tosi Sebastien Requires ImageJ FeatureJ Laplacian Find Maxima Execution Platform … Windows Implementation Type plugin Programming Language ImageJ Macros Supported image dimension 2D Interaction Level … |
| shinyHTM |
2 |
|
2D, 3D, multi-channel, time-series |
|
Software |
… significance Image visualization relies on Fiji/ImageJ, along with its wealth of analytical tools. shinyHTM … used to analyze image features obtained with CellProfiler, ImageJ or any other bioimage analysis software. The output of … significance Image visualization relies on Fiji/ImageJ, along with its wealth of analytical tools. shinyHTM … |
| 3Dscript |
2 |
|
3D, multi-channel |
ImageJ |
Software |
… Type Collection Author Schmid, Benjamin Requires ImageJ Execution Platform Linux Mac Windows Implementation … 2-Clause License Description 3Dscript is a plugin for Fiji/ImageJ for creating 3D and 4D animations of microscope data. … 3Dscript is a plugin for Fiji/ImageJ for creating 3D and 4D animations of microscope data. … |
| Spots colocalization (ComDet) |
2 |
|
2D, multi-channel |
ImageJ, Jama |
Software |
… Type Collection Author Eugene Katrukha Requires ImageJ Jama Execution Platform Linux Mac Windows … Page Fiji Update Site Documentation Link Wiki@Github @ImageJ.net Usage Example Link How to use plugin (Text … |
| GaussFit OnSpot |
2 |
|
2D |
ImageJ |
Software |
… Author Peter Haub Tobias Meckel Nico Stuurman Requires ImageJ Execution Platform Linux Mac Windows Implementation … License GPL Description quote: GaussFit_OnSpot is an ImageJ plugin for fitting Gaussian profiles onto selected … quote: GaussFit_OnSpot is an ImageJ plugin for fitting Gaussian profiles onto selected … |
| BoneJ |
2 |
|
2D, 3D |
ImageJ |
Software |
… Type Collection Author Michael Doube Requires ImageJ Execution Platform Linux Mac Windows Implementation Type plugin is compatible with ImageJ Supported image dimension 2D 3D Interaction Level … |
| MetroloJ |
2 |
|
2D, 3D, multi-channel |
ImageJ |
Software |
… Author Cordelières Fabrice P Matthews Cédric Requires ImageJ Execution Platform Mac Windows Implementation Type … MetroloJ plugin Reference Publication Link MetroloJ: an ImageJ plugin to help monitor microscopes’ health. Backlinks … |
| Watershed (ImageJ ij-1.52i) |
2 |
|
|
|
Software |
… Watershed (ImageJ ij-1.52i) … |
| Maximum (3D) VIB Protocol |
2 |
|
3D |
ImageJ, VIB Protocol |
Software |
… Author Schmid, Benjamin Schindelin, Johannes Requires ImageJ VIB Protocol Execution Platform Linux Mac Windows … Github Documentation Link Minimum/Maximum/Median page at ImageJ.net website Backlinks … |
| ContourLines |
2 |
|
2D |
ImageJ, Fiji |
Software |
… Type Component Author Eugene Katrukha Requires ImageJ Fiji Execution Platform Linux Mac Windows … Free and open source License MIT Description ImageJ/FIJI plugin generating contour lines with equal … ImageJ/FIJI plugin generating contour lines with equal … |
| Automated workflow for parallel Multiview Reconstruction |
2 |
|
3D, multi-channel, time-series |
Fiji, Snakemake |
Software |
|
| MicrobeJ |
2 |
|
2D, 3D, multi-channel |
ImageJ |
Software |
… Author Adrien Ducret, Yves Brun, Ellen Quardokus Requires ImageJ Execution Platform Linux Mac Windows Implementation … Free and open source Description This is an ImageJ plugin to analyze bacterial cells. It provides a … This is an ImageJ plugin to analyze bacterial cells. It provides a … |
| ThunderSTORM |
2 |
|
2D, 3D |
ImageJ |
Software |
… P. Krízek J. Borkovec Z. vindrych G. M. Hagen Requires ImageJ Execution Platform Linux Mac Windows Implementation … is an open-source, interactive, and modular plug-in for ImageJ designed for automated processing, analysis, and … is an open-source, interactive, and modular plug-in for ImageJ designed for automated processing, analysis, and … |
| PSFj |
2 |
|
|
|
Software |
… standalone Programming Language Java is compatible with ImageJ License/Openness Free and open source License GPL 3.0 … e.g. for image restoration purposes. PSFj is based on ImageJ and JAVA, and runs on Windows, Mac, and Linux PCs as a … e.g. for image restoration purposes. PSFj is based on ImageJ and JAVA, and runs on Windows, Mac, and Linux PCs as a … |
| BioImage Model Zoo |
2 |
|
2D, 3D, multi-channel, time-series |
|
Software |
… compatible with Fiji ilastik ImJoy DeepImageJ StarDist - ImageJ Supported image dimension 2D 3D multi-channel … |
| Qualitative annotations Fiji plugins |
2 |
|
2D, 3D, multi-channel, time-series |
ImageJ, Fiji |
Software |
… Franz Gehrig Jochen orcid.org/0000-0002-1193-1324 Requires ImageJ Fiji Execution Platform Linux Mac Windows … Type plugin Programming Language Jython is compatible with ImageJ Fiji Supported image dimension 2D 3D multi-channel … |
| Local Z Projector |
2 |
|
3D, multi-channel, time-series |
ImgLib2, ImageJ 2.x |
Software |
… orcid.org/0000-0002-0998-4718 Valon Léo Requires ImgLib2 ImageJ 2.x Execution Platform Linux Mac Windows … |
| FLIM / SLIM Analysis |
2 |
|
2D, time-series |
ImageJ |
Software |
… Type Collection Author Paul Barber Requires ImageJ Execution Platform Linux Mac Windows Programming … |
| Blob segmentation |
2 |
|
2D |
Fiji, MorphoLibJ |
Software |
… Execution Platform Linux Mac Windows Programming Language ImageJ Macros Supported image dimension 2D Interaction Level … |
| MosaicExplorerJ |
2 |
|
2D, 3D |
ImageJ |
Software |
… Type Component Author Sebastien Tosi Requires ImageJ Execution Platform Linux Mac Windows Programming Language ImageJ Macros Supported image dimension 2D 3D Interaction … |
| Quantitative analysis of focal adhesions |
2 |
|
2D |
ImageJ, Log3D, CLAHE |
Software |
… Utku Horzum Berrin Ozdil Devrim Pesen-Okvur Requires ImageJ Log3D CLAHE Execution Platform Linux Mac Windows … open source Description Simple workflow description for ImageJ, step-by-step description for delineating focal … Simple workflow description for ImageJ, step-by-step description for delineating focal … |
| Microtubule end tracking in Drosophila Oocyte |
2 |
|
2D, time-series |
Fiji, TrackMate, Bleach Correction, Fourier Bandpass Filter, Temporal Medial Filter |
Software |
… e.g. using Image->Adjust->Bleach Correction in Fiji/ImageJ uneven illumination : Fourier bandpass filtering (e.g. … Temporal Median filter tracking : e.g. TrackMate in Fiji/ImageJ (segmentation using DoG detector) has function Object … e.g. using Image->Adjust->Bleach Correction in Fiji/ImageJ uneven illumination : Fourier bandpass filtering (e.g. … |
| ijRotatedCrop |
2 |
|
|
|
Software |
… box size and orientation(s). The RotCrop Plugins for ImageJ allow to perform rotated crop of 2D/3D images. In … crop has topic Bioimage informatics Additional keywords imagej-plugin Post date 10/25/2024 - 14:58 Last modified … box size and orientation(s). The RotCrop Plugins for ImageJ allow to perform rotated crop of 2D/3D images. In … |
| ABBA |
2 |
|
2D |
ImageJ |
Software |
… Nicolas (orcid.org/0000-0003-4722-6245) Requires ImageJ Execution Platform Linux Mac Windows Implementation … Type plugin Programming Language Java is compatible with ImageJ Supported image dimension 2D Interaction Level … |
| Autofocus |
2 |
|
3D |
ImageJ, Autofocus |
Software |
… Type Component Author Richard Mort Requires ImageJ Autofocus Execution Platform Linux Mac Windows Programming Language ImageJ Macros Supported image dimension 3D Interaction Level … |
| Blood vessel segmentation and network analysis |
2 |
|
3D |
Fiji |
Software |
… Execution Platform Linux Mac Windows Programming Language ImageJ Macros Supported image dimension 3D Interaction Level … - 15:09 Last modified 04/28/2023 - 16:16 Download Page ImageJ Macro: Blood vessel segmentation and network analysis … |
| ImmunoRatio |
2 |
|
2D |
ImageJ, Colour Deconvolution |
Software |
… Type Workflow Author Vilppu Tuominen Jorma Isola Requires ImageJ Colour Deconvolution Execution Platform Linux Mac … ER, PR, and Ki-67 immunohistochemistry ImmunoRatio is an ImageJ plugin to quantify haematoxylin and DAB-stained tissue … ER, PR, and Ki-67 immunohistochemistry ImmunoRatio is an ImageJ plugin to quantify haematoxylin and DAB-stained tissue … |
| Cells tracking in tissue |
2 |
|
|
ImageJ, MATLAB, Graylevel Watershed for ImageJ |
Software |
… Type Workflow Author Sébastien Tosi Requires ImageJ MATLAB Graylevel Watershed for ImageJ Interaction Level Automated License/Openness I do not … |
| White Balance |
2 |
|
|
ImageJ |
Software |
… Type Component Author Laurent Gelman Requires ImageJ Execution Platform Linux Mac Windows Interaction Level … Description The Macro processes a composite picture in ImageJ/Fiji and outputs a color-balanced merged RGB image. To … The Macro processes a composite picture in ImageJ/Fiji and outputs a color-balanced merged RGB image. To … |
| Noise Suppression using Simple Spatial Filters |
2 |
|
|
ImageJ |
Software |
… Type Component Author Graeme Ball Requires ImageJ Programming Language Java Interaction Level Automated … above describes the simple 2D spatial filters available in ImageJ, but similar filters are available in most software. … above describes the simple 2D spatial filters available in ImageJ, but similar filters are available in most software. … |
| Measuring confluence in adherent cell cultures |
2 |
|
|
ImageJ |
Software |
… Sharon OTooleb, John J. OLearya, Britta Stordal Requires ImageJ Interaction Level Automated License/Openness I do not … cell cultures over time and how to process these images in ImageJ to measure the area fraction (confluence). Entry … cell cultures over time and how to process these images in ImageJ to measure the area fraction (confluence). … |
| SparkMaster |
2 |
|
2D, time-series |
ImageJ |
Software |
… Aleksey V. Zima Lothar A. Blatter Donald M. Bers Requires ImageJ Execution Platform Linux Mac Windows Implementation … Free and open source Description Analyzing Ca2+ sparks ImageJ plugin to detect and measure Ca2+ sparks in linescan … Analyzing Ca2+ sparks ImageJ plugin to detect and measure Ca2+ sparks in linescan … |
| Uneven illumination correction |
2 |
|
|
CellProfiler, ImageJ |
Software |
… Type Workflow Author Tutorial under ImageJ: Gabriel Landini Requires CellProfiler ImageJ Interaction Level Automated License/Openness I do not … Tutorial under ImageJ: Gabriel Landini … |
| LIF Extractor |
2 |
|
3D |
ImageJ, Bio-Formats |
Software |
… Type Component Author Christophe Leterrier Requires ImageJ Bio-Formats Programming Language ImageJ Macros Supported image dimension 3D Interaction Level … |
| LIF Projector |
2 |
|
3D |
ImageJ, Bio-Formats |
Software |
… Type Component Author Christophe Leterrier Requires ImageJ Bio-Formats Programming Language ImageJ Macros Supported image dimension 3D Interaction Level … |
| Extract_Images |
2 |
|
2D, 3D, multi-channel, time-series |
ImageJ, LOCI Bioformats plugin |
Software |
… Type Component Author Christophe ????Leterrier Requires ImageJ LOCI Bioformats plugin Execution Platform Linux Mac Windows Programming Language ImageJ Macros Supported image dimension 2D 3D multi-channel … |
| 2D cell tracking and analysis of morphological dynamics |
2 |
|
2D, time-series |
ImageJ, QuimP |
Software |
… Epstein, K.I. Anderson and T. Bretschneider Requires ImageJ QuimP Execution Platform Linux Mac Windows Supported … |
| Find, Draw and Measure Wells in a Multi-Well Plate Picture |
2 |
|
2D |
ImageJ |
Software |
… Type Component Author Laurent Gelman Requires ImageJ Execution Platform Linux Mac Windows Programming Language ImageJ Macros Supported image dimension 2D Interaction Level … |
| Performing a Fluorescence Recovery after Photobleaching (FRAP) experiment |
2 |
|
2D, time-series |
ImageJ, Excel |
Software |
… Ronald S. Petralia Ya-Xian Wang Bechara Kachar Requires ImageJ Excel Supported image dimension 2D time-series … and subsequently analyzed. This includes steps in ImageJ and subsequent normalization of the intensity data. … and subsequently analyzed. This includes steps in ImageJ and subsequent normalization of the intensity data. … |
| ImmunoMembrane |
2 |
|
2D |
ImageJ |
Software |
… Type Component Author Vilppu Tuominen Jorma Isola Requires ImageJ Execution Platform Linux Mac Windows Implementation … |
| Leaf Segmentation using Trainable Weka Segmentation plugin |
2 |
|
2D |
Fiji |
Software |
… Execution Platform Linux Mac Windows Programming Language ImageJ Macros Supported image dimension 2D Interaction Level … example macro introduced in the documentation page of the ImageJ plugin Trainable Weka Segmentation (in Fiji, it's … example macro introduced in the documentation page of the ImageJ plugin Trainable Weka Segmentation (in Fiji, it's … |
| CytooChip Analysis |
2 |
|
2D |
ImageJ |
Software |
… Type Workflow Author Sébastien Requires ImageJ Execution Platform Linux Mac Windows Programming Language ImageJ Macros Supported image dimension 2D Interaction Level … |
| Root tools |
2 |
|
2D |
ImageJ |
Software |
… Type Workflow Author Volker Baecker Requires ImageJ Execution Platform Linux Mac Windows Implementation Type plugin Programming Language ImageJ Macros Supported image dimension 2D Interaction Level … |
| OpenComet |
2 |
|
2D |
ImageJ |
Software |
… Author Benjamin Gyori Gireedhar Venkatachalam Requires ImageJ Execution Platform Linux Mac Windows Programming … does not match with this orientation (Rotate images, Using ImageJ/Transform Image or TransformJ plugin for example). … does not match with this orientation (Rotate images, Using ImageJ/Transform Image or TransformJ plugin for example). … |
| ADAPT |
2 |
|
2D, time-series |
ImageJ |
Software |
… Type Component Author Dave Barry Requires ImageJ Execution Platform Linux Mac Windows Implementation … Analysis of ProTrusions) is a plug-in developed for the ImageJ/Fiji platform to automatically detect and analyse cell … Analysis of ProTrusions) is a plug-in developed for the ImageJ/Fiji platform to automatically detect and analyse cell … |
| Image Stitching |
2 |
|
2D, 3D, multi-channel, time-series |
ImageJ, EBImage tile |
Software |
… Type Component Author Preibisch Stephan Requires ImageJ EBImage tile Execution Platform Linux Mac Windows … http://fiji.sc/Image_Stitching Documentation Link https://imagej.net/Image_Stitching Reference Publication Link … |
| Graph Cut |
2 |
|
|
ImageJ, Graph Cut |
Software |
… Type Component Author Funke Jan Requires ImageJ Graph Cut Execution Platform Linux Mac Windows … Page http://fiji.sc/Graph_Cut Documentation Link https://imagej.net/Graph_Cut Reference Publication Link Based on this … |
| Chess |
2 |
|
|
ImageJ |
Software |
… Type Component Requires ImageJ Execution Platform Linux Mac Windows Implementation … Type plugin Programming Language Jython is compatible with ImageJ Interaction Level Automated License/Openness Free and … |
| RATS: Robust Automatic Threshold Selection |
2 |
|
2D |
ImageJ |
Software |
… Type Component Author Ben Tupper Requires ImageJ Execution Platform Linux Mac Windows Implementation … Documentation Link https://imagej.net/RATS:_Robust_Automatic_Threshold_Selection … |
| Colour Deconvolution |
2 |
|
2D |
Fiji |
Software |
… colour deconvolution plugin ( java and class files ) for ImageJ and Fiji implements stain separation using Ruifrok and … colour deconvolution plugin ( java and class files ) for ImageJ and Fiji implements stain separation using Ruifrok and … |
| Analyze Skeleton 2D time series |
2 |
|
time-series |
ImageJ, ImageJ Analyze Skeleton |
Software |
… Type Component Requires ImageJ ImageJ Analyze Skeleton Execution Platform Linux Mac Windows … |
| Test Java3D |
2 |
|
3D |
ImageJ |
Software |
… Type Component Author Schmid Benjamin Requires ImageJ Execution Platform Linux Mac Windows Implementation … Page http://fiji.sc/Test_Java3D Documentation Link https://imagej.net/Test_Java3D Backlinks … |
| Upload Sample Image |
2 |
|
|
ImageJ |
Software |
… Type Component Author Johannes Schindelin Requires ImageJ Execution Platform Linux Mac Windows Interaction Level … is used to upload a file (not just images) meant for the ImageJ developers. You might need to do this e.g. when the … It is used to upload a file (not just images) meant for the ImageJ developers. You might need to do this e.g. when the … |
| Auto Threshold |
2 |
|
2D |
Fiji |
Software |
… Last modified 04/25/2023 - 19:22 Download Page https://imagej.net/Auto_Threshold Documentation Link https://imagej.net/plugins/auto-threshold Usage Example Link see … |
| BUnwarpJ |
2 |
|
2D |
ImageJ |
Software |
… Type Component Author Ignacio Arganda-Carreras Requires ImageJ Execution Platform Linux Mac Windows Implementation … Page http://fiji.sc/BUnwarpJ Documentation Link https://imagej.net/BUnwarpJ Backlinks … |
| Dynamic ROI Profiler |
2 |
|
2D |
Fiji |
Software |
|
| Cicardian Gene Expression |
2 |
|
2D, time-series |
ImageJ |
Software |
… Type Component Author Daniel Sage Requires ImageJ Execution Platform Linux Mac Windows Implementation … License/Openness Free and open source Description "This ImageJ plugin (CGE) is a semi-automatic tool to detect and … "This ImageJ plugin (CGE) is a semi-automatic tool to detect and … |
| Stitching 2D/3D |
2 |
|
2D, 3D |
ImageJ |
Software |
… Type Component Author Preibisch Stephan Requires ImageJ Execution Platform Linux Mac Windows Implementation … http://fiji.sc/Stitching_2D/3D Documentation Link https://imagej.net/Stitching_2D/3D Reference Publication Link … |
| SteerableJ |
2 |
|
2D |
ImageJ |
Software |
… Type Component Author François Aguet Requires ImageJ Execution Platform Linux Mac Windows Implementation Type plugin is compatible with ImageJ Supported image dimension 2D Interaction Level … |
| Differentials |
2 |
|
2D |
ImageJ |
Software |
… Type Component Author Philippe Thévenaz Requires ImageJ Execution Platform Linux Mac Windows Implementation … Six 2D differential operations are implemented in this ImageJ plugin. - Gradient Magnitude - Gradient Direction - … Six 2D differential operations are implemented in this ImageJ plugin. - Gradient Magnitude - Gradient Direction - … |
| FijiArchipelago |
2 |
|
|
ImageJ |
Software |
… Type Component Author Larry Lindsey Requires ImageJ Execution Platform Mac Windows Implementation Type … designed to make it easy for programmers to export Fiji/ImageJ functionality over a network to several other … designed to make it easy for programmers to export Fiji/ImageJ functionality over a network to several other … |
| Multithreaded Image Processing |
2 |
|
|
ImageJ |
Software |
… Type Component Requires ImageJ Execution Platform Linux Mac Windows Interaction Level … Last modified 10/16/2019 - 15:19 Download Page https://imagej.net/Multithreaded_Image_Processing_in_Clojure Backlinks … |
| Spheres and Tubes in 3D |
2 |
|
3D |
ImageJ, 3D Viewer |
Software |
… Type Component Requires ImageJ 3D Viewer Execution Platform Linux Mac Windows … Free and open source Description An example ImageJ plugin illustrating how to create and display 3D tubes … An example ImageJ plugin illustrating how to create and display 3D tubes … |
| 3D Viewer |
2 |
|
3D |
ImageJ, 3D Viewer |
Software |
… Author Schmid Benjamin Schindelin Johannes Requires ImageJ 3D Viewer Execution Platform Linux Mac Windows … Page http://fiji.sc/3D_Viewer Documentation Link https://imagej.net/3D_Viewer:_User_FAQs Reference Publication Link … |
| TrakEM2 |
2 |
|
2D, 3D |
ImageJ, 3D Viewer |
Software |
… Albert Cardona Stephan Saalfeld Curtis Rueden Requires ImageJ 3D Viewer Execution Platform Linux Mac Windows … and open source License GPLv3 Description TrakEM2 is an ImageJ plugin for morphological data mining, … TrakEM2 is an ImageJ plugin for morphological data mining, … |
| FlowJ |
2 |
|
2D, time-series |
ImageJ, Fiji |
Software |
… Author Michael Abràmoff Jean-Yves Tinevez Requires ImageJ Fiji Execution Platform Linux Mac Windows … |
| CIDRE |
2 |
|
2D, time-series |
ImageJ, MATLAB |
Software |
… Type Collection Author Kevin Smith Requires ImageJ MATLAB Execution Platform Linux Mac Windows is compatible with ImageJ MATLAB Supported image dimension 2D time-series … |
| Parallel Iterative Deconvolution |
2 |
|
2D, 3D |
ImageJ, Huygens, PSF Generator |
Software |
… Type Component Author Piotr Wendykier Requires ImageJ Huygens PSF Generator Execution Platform Linux Mac … know License/Openness Free and open source Description An ImageJ plugin for iterative deblurring. has function Image … An ImageJ plugin for iterative deblurring. … |
| SpotDistance |
2 |
|
3D |
ImageJ |
Software |
… Type Component Author Daniel Sage Requires ImageJ Execution Platform Linux Mac Windows Implementation … License/Openness Free and open source Description An ImageJ plugin for evaluate intra-nuclear 3D cross-distances … An ImageJ plugin for evaluate intra-nuclear 3D cross-distances … |
| Shepp-Logan Phantom |
2 |
|
2D |
ImageJ |
Software |
… Type Component Author Philippe Thévenaz Requires ImageJ Execution Platform Linux Mac Windows Implementation … Link http://bigwww.epfl.ch/thevenaz/shepplogan/ https://imagej.net/Shepp-Logan_Phantom Reference Publication Link The … |
| Colour merge |
2 |
|
|
ImageJ |
Software |
… Type Component Requires ImageJ Interaction Level Automated License/Openness I do not … Last modified 12/20/2018 - 18:37 Download Page https://imagej.net/Colour_merge Backlinks … |
| mcib3d library |
2 |
|
3D |
Icy MereoTopology |
Software |
… Plugins for 3D Image processing and Analyisis in ImageJ. Previously (?) known as 3D ImageJ Suite . has function Image analysis Image segmentation … Plugins for 3D Image processing and Analyisis in ImageJ. Previously (?) known as 3D ImageJ Suite . … |
| Delayed Snapshot |
2 |
|
2D |
ImageJ, Fiji |
Software |
… Type Component Author Albert Cardona Requires ImageJ Fiji Execution Platform Linux Mac Windows … Bioimage informatics Additional keywords screen capturing ImageJ Jython Entry Curator migration Post date 10/11/2013 - … |
| Shape Index Map |
2 |
|
2D, 3D, multi-channel, time-series |
ImageJ |
Software |
… Type Component Author Johannes Schindelin Requires ImageJ Execution Platform Linux Mac Windows Supported image … Download Page http://fiji.sc/ Documentation Link https://imagej.net/Shape_Index_Map Backlinks … |
| Cover Maker |
2 |
|
|
ImageJ |
Software |
… Author Tomancak, Pavel Schindelin, Johannes Requires ImageJ Execution Platform Linux Mac Windows Implementation … Last modified 10/15/2019 - 18:27 Download Page https://imagej.net/Cover_Maker Backlinks … |
| MIJ |
2 |
|
|
ImageJ, MATLAB |
Software |
… Type Component Author Daniel Sage Requires ImageJ MATLAB Execution Platform Linux Mac Windows … and open source Description A Java package for running ImageJ and Fiji within Matlab. has function Conversion has … A Java package for running ImageJ and Fiji within Matlab. … |
| Colocalization Test |
2 |
|
|
ImageJ |
Software |
… Type Component Author Daniel James White Requires ImageJ Interaction Level Automated License/Openness I do not … Last modified 12/20/2018 - 18:39 Download Page https://imagej.net/Colocalization_Test Backlinks … |
| Volume Viewer |
2 |
|
3D |
ImageJ, Fiji |
Software |
… Type Component Author Kai Uwe Barthel Requires ImageJ Fiji Execution Platform Linux Mac Windows … http://fiji.sc/Volume_Viewer Documentation Link http://imagej.net/plugins/volume-viewer.html Backlinks … |
| Time Stamper |
2 |
|
time-series |
ImageJ |
Software |
… Type Component Author White Daniel James Requires ImageJ Execution Platform Linux Mac Windows Implementation … http://fiji.sc/Time_Stamper Documentation Link https://imagej.net/Time_Stamper Backlinks … |
| Mixture Modeling Thresholding |
2 |
|
2D |
ImageJ, Histogram |
Software |
… Component Author Christopher Mei, Maxime Dauphin Requires ImageJ Histogram Execution Platform Linux Mac Windows … modified 10/16/2019 - 16:47 Documentation Link https://imagej.net/Mixture_Modeling_Thresholding Backlinks … |
| Bleach Correction |
2 |
|
2D, 3D, time-series |
ImageJ |
Software |
… Type Component Author Kota Miura Jens Rietdorf Requires ImageJ Execution Platform Linux Mac Windows Implementation … Reference Publication Link Bleach correction ImageJ plugin for compensating the photobleaching of … |
| Strahler Analysis |
2 |
|
2D, 3D |
ImageJ, Skeletonize3D, ImageJ Analyze Skeleton |
Software |
… Type Component Author Tiago Ferreira Requires ImageJ Skeletonize3D ImageJ Analyze Skeleton Execution Platform Linux Mac Windows … |
| Helmholtz Analysis |
2 |
|
|
ImageJ, Fiji |
Software |
… Author Dougherty Bob Schindelin Johannes Requires ImageJ Fiji Execution Platform Linux Mac Windows … Helmholtz Analysis Explanation of the Helmholtz Analysis ImageJ Plugin Reference Publication Link Measurement of … |
| ImarisXT |
2 |
|
|
ImageJ, Imaris, MATLAB, ImarisCell, ImarisMeasurementPro, ImarisTrack, ImarisFilamentTracer, Python |
Software |
… Type Component Author Oxford Instruments Requires ImageJ Imaris MATLAB ImarisCell ImarisMeasurementPro … http://www.bitplane.com/imaris/imarisxt Documentation Link ImageJ and Fiji Support in ImarisXT Backlinks … |
| Background Subtractor |
2 |
|
|
Fiji, MosaicSuite |
Software |
… know Description Histogram-based background subtractor for ImageJ. The implemented algorithm is based on the assumption … 14:31 Download Page http://mosaic.mpi-cbg.de/?q=downloads/imageJ Documentation Link … Histogram-based background subtractor for ImageJ. The implemented algorithm is based on the assumption … |
| Convolve with 2D Bessel function |
2 |
|
|
ImageJ |
Software |
… Type Component Requires ImageJ Execution Platform Linux Mac Windows Implementation … 18:03 Download Page http://mosaic.mpi-cbg.de/?q=downloads/imageJ Documentation Link … |
| OMERO.insight-ij client |
2 |
|
|
ImageJ, OMERO |
Software |
… Type Component Requires ImageJ OMERO Interaction Level Automated License/Openness I … enmicroscopy.org/site/support/omero5/users/client-tutorials/imagej… Backlinks Quantification of outer ring diameters of … |
| PSF Tool 2D |
2 |
|
2D |
ImageJ |
Software |
… Type Component Requires ImageJ Execution Platform Linux Mac Windows Implementation … 11:31 Download Page http://mosaic.mpi-cbg.de/?q=downloads/imageJ Documentation Link tutorial pdf Backlinks … |
| Endrov |
2 |
|
|
ICY Annotation, OMERO, Processing, ImgLib2, ImgLib2 |
Software |
… C. elegans embryogenesis. It was decided to not base it on ImageJ because little of it could be reused, many of the … be useful for all image processing and be able to replace ImageJ. Entry Curator kota Post date 10/23/2013 - 02:47 Last … C. elegans embryogenesis. It was decided to not base it on ImageJ because little of it could be reused, many of the … |
| MATLAB |
1 |
|
2D, 3D, multi-channel, time-series |
ImageJ Feature Extraction, Connected Components |
Software |
… Type Collection Author Mathworks Requires ImageJ Feature Extraction Connected Components Execution … |
| Microscope Image Correlation Spectroscopy MICS |
1 |
|
2D, time-series |
ImageJ |
Software |
… Chen Paul-Gilloteaux Perrine Waharte François Requires ImageJ Execution Platform Linux Mac Windows Implementation … |
| ICS tools |
1 |
|
|
ImageJ |
Software |
… Type Collection Author Fitz Elliott Requires ImageJ Execution Platform Linux Mac Windows Implementation … |
| FindFoci |
1 |
|
2D, 3D |
Spot Detection (KNIME) |
Software |
… Page http://www.sussex.ac.uk/gdsc/intranet/microscopy/imagej/findfoci Documentation Link pdf Reference Publication … |
| MTrackJ |
1 |
|
|
ImageJ, ImageScience.jar |
Software |
… Type Component Author Erik Meijering Requires ImageJ ImageScience.jar Execution Platform Linux Mac Windows … |
| TransformJ |
1 |
|
2D, 3D |
ImageJ |
Software |
… Type Collection Author Erik Meijering Requires ImageJ Execution Platform Linux Mac Windows Implementation … |
| Find Maxima |
1 |
|
2D |
ImageJ |
Software |
… Type Component Author Michael Schmid Requires ImageJ Execution Platform Linux Mac Windows Supported image … comparison /find-maxima-python Backlinks Spot detection (ImageJ) / Workflow SpotDetectionIJ / Workflow … |
| TANGO Tools for Analysis of Nuclear Genome Organization |
1 |
|
3D |
|
Software |
… of Nuclear Genome Organization. It is composed of an ImageJ plugin for batch processing and analysis, and a R … of Nuclear Genome Organization. It is composed of an ImageJ plugin for batch processing and analysis, and a R … |
| FeatureJ Derivatives |
1 |
|
2D, 3D, multi-channel, time-series |
ImageJ |
Software |
… Type Component Author Erik Meijering Requires ImageJ Execution Platform Linux Mac Windows Implementation … |
| MosaicIA |
1 |
|
3D, time-series |
Fiji, MosaicSuite |
Software |
… Last modified 10/21/2019 - 11:06 Download Page http://imagej.net/MosaicIA Backlinks … |
| ABSnake |
1 |
|
2D, 3D |
ImageJ |
Software |
… Type Component Author P. Andrey T. Boudier Requires ImageJ Execution Platform Linux Mac Windows Implementation … |
| Grayscale granulometry |
1 |
|
|
|
Software |
… Automated License/Openness I do not know Description This imageJ/Fiji plugin provides an analysis of the granulometry … This imageJ/Fiji plugin provides an analysis of the granulometry … |
| MultiStackReg |
1 |
|
3D |
Fiji, TurboReg |
Software |
… License/Openness Free and open source Description This ImageJ plugin aligns the slices of a stack just like the … This ImageJ plugin aligns the slices of a stack just like the … |
| MosaicSuite |
1 |
|
2D, 3D, time-series |
Fiji, ImageJ 2.x |
Software |
… Urs Berger, Phillip Koumoutsakos, Petros Requires Fiji ImageJ 2.x Execution Platform Linux Mac Windows … |
| imageHTS |
1 |
|
|
Segmentation of Clustered Cells in MATLAB, ImageJ Feature Extraction |
Software |
… Huber Requires Segmentation of Clustered Cells in MATLAB ImageJ Feature Extraction Execution Platform Windows Linux … |
| Bigwarp |
1 |
|
2D, 3D, multi-channel |
|
Software |
… Last modified 03/06/2023 - 15:02 Download Page https://imagej.net/BigWarp Reference Publication Link Bogovic et al … |
| Micro-Manager |
1 |
|
|
ImageJ |
Software |
… Type Collection Requires ImageJ Interaction Level Automated License/Openness I do not … |
| Alignment of FIBSEM or SBFSEM images |
1 |
|
|
Fiji, Open Virtual stack in Fiji, TrakEM2, Create new TrakEM project in Fiji, import images into TrakEM, Linear Stack Alignment with SIFT (ImageJ) |
Software |
… images into TrakEM Linear Stack Alignment with SIFT (ImageJ) Interaction Level Semi-automated Post date 01/30/2018 … |
| MaMuT |
1 |
|
2D, 3D, multi-channel, time-series |
Fiji, BigDataViewer, TrackMate |
Software |
… Last modified 10/18/2018 - 17:38 Download Page https://imagej.net/MaMuT Reference Publication Link Reconstruction of … |
| Mean shift |
1 |
|
|
|
Software |
… Last modified 05/20/2018 - 18:28 Download Page https://imagej.nih.gov/ij/plugins/mean-shift.html Documentation Link … |
| Quality metric of 3D SPIM stacks |
1 |
|
|
|
Software |
… License/Openness Free and open source Description An ImageJ/Fiji macro which measures quality through two stacks … An ImageJ/Fiji macro which measures quality through two stacks … |
| Log3D |
1 |
|
2D, 3D |
ImageJ |
Software |
… Type Component Author Daniel Sage Requires ImageJ Execution Platform Linux Mac Windows Implementation … |
| Manual tracking with TrackMate |
1 |
|
2D, 3D, time-series |
Fiji |
Software |
… - 17:36 Download Page GitHub Documentation Link https://imagej.net/Manual_tracking_with_TrackMate Reference … |
| Detection of Molecules - DoM |
1 |
|
|
ImageJ |
Software |
… Type Collection Author Eugene Katrukha Requires ImageJ Execution Platform Linux Mac Windows Implementation … |
| pystackreg |
1 |
|
2D, 3D |
StackReg, TurboReg |
Software |
… Free and open source Description Python/C++ port of the ImageJ extension TurboReg/StackReg written by Philippe … Python/C++ port of the ImageJ extension TurboReg/StackReg written by Philippe … |
| BisQue |
1 |
|
2D, 3D, multi-channel, time-series |
|
Software |
… with Condor Analysis in MATLAB, Python, Java+ImageJ 100+ biological image formats Very large 5D images … with Condor Analysis in MATLAB, Python, Java+ImageJ 100+ biological image formats Very large 5D images … |
| ThreeB 3B Microscopy Analysis Software |
1 |
|
2D, time-series |
ImageJ |
Software |
… Molecular Biophysics at the Kings College London Requires ImageJ Execution Platform Windows Implementation Type plugin … |
| Microscope autopilot |
1 |
|
2D, 3D, multi-channel, time-series |
|
Software |
… Type library Programming Language Java is compatible with ImageJ Fiji Supported image dimension 2D 3D multi-channel … |
| IJ-OpenCV |
1 |
|
|
|
Software |
… modified 11/07/2018 - 15:05 Documentation Link https://imagej.net/IJ-OpenCV Backlinks … |
| SQUIRREL |
1 |
|
2D |
ImageJ, NanoJ |
Software |
… Henriques, Ricardo orcid.org/0000-0002-2043-5234 Requires ImageJ NanoJ Execution Platform Linux Mac Windows … |
| PTA2 |
1 |
|
2D |
Fiji |
Software |
|
| DeconvolutionLab2 |
1 |
|
3D |
ImageJ |
Software |
… Arne Guiet, Romain Vonesch, Cédric Unser, Michael Requires ImageJ Execution Platform Linux Mac Windows Implementation … |
| AssayScope |
1 |
|
2D, 3D, multi-channel, time-series |
|
Software |
… Windows Implementation Type standalone is compatible with ImageJ Supported image dimension 2D 3D multi-channel … |
| MIPs for PSFs |
1 |
|
3D |
ImageJ, Fiji |
Software |
… Type Component Author Laurent Gelman Jens Rietdorf Requires ImageJ Fiji Execution Platform Linux Mac Windows Programming … |
| ConfocalCheck |
1 |
|
2D, 3D, multi-channel, time-series |
ImageJ |
Software |
… Imm Dormann Dirk orcid.org/0000-0001-6309-7522 Requires ImageJ Execution Platform Mac Windows Implementation Type … |
| 3D vessel segmentation of synchrotron phase contrast tomography |
1 |
|
3D |
Fiji, ilastik |
Software |
|
| HAWK |
1 |
|
2D, 3D |
ImageJ |
Software |
… Type Component Author Marsh Richard Cox Susan Requires ImageJ Execution Platform Linux Mac Windows Implementation … |
| NanoJ |
1 |
|
2D, 3D |
ImageJ |
Software |
… Type Collection Requires ImageJ Execution Platform Linux Mac Windows Implementation … |
| Minimum (3D) Filter VIB Protocol |
1 |
|
3D |
VIB Protocol |
Software |
… Github Documentation Link Minimum/Maximum/Median page at ImageJ.net website Backlinks … |
| 3D Fill holes (mcib3d) |
1 |
|
3D |
mcib3d library, ImageJ |
Software |
… Component Author Boudier, Thomas Requires mcib3d library ImageJ Execution Platform Linux Mac Windows Implementation … |
| fairSIM |
1 |
|
|
|
Software |
… for a wide range of SR-SIM platforms directly within ImageJ. For research groups developing their own … for a wide range of SR-SIM platforms directly within ImageJ. For research groups developing their own … |
| Filopodyan |
1 |
|
2D, time-series |
ImageJ, Fiji |
Software |
… Type Collection Author Butler Richard Requires ImageJ Fiji Execution Platform Linux Mac Windows … |
| WormScan |
1 |
|
|
Fiji |
Software |
… Execution Platform Linux Mac Windows Programming Language ImageJ Macros License/Openness Free and open source … |
| SME |
1 |
|
3D |
|
Software |
… microscopy 3D image stacks. We provide a parameter-free ImageJ/Fiji plugin that allows 2D visualization and … microscopy 3D image stacks. We provide a parameter-free ImageJ/Fiji plugin that allows 2D visualization and … |
| DropSnake |
1 |
|
2D |
ImageJ |
Software |
… Type Component Author Aurélien Stalder Requires ImageJ Execution Platform Linux Mac Windows Implementation … |
| LBADSA |
1 |
|
2D |
ImageJ |
Software |
… Type Component Author Aurélien Stalder Requires ImageJ Execution Platform Linux Mac Windows Implementation … |
| FeatureJ Hessian |
1 |
|
2D, 3D |
ImageJ |
Software |
… Type Component Author Meijering, Erik Requires ImageJ Execution Platform Linux Mac Windows Implementation … Backlinks Oocytor / Component Spot Detection 3D Hessian (ImageJ) / Workflow … |
| Nuclei Tracking (TrackMate) |
1 |
|
2D, time-series |
TrackMate, pyimagej |
Software |
|
| MorphoNet |
1 |
|
2D, 3D, multi-channel, time-series |
|
Software |
… Mac Windows Implementation Type web is compatible with ImageJ Fiji Supported image dimension 2D 3D multi-channel … |
| ImageM |
1 |
|
2D, 3D |
Matlab Image Processing Toolbox, MATLAB, MATLAB Statistics toolbox |
Software |
… is largely inspired from the open source software "ImageJ". ImageM can also be run on the open source … is largely inspired from the open source software "ImageJ". ImageM can also be run on the open source … |
| CAREless |
1 |
|
2D, 3D, multi-channel, time-series |
ImageJ, Python |
Software |
… Type Collection Author csommer Requires ImageJ Python Execution Platform Linux Mac Windows … |
| ndpi_extractroi |
1 |
|
2D |
OpenSlide |
Software |
… the use of OpenSlide in java: it will extract an imageJ roi drawn from the thumbnail of the whole slide image, … the use of OpenSlide in java: it will extract an imageJ roi drawn from the thumbnail of the whole slide image, … |
| Analyze Spheroid Cell Invasion In 3D Matrix |
1 |
|
3D |
MorphoLibJ |
Software |
… Execution Platform Linux Mac Windows Programming Language ImageJ Macros Supported image dimension 3D Interaction Level … |
| AnnotatorJ |
1 |
|
2D, multi-channel |
Fiji |
Software |
… Link Git HUB Reference Publication Link AnnotatorJ: an ImageJ plugin to ease hand annotation of cellular … |
| BaSiC |
1 |
|
2D, time-series |
Fiji |
Software |
… single-cell quantification. BaSiC is available as a Fiji/ImageJ plugin. has function Image correction has topic … single-cell quantification. BaSiC is available as a Fiji/ImageJ plugin. … |
| Golgi Segmentation by Active Mask framework |
1 |
|
2D |
ImageJ, Matlab Image Processing Toolbox |
Software |
… Fickus, Y. Guo, A. D. Linstedt and J. Kova?evi? Requires ImageJ Matlab Image Processing Toolbox Implementation Type … |
| Cell segmentation by EBImage, R |
1 |
|
|
Graylevel Watershed for ImageJ, Segmentation of Clustered Cells in MATLAB |
Software |
… Author takeo katsuki Requires Graylevel Watershed for ImageJ Segmentation of Clustered Cells in MATLAB Interaction … |
| SynActJ |
1 |
|
2D, time-series |
Fiji |
Software |
… MIT License Description SynActJ (Synaptic Activity in ImageJ) is an easy-to-use fully open-source workflow that … SynActJ (Synaptic Activity in ImageJ) is an easy-to-use fully open-source workflow that … |
| spot detection and codistribution analysis |
1 |
|
2D, multi-channel |
ImageJ, MATLAB |
Software |
… Paul-Gilloteaux orcid.org/0000-0003-3903-4841 Requires ImageJ MATLAB Execution Platform Unsure Supported image … |
| OrganoSeg |
1 |
|
2D |
Matlab Image Processing Toolbox |
Software |
… Compare OrganoSeg against CellProfiler1, MorphoLibJ1, and ImageJ Backlinks … |
| ELEPHANT |
1 |
|
2D, 3D, time-series |
|
Software |
… Mac Windows Implementation Type plugin is compatible with ImageJ Supported image dimension 2D 3D time-series … |
| faim-ipa |
1 |
|
2D, 3D, multi-channel, time-series |
|
Software |
|
| Fast4DReg |
1 |
|
2D, 3D, multi-channel, time-series |
|
Software |
… Windows Implementation Type plugin Programming Language ImageJ Macros is compatible with Fiji Supported image … |
| ThicknessTool |
1 |
|
|
|
Software |
… I do not know Description A plugin for the ImageJ platform that automates measurement of retinal nuclear … A plugin for the ImageJ platform that automates measurement of retinal nuclear … |
| FISH signals detection |
1 |
|
2D |
Fiji |
Software |
… Author Sébastien Tosi Requires Fiji Programming Language ImageJ Macros Supported image dimension 2D Interaction Level … |
| Tissue analysis from histological sections |
1 |
|
2D |
Fiji, Trainable Weka Segmentation |
Software |
… Execution Platform Linux Mac Windows Programming Language ImageJ Macros Supported image dimension 2D Interaction Level … |
| SPIM de-striper |
1 |
|
|
Fiji |
Software |
… Execution Platform Linux Mac Windows Programming Language ImageJ Macros Interaction Level Automated License/Openness … |
| Tube un-winder |
1 |
|
3D |
Fiji |
Software |
… Execution Platform Linux Mac Windows Programming Language ImageJ Macros Supported image dimension 3D Interaction Level … |
| FigureJ |
1 |
|
2D, 3D, multi-channel, time-series |
ImageJ |
Software |
… Type Component Author Jerome Mutterer Edda Zinck Requires ImageJ Execution Platform Linux Mac Windows Implementation … |
| Image anonymisation |
1 |
|
|
ImageJ |
Software |
… Type Workflow Author Christophe Leterrier Requires ImageJ Interaction Level Automated License/Openness I do not … |
| Lymphatic Vessel Density calculation |
1 |
|
|
MATLAB, Pandore, Moment thresholding (ImageJ) |
Software |
… Signolle Requires MATLAB Pandore Moment thresholding (ImageJ) Interaction Level Manual License/Openness I do not … |
| 3D intensity profile |
1 |
|
3D |
Fiji |
Software |
… Free and open source Description This Javascript works in ImageJ to measure 3D intensity profile along cylindrical … This Javascript works in ImageJ to measure 3D intensity profile along cylindrical … |
| Splitting clustered cells |
1 |
|
|
MATLAB, Graylevel Watershed for ImageJ |
Software |
… Steve Eddins Requires MATLAB Graylevel Watershed for ImageJ Interaction Level Automated License/Openness Free and … |
| Segmentation and quantification of subcellular structures in fluorescence microscopy images using Squassh |
1 |
|
2D, 3D |
ImageJ, Squassh |
Software |
… M Niemann A Ziegler U Berger P Sbalzarini IF Requires ImageJ Squassh Execution Platform Linux Mac Windows … |
| Myotracker |
1 |
|
2D |
Fiji |
Software |
|
| Kymoquant |
1 |
|
2D, time-series |
ImageJ |
Software |
… Type Component Author Kota Miura Requires ImageJ Supported image dimension 2D time-series Interaction … |
| MorphoLibJ: using morphological reconstructions to isolate objects |
1 |
|
3D |
ImageJ, MorphoLibJ |
Software |
… Type Workflow Author Fabrice Cordelières Requires ImageJ MorphoLibJ Execution Platform Linux Mac Windows … |
| ImarisIsoSurface |
1 |
|
|
Graylevel Watershed for ImageJ, Imaris |
Software |
… Type Component Requires Graylevel Watershed for ImageJ Imaris Interaction Level Automated License/Openness I … |
| CellProfiler |
1 |
|
2D, 3D, multi-channel, time-series |
|
Software |
… is extensible through plugins written in Python or for ImageJ. Strengths: Cells, Neurons, C. Elegans, 2D Fluorescent … is extensible through plugins written in Python or for ImageJ. Strengths: Cells, Neurons, C. Elegans, 2D Fluorescent … |
| NeuronJ |
1 |
|
2D |
ImageJ |
Software |
… Type Component Author Erik Meijering Requires ImageJ Execution Platform Linux Mac Windows Implementation … |
| Auto Local Threshold |
1 |
|
2D |
ImageJ |
Software |
… Type Component Author Gabriel Landini Requires ImageJ Execution Platform Linux Mac Windows Implementation … |
| List all threads |
1 |
|
|
ImageJ |
Software |
… Type Component Requires ImageJ Interaction Level Automated License/Openness I do not … |
| RGB Measure Plus |
1 |
|
multi-channel |
ImageJ |
Software |
… Type Component Author Dimiter Prodanov Requires ImageJ Execution Platform Linux Mac Windows Implementation … |
| RGB Profiler |
1 |
|
multi-channel |
ImageJ |
Software |
… Author Christophe Laummonerie Jerome Mutterer Requires ImageJ Execution Platform Linux Mac Windows Implementation … |
| Replace Red with Magenta |
1 |
|
2D |
ImageJ |
Software |
… Type Component Author Johannes Schindelin Requires ImageJ Implementation Type plugin Programming Language Java … |
| Sync Windows |
1 |
|
2D, 3D, time-series |
ImageJ |
Software |
… Schindelin Johannes Hiner Mark Walter Joachim Requires ImageJ Execution Platform Linux Mac Windows Implementation … |
| Blend two images (Fiji scripting example) |
1 |
|
2D |
Fiji |
Software |
… Last modified 12/20/2018 - 18:31 Download Page https://imagej.net/Blend_two_images Backlinks … |
| Integral Image Filters |
1 |
|
2D |
ImageJ |
Software |
… Type Component Author Stephan Saalfeld Requires ImageJ Execution Platform Linux Mac Windows Implementation … |
| IsoData Classifier |
1 |
|
2D |
ImageJ |
Software |
… Type Component Requires ImageJ Execution Platform Linux Mac Windows Supported image … |
| PSF Generator |
1 |
|
3D |
|
Software |
… standalone Programming Language Java is compatible with ImageJ Icy Supported image dimension 3D Interaction Level … |
| Make Fiji Package |
1 |
|
|
ImageJ |
Software |
… Type Component Author Johannes Schindelin Requires ImageJ Interaction Level Automated License/Openness Free and … |
| E-Snake |
1 |
|
|
ImageJ |
Software |
… Type Component Author Ricard Delgado-Gonzalo Requires ImageJ Execution Platform Linux Mac Windows Implementation … |
| Diffraction PSF 3D |
1 |
|
3D |
ImageJ |
Software |
… Type Component Author Bob Dougherty Requires ImageJ Execution Platform Linux Mac Windows Implementation … |
| Image Stabilizer |
1 |
|
2D, time-series |
ImageJ |
Software |
… Type Component Author Kang Li Requires ImageJ Execution Platform Linux Mac Windows Implementation … |
| SpotTracker |
1 |
|
2D, time-series |
ImageJ |
Software |
… Type Component Requires ImageJ Execution Platform Linux Mac Windows Implementation … |
| PlugIn Design Guidelines |
1 |
|
|
ImageJ |
Software |
… Type I do not know Requires ImageJ Execution Platform Linux Mac Windows Implementation … |
| Bio-Formats |
1 |
|
|
|
Software |
… Platform Linux Mac Windows is compatible with CellProfiler ImageJ Interaction Level Automated License/Openness I do not … |
| Rolling Ball Background Subtraction |
1 |
|
2D |
ImageJ |
Software |
… Type Component Author Michael Castle Janice Keller Requires ImageJ Execution Platform Linux Mac Windows Supported image … |
| Align Image by line ROI |
1 |
|
2D |
Fiji |
Software |
… Last modified 12/18/2018 - 04:43 Download Page https://imagej.net/Align_Image_by_line_ROI Backlinks … |
| Extended Depth of Field |
1 |
|
3D |
ImageJ |
Software |
… Type Component Author Prudencio, Alex Sage, Daniel Requires ImageJ Execution Platform Linux Mac Windows Implementation … |
| PIV analyser |
1 |
|
2D |
ImageJ, Optical Flow |
Software |
… Type Component Requires ImageJ Optical Flow Execution Platform Linux Mac Windows … |
| PureDenoise |
1 |
|
3D, multi-channel, time-series |
ImageJ |
Software |
… Type Component Author Florian Luisier Requires ImageJ Execution Platform Linux Mac Windows Implementation … |
| Stochastic Denoising |
1 |
|
2D |
ImageJ |
Software |
… Type Component Author Funke Jan Requires ImageJ Execution Platform Linux Mac Windows Implementation … |
| Extended Depth of Focus |
1 |
|
3D |
ImageJ, Fiji |
Software |
… D. Van De Ville J. Berent D. Sage M. Unser Requires ImageJ Fiji Execution Platform Linux Mac Windows … |
| Otsu Thresholding |
1 |
|
|
ImageJ, Histogram |
Software |
… Type Component Requires ImageJ Histogram Interaction Level Automated License/Openness … |
| MonogenicJ |
1 |
|
2D |
ImageJ |
Software |
… Type Component Requires ImageJ Execution Platform Linux Mac Windows Implementation … |
| Report a Bug |
1 |
|
|
ImageJ |
Software |
… Component Author Mark Longair Johannes Schindelin Requires ImageJ Execution Platform Linux Mac Windows Interaction Level … |
| Multithreaded Image Processing in Javascript |
1 |
|
|
ImageJ |
Software |
… Type Component Author Albert Cardona Requires ImageJ Interaction Level Automated License/Openness Free and … |
| Reconstruct Reader |
1 |
|
|
ImageJ, TrakEM2 |
Software |
… Type Component Author Larry Lindsey Requires ImageJ TrakEM2 Execution Platform Linux Mac Windows … |
| Name Landmarks and Register |
1 |
|
|
ImageJ |
Software |
… Type Component Requires ImageJ Interaction Level Automated License/Openness I do not … |
| File Import |
1 |
|
|
ImageJ |
Software |
… Type Component Requires ImageJ Execution Platform Linux Mac Windows Interaction Level … |
| StackReg |
1 |
|
3D, time-series |
ImageJ, TurboReg |
Software |
… Type Component Author Philippe Thévenaz Requires ImageJ TurboReg Execution Platform Linux Mac Windows … |
| Multiple Image Processor |
1 |
|
2D, 3D, multi-channel, time-series |
ImageJ, Fiji |
Software |
… Type Component Author Nathaniel Gonzalez Santiago Requires ImageJ Fiji Execution Platform Linux Mac Windows … |
| FastFilters3D |
1 |
|
3D |
ImageJ |
Software |
… Type Collection Author Thomas Boudier Requires ImageJ Execution Platform Linux Mac Windows Implementation … |
| Particle Tracker |
1 |
|
3D, time-series |
ImageJ, MosaicSuite |
Software |
… Type Component Author MOSAIC Group Requires ImageJ MosaicSuite Execution Platform Linux Mac Windows … |
| 3View import list |
1 |
|
3D |
ImageJ, TrakEM2 |
Software |
… Type Component Requires ImageJ TrakEM2 Execution Platform Linux Mac Windows … |
| Anaglyph for Red Cyan glasses |
1 |
|
3D |
ImageJ |
Software |
… Type Component Requires ImageJ Execution Platform Linux Mac Windows Implementation … |
| BEEPS (Bi-Exponential Edge-Preserving Smoother) |
1 |
|
2D |
ImageJ |
Software |
… Type Component Requires ImageJ Execution Platform Linux Mac Windows Implementation … |
| MorphoMaths |
1 |
|
|
Graylevel Watershed for ImageJ, EBImage closing, EBImage opening |
Software |
… Type Component Requires Graylevel Watershed for ImageJ EBImage closing EBImage opening Execution Platform … |
| 3D Surface Plot |
1 |
|
3D |
ImageJ |
Software |
… Type Component Author Kai Uwe Barthel Requires ImageJ Execution Platform Linux Mac Windows Implementation … |
| QuimP |
1 |
|
2D, multi-channel, time-series |
|
Software |
… Type plugin Programming Language Java is compatible with ImageJ Supported image dimension 2D multi-channel time-series … |
| Fractional Splines Wavelets |
1 |
|
2D |
ImageJ, MATLAB |
Software |
… Dimitri Blu, Thierry Sage, Daniel Unser, Michael Requires ImageJ MATLAB Execution Platform Linux Mac Windows … |
| IdentifyPrimaryObjects |
1 |
|
2D |
CellProfiler, Spot Detector (Icy), Graylevel Watershed for ImageJ |
Software |
… CellProfiler Spot Detector (Icy) Graylevel Watershed for ImageJ Execution Platform Mac Windows Implementation Type … |
| Level Sets |
1 |
|
2D |
ImageJ |
Software |
… Type Component Author Curtis Rueden Requires ImageJ Execution Platform Linux Mac Windows Implementation … |
| Simulate Color Blindness |
1 |
|
|
ImageJ, Fiji |
Software |
… Type Component Author Johannes Schindelin Requires ImageJ Fiji Execution Platform Linux Mac Windows … |
| Parallel Spectral Deconvolution |
1 |
|
2D, 3D |
ImageJ |
Software |
… Type Component Author Piotr Wendykier Requires ImageJ Execution Platform Linux Mac Windows Implementation … |
| Landmark Correspondences |
1 |
|
2D |
ImageJ, Fiji |
Software |
… Type Component Author Stephan Saalfeld Requires ImageJ Fiji Execution Platform Linux Mac Windows … |
| Skeletonize3D |
1 |
|
2D, 3D |
ImageJ |
Software |
… Type Component Author Ignacio Arganda-Carreras Requires ImageJ Execution Platform Linux Mac Windows Implementation … |
| Using the Script Editor |
1 |
|
|
ImageJ |
Software |
… Component Author Johannes Schindelin Sumit Dubey Requires ImageJ Execution Platform Linux Mac Windows Interaction Level … |
| Fiji Logo 3D |
1 |
|
|
ImageJ |
Software |
… Type Component Requires ImageJ Interaction Level Automated License/Openness I do not … |
| OrientationJ |
1 |
|
|
ImageJ |
Software |
… Type Component Author Daniel Sage Requires ImageJ Execution Platform Linux Mac Windows Implementation … |
| PixBleach |
1 |
|
|
ImageJ |
Software |
… Type Component Requires ImageJ Interaction Level Automated License/Openness I do not … |
| Image Stitching Fiji |
1 |
|
2D, 3D, multi-channel, time-series |
Fiji |
Software |
… open source License GPL-v2.0 Description Quote from the ImageJ wiki: The Stitching Plugin (2d-5d) is able to … Quote from the ImageJ wiki: The Stitching Plugin (2d-5d) is able to … |
| Resize using high-quality interpolation |
1 |
|
2D |
ImageJ |
Software |
… Muñoz David Leroux Daniel Sage Michael Unser Requires ImageJ Execution Platform Linux Mac Windows Implementation … |
| View5D |
1 |
|
2D, 3D, multi-channel, time-series |
ImageJ |
Software |
… Author Rainer Heintzmann Jean-Yves Tinevez Requires ImageJ Execution Platform Linux Mac Windows Implementation … |
| SPIM Bead Registration |
1 |
|
|
ImageJ |
Software |
… Saalfeld Johannes Schindelin Pavel Tomancak Requires ImageJ Interaction Level Automated License/Openness Free and … |
| Miniature Faking |
1 |
|
2D |
ImageJ |
Software |
… Type Component Requires ImageJ Execution Platform Linux Mac Windows Implementation … |
| Sigma Filter |
1 |
|
2D |
ImageJ |
Software |
… Type Component Requires ImageJ Execution Platform Linux Mac Windows Implementation … |
| KNIME Image Processing and Analysis |
1 |
|
|
ImageJ, ICY Annotation, Graph Cut, OMERO, Bio-Formats, KNIME Anisotropic Diffusion , Processing, Image Calculator (KNIME), Image Normalizer (KNIME), ImgLib2, ImgLib2, Max Filter (KNIME), Max Homogeneity (KNIME), Quantile Filter (KNIME), Sigma Filter, Sigma Filter, Sobel Filter (KNIME), KNIME Variance Filter |
Software |
… Type Collection Requires ImageJ ICY Annotation Graph Cut OMERO Bio-Formats KNIME … |
| Same Slice in Multiple Images |
1 |
|
3D, time-series |
ImageJ |
Software |
… Type Component Requires ImageJ Execution Platform Linux Mac Windows Supported image … |
| Transform Virtual Stack Slices |
1 |
|
3D |
ImageJ |
Software |
… Arganda-Carreras Albert Cardona Stephan Saalfeld Requires ImageJ Execution Platform Linux Mac Windows Implementation … |
| Image Expression Parser |
1 |
|
|
ImageJ |
Software |
… Type Component Author Tinevez Jean-Yves Requires ImageJ Execution Platform Linux Mac Windows Implementation … |
| Snakuscule |
1 |
|
2D |
ImageJ |
Software |
… Type Component Requires ImageJ Execution Platform Linux Mac Windows Implementation … |
| SIOX: Simple Interactive Object Extraction |
1 |
|
2D, multi-channel |
ImageJ |
Software |
… Type Component Author Ignacio Arganda-Carreras Requires ImageJ Execution Platform Linux Mac Windows Implementation … |
| RodCellJ |
1 |
|
2D, 3D, time-series |
ImageJ |
Software |
… Type Component Author Daniel Schmitter Daniel Sage Requires ImageJ Execution Platform Linux Mac Windows Implementation … |
| Grid |
1 |
|
2D, 3D |
ImageJ, Grid |
Software |
… Type Component Author Wayne Rasband Requires ImageJ Grid Execution Platform Linux Mac Windows … |
| Segmentation Editor |
1 |
|
2D, 3D |
ImageJ |
Software |
… Schindelin, Francois Kusztos, Benjamin Schmid Requires ImageJ Execution Platform Linux Mac Windows Implementation … |
| Enhance Local Contrast (CLAHE) |
1 |
|
2D |
ImageJ |
Software |
… Type Component Author Stephan Saalfeld Requires ImageJ Execution Platform Linux Mac Windows Implementation … |
| Straighten |
1 |
|
2D |
ImageJ |
Software |
… Type Component Requires ImageJ Execution Platform Linux Mac Windows Supported image … |
| Statistical Region Merging |
1 |
|
2D |
ImageJ |
Software |
… Type Component Requires ImageJ Execution Platform Linux Mac Windows Implementation … |
| Spline Deformation Generator |
1 |
|
2D |
ImageJ |
Software |
… Type Component Requires ImageJ Execution Platform Linux Mac Windows Implementation … |
| Moving Least Squares |
1 |
|
|
ImageJ |
Software |
… Type Component Requires ImageJ Interaction Level Automated License/Openness I do not … |
| Ovuscule |
1 |
|
2D |
ImageJ |
Software |
… Type Component Author Philippe Thévenaz Requires ImageJ Execution Platform Linux Mac Windows Implementation … |
| UnwarpJ |
1 |
|
|
ImageJ |
Software |
… Sánchez Sorzano Philippe Thévenaz Michael Unser Requires ImageJ Interaction Level Automated License/Openness Free and … |
| Copy Pixel Size |
1 |
|
2D |
ImageJ |
Software |
… Type Component Author J. Anthony Parker Requires ImageJ Execution Platform Linux Mac Windows Implementation … |
| Series Labeler |
1 |
|
2D, 3D, multi-channel, time-series |
ImageJ |
Software |
… Type Component Requires ImageJ Execution Platform Linux Mac Windows Implementation … |
| DeconvolutionLab |
1 |
|
2D |
ImageJ |
Software |
… Type Component Author Daniel Sage Requires ImageJ Execution Platform Linux Mac Windows Implementation … |
| Coloc 2 |
1 |
|
2D |
Fiji |
Software |
… Last modified 12/18/2018 - 05:05 Download Page https://imagej.net/Coloc_2 Backlinks … |
| TopoJ |
1 |
|
2D |
ImageJ |
Software |
… Type Component Author Hovis David Requires ImageJ Execution Platform Linux Mac Windows Implementation … |
| Stack Manipulation |
1 |
|
2D, 3D, multi-channel, time-series |
ImageJ |
Software |
… Type Component Requires ImageJ Execution Platform Linux Mac Windows Implementation … |
| ImarisFilamentTracer |
1 |
|
|
Imaris, Sholl Analysis (ImageJ) |
Software |
… Type Collection Requires Imaris Sholl Analysis (ImageJ) Implementation Type standalone Interaction Level … |
| RGB to Montage |
1 |
|
multi-channel |
ImageJ |
Software |
… Type Component Author unknown Requires ImageJ Execution Platform Linux Mac Windows Implementation … |
| Retinex |
1 |
|
|
ImageJ |
Software |
… Type Component Author Francisco Jiménez Hernández Requires ImageJ Interaction Level Automated License/Openness Free and … |
| Drop Shape Analysis |
1 |
|
|
ImageJ |
Software |
… Type Collection Author Aurélien Stalder Requires ImageJ Interaction Level Automated License/Openness Free and … |
| VIB Protocol |
1 |
|
3D |
ImageJ, CellProfiler Align |
Software |
… Mark Longair Johannes Schindelin Benjamin Schmid Requires ImageJ CellProfiler Align Execution Platform Linux Mac … |
| Volume Calculator |
1 |
|
3D |
ImageJ, Skeletonize3D |
Software |
… Type Component Author Peter C. Marks Requires ImageJ Skeletonize3D Execution Platform Linux Mac Windows … |
| Iterative Deconvolve 3D |
1 |
|
2D, 3D |
ImageJ |
Software |
… Type Component Requires ImageJ Execution Platform Linux Mac Windows Implementation … |
| Interactive Similarity |
1 |
|
|
ImageJ |
Software |
… Author https://orcid.org/0000-0002-4106-1761 Requires ImageJ Execution Platform Linux Mac Windows Implementation … |
| MosaicJ |
1 |
|
2D |
ImageJ, TurboReg |
Software |
… Type Component Author Philippe Thévenaz Requires ImageJ TurboReg Execution Platform Linux Mac Windows … |
| Temporal-Color Code |
1 |
|
3D, time-series |
ImageJ |
Software |
… Component Author Miura Kota Schindelin Johannes Requires ImageJ Execution Platform Linux Mac Windows Implementation … |
| TurboReg |
1 |
|
|
ImageJ |
Software |
… Type Component Author Philippe Thévenaz Requires ImageJ Execution Platform Linux Mac Windows Implementation … |
| Interactive Perspective |
1 |
|
2D |
ImageJ |
Software |
… Type Component Author Stephan Saalfeld Requires ImageJ Execution Platform Linux Mac Windows Implementation … |
| CellProfiler Align |
1 |
|
2D |
CellProfiler |
Software |
… Image Processing Align Backlinks VIB Protocol / Component ImageJ Align RGB planes / Component … |
| Insert Poisson noise |
1 |
|
|
|
Software |
… 15:05 Download Page http://mosaic.mpi-cbg.de/?q=downloads/imageJ Documentation Link … |
| Interaction Analysis |
1 |
|
|
Fiji, MosaicSuite |
Software |
… 13:50 Download Page http://mosaic.mpi-cbg.de/?q=downloads/imageJ Documentation Link … |
| Region Competition |
1 |
|
|
Fiji, MosaicSuite |
Software |
… 13:28 Download Page http://mosaic.mpi-cbg.de/?q=downloads/imageJ Documentation Link Tutorials Installation Reference … |
| Bio7 |
1 |
|
|
ImageJ |
Software |
… Type Collection Author Dr. Marcel Austenfeld Requires ImageJ Execution Platform Windows Linux Mac Programming … |
| ClearVolume |
0.993 |
|
3D, multi-channel, time-series |
ClearCL, ClearGL |
Software |
|
| Simple Neurite Tracer |
0.969 |
|
2D, 3D |
Fiji |
Software |
… http://snyderlab.com/2016/05/25/tracing-neurons-using-fiji-imagej/ Backlinks … |
| Junction Mapper |
0.957 |
|
2D, multi-channel |
|
Software |
|
| Particle Tracker 2D/3D |
0.886 |
|
2D, 3D, multi-channel, time-series |
Fiji, MosaicSuite |
Software |
… - 13:08 Download Page https://git.mpi-cbg.de/git/ImageJ.git Documentation Link Website Manual Addendum for 3D … |
| Effective image visualization for publications – a workflow using open access tools and concepts |
0.836 |
|
|
|
Software |
… Usage Example Link https://imagej.nih.gov/ij/images/hela-cells.zip DOI link … |
| Trainable Weka Segmentation |
0.836 |
|
2D, 3D, multi-channel, time-series |
Fiji |
Software |
… Page Releases in the Github repo Documentation Link http://imagej.net/Trainable_Weka_Segmentation Reference Publication … |
| Icy |
0.792 |
|
2D, 3D, multi-channel, time-series |
|
Software |
… in javascript or python Automatic bug reports Native ImageJ integration 100% compatible Native Micro-Manager … in javascript or python Automatic bug reports Native ImageJ integration 100% compatible Native Micro-Manager … |
