| Fiji |
9 |
|
2D, 3D, multi-channel, time-series |
|
Software |
… Free and open source License GPL v2 (and others: http://fiji.sc/Fiji:About) Description Fiji is just ImageJ: a distribution of ImageJ (and ImageJ2) … |
| FijiArchipelago |
8 |
|
|
ImageJ |
Software |
… Free and open source License GPLv2 Description Fiji Archipelago is a tool designed to make it easy for programmers to export Fiji/ImageJ functionality over a network to several other … Last modified 10/16/2019 - 17:32 Download Page http://fiji.sc/FijiArchipelago Documentation Link … |
| Effective image visualization for publications – a workflow using open access tools and concepts |
7.347 |
|
|
|
Software |
… images. The workflow is based on the open source software Fiji, but its principles can be applied with other software … 05/24/2023 - 14:07 Workflow steps Step 1: Open & save Fiji Data handling Step 2: Brightness & contrast Fiji Image visualisation Step 3: Image processing Fiji Image … |
| Update Fiji |
7 |
|
|
Fiji, ImageJ 2.x |
Software |
… Author Johannes Schindelin Curtis Rueden Requires Fiji ImageJ 2.x Execution Platform Linux Mac Windows … to keep you up-to-date with all components of ImageJ (or Fiji), i.e. the macros, scripts, plugins and the core … Last modified 10/17/2019 - 18:22 Download Page http://fiji.sc/Update_Fiji Documentation Link … |
| 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 Implementation Type … storing extremely large and complex data collections. This Fiji/ImageJ HDF5 plugin saves and loads 2D - 5D datasets with flexible options. In Fiji, the plugin is downloadable via update site " HDF5 ". … |
| Make Fiji Package |
7 |
|
|
ImageJ |
Software |
… License/Openness Free and open source Description The Fiji Packager allows you to bundle an existing Fiji installation so you can share all the plugins and update … .tar.bz2 are supported at the moment) from the files in Fiji.app/ . Entry Curator migration Post date 10/11/2013 - … |
| Qualitative annotations Fiji plugins |
7 |
|
2D, 3D, multi-channel, time-series |
ImageJ, Fiji |
Software |
… Jochen orcid.org/0000-0002-1193-1324 Requires ImageJ Fiji Execution Platform Linux Mac Windows Implementation Type … Programming Language Jython is compatible with ImageJ Fiji Supported image dimension 2D 3D multi-channel … Free and open source License GPL-v3 Description Set of Fiji plugins facilitating the systematic manual annotation of … |
| MoBIE Fiji Viewer |
6 |
|
2D, 3D, multi-channel |
Fiji, BigDataViewer |
Software |
… Component Author Tisher Christian Pape Constantin Requires Fiji BigDataViewer Execution Platform Linux Mac Windows … browsing of multimodal big image data. The MoBIE Fiji viewer is based on BigDataViewer and enables browsing … 13:25 Last modified 03/06/2023 - 16:32 Download Page From Fiji add the MoBie site Documentation Link Git Hub Reference … |
| ROI 1-click tools for ImageJ/Fiji |
6 |
|
2D, multi-channel, time-series |
ImageJ, Fiji |
Software |
… Laurent orcid.org/0000-0001-7686-3249 Requires ImageJ Fiji Implementation Type plugin Programming Language ImageJ … click tools for the rapid annotations of ROI in ImageJ/Fiji. The ROI 1-click tools can be setup with a predefined … Go to next slice, run a macro command...) To install in Fiji, just activate the ROI 1-click tools has function … |
| Register Virtual Stack Slices (Fiji) |
5.989 |
|
3D, time-series |
Fiji |
Software |
… Cardona Ignacio Arganda-Carreras Stephan Saalfeld Requires Fiji Execution Platform Linux Mac Windows Implementation Type … Last modified 03/02/2020 - 21:24 Documentation Link http://fiji.sc/Register_Virtual_Stack_Slices … migration.tool … 4658 … with the Fijij package. … Register Virtual Stack Slices (Fiji) … |
| DeepCLEM |
5.766 |
|
2D |
Fiji, Register Virtual Stack Slices (Fiji), CSBDeep a toolbox for Content-aware Image Restoration (CARE) in Fiji |
Software |
… Kollmannsberger orcid.org/0000-0002-8049-61861 Requires Fiji Register Virtual Stack Slices (Fiji) CSBDeep a toolbox for Content-aware Image Restoration (CARE) in Fiji Execution Platform Linux Mac Windows Implementation Type … |
| VSI File Extractor (ImageJ) |
5 |
|
2D |
Fiji |
Software |
… Author Olivier Burri Romain Guiet Arne Seitz Requires Fiji Execution Platform Linux Mac Windows Implementation Type … memory (>50k x 50k pixels). It was written and tested on Fiji and is available from a Fiji Update Site: http://fiji.sc/List_of_update_sites has … |
| PHANTAST for FIJI |
5 |
|
2D |
Fiji |
Software |
… Type Component Author Nicolas Jaccard Requires Fiji Execution Platform Linux Mac Windows Implementation Type … and open source License https://github.com/nicjac/PHANTAST-FIJI/blob/master/LICENSE Description The phase contrast … of Biochemical Engineering and CoMPLEX . … PHANTAST for FIJI … |
| 2D tracking using KNIME and Fiji |
5 |
|
2D, time-series |
KNIME Image Processing and Analysis, Fiji |
Software |
… Reymann Requires KNIME Image Processing and Analysis Fiji Execution Platform Linux Mac Windows Programming … steps, objects/cells are segmented first, then it uses Fiji TrackMate LAP method for the tracking task. … steps, objects/cells are segmented first, then it uses Fiji TrackMate LAP method for the tracking task. … |
| Fiji CMTK GUI |
5 |
|
2D, 3D |
Fiji, CMTK |
Software |
… Jefferis Gregory orcid.org/0000-0002-0587-9355 Requires Fiji CMTK Execution Platform Linux Mac Windows Implementation … a simple GUI frontend for CMTK image registration tools in Fiji has function Image registration Affine registration … - 20:52 Download Page https://github.com/jefferis/fiji-cmtk-gui … johnbogovic … Jefferis Gregory … |
| Z-spacing correction for Fiji |
5 |
|
3D |
Fiji |
Software |
… Type Component Author Hanslovsky Philipp Requires Fiji Execution Platform Linux Mac Windows Implementation Type … of 2-dimensional sections. We provide plugins for both Fiji and TrakEM2. has function Warping Image correction has … of 2-dimensional sections. We provide plugins for both Fiji and TrakEM2. … Z-spacing correction for Fiji … |
| 2D Gaussian fitting macro (Fiji/ImageJ) for multiple signals. |
5 |
|
2D |
ImageJ, Fiji |
Software |
… dominic orcid.org/0000-0003-2685-4226 Requires ImageJ Fiji Programming Language ImageJ Macros Supported image … detected regions. This macro is unique because the ImageJ/Fiji curve fitting API only supports 1-D curve. I get around … detected regions. This macro is unique because the ImageJ/Fiji curve fitting API only supports 1-D curve. I get around … |
| Protein Micro-array Analysis |
4 |
|
2D |
Fiji |
Software |
… Type Workflow Author Sébastien Tosi Requires Fiji Execution Platform Linux Mac Windows Programming … "ImageJ plugins toolkit". To ensure compatibility with Fiji you should download the version 1.6.1 . The … un-compressing the .jar file from the previous archive to Fiji plugins folder. sample image: link has function Image … |
| PlugIn Design Guidelines |
4 |
|
|
ImageJ |
Software |
… Last modified 10/18/2019 - 14:16 Download Page http://fiji.sc/PlugIn_Design_Guidelines Documentation Link http://fiji.sc/PlugIn_Design_Guidelines Reference Publication Link http://fiji.sc/PlugIn_Design_Guidelines Usage Example Link … |
| Spark Stitcher |
4 |
|
3D, multi-channel |
Fiji |
Software |
… Type Component Author Pisarev Igor Requires Fiji Execution Platform Linux Mac Windows Implementation Type … cluster. The code is based on the Stitching plugin for Fiji https://github.com/fiji/Stitching has function Image registration Illumination … |
| Fiji Logo 3D |
4 |
|
|
ImageJ |
Software |
… Last modified 09/13/2017 - 12:07 Download Page http://fiji.sc/Fiji_Logo_3D … migration.tool … migration … Fiji Logo 3D … |
| Blend two images (Fiji scripting example) |
4 |
|
2D |
Fiji |
Software |
… Type Component Author Albert Cardona Requires Fiji Execution Platform Linux Mac Windows Implementation Type … Free and open source I do not know Description This is a Fiji scripting demo using Clojure. Entry Curator migration … … Albert Cardona … basic_html … migration … This is a Fiji scripting demo using Clojure. … Blend two images (Fiji … |
| CSBDeep a toolbox for Content-aware Image Restoration (CARE) in Fiji |
4 |
|
2D, 3D, multi-channel |
Fiji |
Software |
… Jug, Florian orcid.org/0000-0002-8499-5812 Requires Fiji Execution Platform Linux Mac Windows Implementation Type … Last modified 04/27/2023 - 12:26 Download Page CSBDeep in Fiji Documentation Link general website for csbdeep Reference … a toolbox for Content-aware Image Restoration (CARE) in Fiji … |
| Delayed Snapshot |
4 |
|
2D |
ImageJ, Fiji |
Software |
… Type Component Author Albert Cardona Requires ImageJ Fiji Execution Platform Linux Mac Windows Implementation Type … scripting example (but is included as a menu item in Fiji) for screen capturing with certain time delay. has topic … modified 03/10/2019 - 03:44 Download Page Bundled with Fiji Documentation Link http://fiji.sc/Delayed_Snapshot … … |
| Manual Tracking Components of ImageJ |
4 |
|
2D, time-series |
Fiji |
Software |
… Cordelieres TrackMate developers E. Meijering Requires Fiji Execution Platform Linux Mac Windows Programming … License/Openness Free and open source Description The Fiji distribution of ImageJ comes with several manual … ( see the component page here ) can be installed via Fiji update sites. It has many shortcut keys enabled so for … |
| Simple Neurite Tracer |
3.993 |
|
2D, 3D |
Fiji |
Software |
… Type Component Author Longair Mark Ferreira Tiago Requires Fiji Execution Platform Linux Mac Windows Implementation Type … or statistical software. This plugin is included in Fiji by default. has function Filament tracing Image … Last modified 05/03/2023 - 10:58 Download Page http://fiji.sc/Simple_Neurite_Tracer Reference Publication Link … |
| Colour Deconvolution |
3.784 |
|
2D |
Fiji |
Software |
… Type Component Author Gabriel Landini Requires Fiji Execution Platform Linux Mac Windows Implementation Type … and open source Description This plugin is bundled with Fiji. For installation in ImageJ1, download from the link … plugin ( java and class files ) for ImageJ and Fiji implements stain separation using Ruifrok and Johnston's … |
| Morphological Segmentation (ImageJ) |
3.716 |
|
2D, 3D |
ImageJ |
Software |
… source Description Morphological Segmentation is an ImageJ/Fiji plugin that combines morphological operations, such as … Last modified 03/02/2020 - 21:05 Download Page http://fiji.sc/Morphological_Segmentation Documentation Link http://fiji.sc/Morphological_Segmentation Usage Example Link … |
| Marker-controlled Watershed (ImageJ) |
3.57 |
|
2D, 3D |
ImageJ |
Software |
… Description Marker-controlled Watershed is an ImageJ/Fiji plugin to segment grayscale images of any type (8, 16 … Last modified 03/02/2020 - 21:01 Download Page http://fiji.sc/Marker-controlled_Watershed Documentation Link http://fiji.sc/Marker-controlled_Watershed Usage Example Link … |
| SynActJ |
3 |
|
2D, time-series |
Fiji |
Software |
… Type Workflow Author Schmied Christopher Requires Fiji Execution Platform Linux Mac Windows Implementation Type … analysis of synaptic activity. The workflow consists of a Fiji plugin performing the automated image analysis of active … 09:39 Workflow steps Step 1: Maximum intensity projection Fiji Image processing Step 2: Laplacian of Gaussian for … |
| Parallel Spectral Deconvolution |
3 |
|
2D, 3D |
ImageJ |
Software |
… Last modified 10/18/2019 - 12:06 Download Page http://fiji.sc/Parallel_Spectral_Deconvolution Documentation Link http://fiji.sc/Parallel_Spectral_Deconvolution Reference Publication Link book Usage Example Link http://fiji.sc/Parallel_Spectral_Deconvolution … migration.tool … … |
| Same Slice in Multiple Images |
3 |
|
3D, time-series |
ImageJ |
Software |
… Last modified 10/17/2019 - 10:27 Download Page http://fiji.sc/Same_Slice_in_Multiple_Images Documentation Link http://fiji.sc/Same_Slice_in_Multiple_Images Usage Example Link http://fiji.sc/Same_Slice_in_Multiple_Images … migration.tool … 4910 … |
| Interactive Affine |
3 |
|
2D |
Fiji |
Software |
… Type Component Author Stephan Saalfeld Requires Fiji Execution Platform Linux Mac Windows Implementation Type … 05/30/2018 - 10:41 Download Page Source code (Bundled with Fiji) Documentation Link http://fiji.sc/Interactive_Affine Javadoc … migration.tool … Stephan … |
| Microtubule Length Analysis |
3 |
|
2D, 3D |
Fiji, Tubeness |
Software |
… Type Workflow Author Perrine Paul-Gilloteaux Requires Fiji Tubeness Execution Platform Linux Mac Windows … estimated. Script Workflow is written as an ImageJ macro (Fiji) with following steps: 1. The enhancement of tubular … to a 1-pixel thick line using the skeletonize plugin of Fiji. The length of the skeletonized microtubules was then … |
| Manual tracking with TrackMate |
3 |
|
2D, 3D, time-series |
Fiji |
Software |
… Type Component Author Jean-Yves Tinevez Requires Fiji Execution Platform Linux Mac Windows Implementation Type … Manual tracking using Trackmate plugin (comes with FIji, so no installation required if you are using Fiji). has function Object tracking Entry Curator kota Post … |
| MoBIE-Utils-Python |
3 |
|
2D, 3D, multi-channel |
|
Software |
… Programming Language Python is compatible with MoBIE Fiji Viewer Supported image dimension 2D 3D multi-channel … For further information, look to http://biii.eu/mobie-fiji-viewer has function Data handling has topic Data sharing … For further information, look to http://biii.eu/mobie-fiji-viewer … MoBIE-Utils-Python … |
| Copy Pixel Size |
3 |
|
2D |
ImageJ |
Software |
… 10/16/2019 - 12:56 Download Page https://github.com/fiji/cookbook/blob/master/src/main/java/sc/fiji/cookbook/Cop… Documentation Link http://fiji.sc/Copy_Pixel_Size … migration.tool … J. Anthony Parker … |
| Dynamic ROI Profiler |
3 |
|
2D |
Fiji |
Software |
… Type Component Author Albert Cardona Requires Fiji Execution Platform Linux Mac Windows Implementation Type … modified 03/11/2019 - 16:57 Download Page Bundled with Fiji Documentation Link http://fiji.sc/Dynamic_ROI_Profiler … migration.tool … 3599 … 4562 … … |
| Delaunay Voronoi |
3 |
|
2D |
Fiji |
Software |
… Component Author Johannes Schindelin L. Paul Chew Requires Fiji Execution Platform Linux Mac Windows Implementation Type … Diagram for a given point ROI. This plugin comes with Fiji. has topic Bioimage informatics Additional keywords … Last modified 03/08/2019 - 01:55 Documentation Link http://fiji.sc/Delaunay_Voronoi Reference Publication Link Source … |
| Microtubule end tracking in Drosophila Oocyte |
3 |
|
2D, time-series |
Fiji, TrackMate, Bleach Correction, Fourier Bandpass Filter, Temporal Medial Filter |
Software |
… Type Workflow Author Graeme Ball Requires Fiji TrackMate Bleach Correction Fourier Bandpass Filter … 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 … |
| ImageJ Plugin Ridge Detection |
3 |
|
|
Fiji |
Software |
… Type Component Author Thorsten Wagner Requires Fiji Execution Platform Linux Mac Windows Implementation Type … Last modified 10/21/2019 - 14:33 Download Page http://fiji.sc/Ridge_Detection Documentation Link http://fiji.sc/Ridge_Detection Reference Publication Link An … |
| MicrotubuleTracker in FIJI |
3 |
|
2D, 3D, time-series |
Fiji |
Software |
… Type Collection Component Author Varun Kapoor Requires Fiji Execution Platform Linux Mac Windows Implementation Type … more than one movie (batch mode). … MicrotubuleTracker in FIJI … |
| Alignment of FIBSEM or SBFSEM images |
3 |
|
|
Fiji, Open Virtual stack in Fiji, TrakEM2, Create new TrakEM project in Fiji, import images into TrakEM, Linear Stack Alignment with SIFT (ImageJ) |
Software |
… Type Component Requires Fiji Open Virtual stack in Fiji TrakEM2 Create new TrakEM project in Fiji import images into TrakEM Linear Stack Alignment with … |
| clij2 |
3 |
|
2D, 3D |
Fiji, Icy, MATLAB |
Software |
… Author Robert Haase 0000-0001-5949-2327 Requires Fiji Icy MATLAB Execution Platform Linux Mac Windows … Jython Matlab is compatible with Icy Protocols ImageJ Fiji Icy MATLAB Supported image dimension 2D 3D Interaction … is a GPU-accelerated image processing library for ImageJ/Fiji , Icy , Matlab and Java. It comes with hundreds of … |
| Analyze Skeleton 2D time series |
3 |
|
time-series |
ImageJ, ImageJ Analyze Skeleton |
Software |
… Last modified 04/27/2023 - 12:53 Download Page http://fiji.sc/Analyze_Skeleton_2D_time_series Documentation Link http://fiji.sc/Analyze_Skeleton_2D_time_series Usage Example Link http://fiji.sc/Analyze_Skeleton_2D_time_series … migration.tool … … |
| BaSiC |
3 |
|
2D, time-series |
Fiji |
Software |
… Type Collection Author Tingying Peng Carsten Marr Requires Fiji Execution Platform Linux Mac Windows Implementation Type … plugin Programming Language Java Matlab is compatible with Fiji MATLAB Python Supported image dimension 2D time-series … single-cell quantification. BaSiC is available as a Fiji/ImageJ plugin. has function Image correction has topic … |
| Automated workflow for parallel Multiview Reconstruction |
3 |
|
3D, multi-channel, time-series |
Fiji, Snakemake |
Software |
… Tobias Pietzsch Stephan Preibisch Pavel Tomancak Requires Fiji Snakemake Execution Platform Linux Supported image … steps Resave to hdf5 Conversion Detection and Registration Fiji Image registration Timelapse Registration SPIM … deconvolution Image deconvolution Multiview Fusion Fiji Image processing Download Page … |
| FlowJ |
3 |
|
2D, time-series |
ImageJ, Fiji |
Software |
… Author Michael Abràmoff Jean-Yves Tinevez Requires ImageJ Fiji Execution Platform Linux Mac Windows Implementation Type … Uras, Fleet and Jepson, and Singh, in Java. Bundled with Fiji, but can also be simply installed to ImageJ as well. has … Documentation Link Original web page Fiji page Reference Publication Link IEEE Transactions in … |
| Maximum Entropy Threshold (ImageJ) |
3 |
|
2D |
ImageJ |
Software |
… few bright objects on large dark background. In ImageJ/FIJI you can acces this tool in Image->Adjust->Threshold and … Last modified 03/02/2020 - 21:44 Download Page http://fiji.sc/ Documentation Link http://fiji.sc/Maximum_Entropy_Threshold … migration.tool … 4458 … … |
| Distortion Correction |
3 |
|
2D |
Fiji |
Software |
… Type Component Author Verena Kaynig Requires Fiji Execution Platform Linux Mac Windows Implementation Type … Free and open source Description This plugin comes with Fiji This plugin can be used to estimate nonlinear … Last modified 03/08/2019 - 02:29 Download Page http://fiji.sc/Distortion_Correction Documentation Link PDF (Manual) … |
| ImageJ/FIJI |
3 |
|
2D, 3D, multi-channel, time-series |
|
Software |
… open source Description Please also check out ImageJ and Fiji . has function Analysis Annotation Data handling … … Machine learning … Please also check out ImageJ and Fiji . … ImageJ/FIJI … |
| Elastic Alignment and Montage |
3 |
|
2D |
Fiji |
Software |
… Type Collection Author Stephan Saalfeld Requires Fiji Execution Platform Linux Mac Windows Implementation Type … modified 04/26/2023 - 19:15 Download Page Bundled with Fiji Documentation Link http://fiji.sc/Elastic_Alignment_and_Montage Reference Publication … |
| AnnotatorJ |
3 |
|
2D, multi-channel |
Fiji |
Software |
… Type Component Author Peter Horvath Réka Hollandi Requires Fiji Execution Platform Linux Mac Windows Implementation Type … Free and open source Description AnnotatorJ is a Fiji Plugin to ease annotation of images, particulrly useful … - 09:49 Last modified 07/09/2021 - 10:03 Download Page Fiji Update Site to add Documentation Link Git HUB Reference … |
| Dynamic Reslice |
3 |
|
3D |
Fiji |
Software |
… Component Author Jean-Yves Tinevez Albert Cardona Requires Fiji Execution Platform Linux Mac Windows Implementation Type … a dynamic version of the Reslice command. Bundled with Fiji. has function Visualisation has topic Bioimage … Last modified 03/09/2019 - 03:12 Documentation Link http://fiji.sc/Dynamic_Reslice Usage Example Link Scripting … … |
| Creating an ImageJ plugin / command |
3 |
|
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 Windows Implementation Type … Programming Language Java is compatible with ImageJ2 Fiji Supported image dimension 2D 3D multi-channel … |
| 3D Objects Counter |
2.899 |
|
3D |
Fiji, ImageJ |
Software |
… Cordelires Jonathan Jackson Daniel James White Requires Fiji ImageJ Execution Platform Linux Mac Windows … Object counter and 3D OC Options are now in the default Fiji "Analyze" menu. has function Object feature extraction … modified 08/07/2018 - 15:43 Download Page Contained in Fiji Documentation Link wiki attribution instructions S. … |
| Interactive Perspective |
2 |
|
2D |
ImageJ |
Software |
… Last modified 03/01/2020 - 14:04 Download Page http://fiji.sc/Interactive_Perspective Documentation Link http://fiji.sc/Interactive_Perspective … migration.tool … 5003 … … |
| Statistical Region Merging |
2 |
|
2D |
ImageJ |
Software |
… Last modified 10/17/2019 - 15:33 Download Page http://fiji.sc/Statistical_Region_Merging Documentation Link http://fiji.sc/Statistical_Region_Merging … migration.tool … 4756 … … |
| Volume Viewer |
2 |
|
3D |
ImageJ, Fiji |
Software |
… Type Component Author Kai Uwe Barthel Requires ImageJ Fiji Execution Platform Linux Mac Windows Implementation Type … Last modified 10/17/2019 - 18:27 Download Page http://fiji.sc/Volume_Viewer Documentation Link … |
| 2D brain slice region annotation: SliceMap |
2 |
|
2D |
|
Software |
… or by an automated region annotation tool. SliceMap is a FIJI/ImageJ plugin for automated brain region annotation of … of the sample. The resulting brain regions are saved as FIJI/ImageJ ROI’s (Regions Of Interest) as a single zip-file … or by an automated region annotation tool. SliceMap is a FIJI/ImageJ plugin for automated brain region annotation of … |
| LimeSeg |
2 |
|
3D |
ImageJ |
Software |
… plugin Programming Language Java is compatible with ImageJ Fiji Update Fiji Supported image dimension 3D Interaction Level … |
| ScientiFig |
2 |
|
|
Fiji |
Software |
… Type Component Author Aigouy Benoit Requires Fiji Implementation Type plugin standalone Interaction Level … It comes either as a stand alonesoftware, either as a Fiji/IJ plugin. has function Montage has topic Data sharing … It comes either as a stand alonesoftware, either as a Fiji/IJ plugin. … ScientiFig … |
| PIV analyser |
2 |
|
2D |
ImageJ, Optical Flow |
Software |
… Last modified 10/16/2019 - 17:35 Download Page http://fiji.sc/PIV_analyser Documentation Link http://fiji.sc/PIV_analyser … migration.tool … 4059 … 4155 … … |
| Particle Tracker |
2 |
|
3D, time-series |
ImageJ, MosaicSuite |
Software |
… Last modified 10/18/2019 - 11:05 Download Page http://fiji.sc/Particle_Tracker Documentation Link http://fiji.sc/Particle_Tracker Reference Publication Link Feature … |
| Filopodyan |
2 |
|
2D, time-series |
ImageJ, Fiji |
Software |
… Type Collection Author Butler Richard Requires ImageJ Fiji Execution Platform Linux Mac Windows Implementation Type … License/Openness Free but not open source Description Fiji plugin for detecting, tracking and quantifying filopodia … tracing … Object tracking … Fluorescence microscopy … Fiji plugin for detecting, tracking and quantifying filopodia … |
| Kalman Stack Filter (ImageJ) |
2 |
|
2D |
ImageJ |
Software |
… Last modified 03/02/2020 - 22:18 Download Page http://fiji.sc/Kalman_Stack_Filter Documentation Link http://fiji.sc/Kalman_Stack_Filter … migration.tool … 5026 … … |
| Analyze Complex Roots Tool |
2 |
|
2D |
Fiji |
Software |
… Bäcker Volker orcid.org/0000-0002-9129-6403 Requires Fiji Execution Platform Linux Mac Windows Implementation Type … Programming Language ImageJ Macros is compatible with Fiji Supported image dimension 2D Interaction Level Automated … |
| Slice Labeler (ImageJ) |
2 |
|
3D, time-series |
ImageJ |
Software |
… Last modified 03/02/2020 - 12:35 Download Page http://fiji.sc/Slice_Labeler Documentation Link http://fiji.sc/Slice_Labeler … migration.tool … Pedro Ramos-Cabrer … … |
| Stack Manipulation |
2 |
|
2D, 3D, multi-channel, time-series |
ImageJ |
Software |
… Last modified 10/17/2019 - 11:22 Download Page http://fiji.sc/Stack_Manipulation Documentation Link http://fiji.sc/Stack_Manipulation … migration.tool … 4184 … 4044 … … |
| Moment thresholding (ImageJ) |
2 |
|
2D, 3D |
ImageJ |
Software |
… that preserves the moments of an image. In ImageJ/Fiji, you can access it in Image->Ajust->Threshold and choose … Last modified 03/02/2020 - 21:47 Documentation Link http://fiji.sc/Auto_Threshold#Moments Reference Publication Link … that preserves the moments of an image. In ImageJ/Fiji, you can access it in Image->Ajust->Threshold and choose … |
| Directionality |
2 |
|
2D |
ImageJ |
Software |
… or location orientation. The plugin is part of Fiji, can be launched through the menu: Analyze > … 09/13/2017 - 12:45 Download Page https://github.com/fiji/Directionality/releases/tag/Directionality_-2.0.2 … or location orientation. The plugin is part of Fiji, can be launched through the menu: Analyze > … |
| Sigma Filter |
2 |
|
2D |
ImageJ |
Software |
… Last modified 10/17/2019 - 11:03 Download Page http://fiji.sc/Sigma_Filter Documentation Link http://fiji.sc/Sigma_Filter … migration.tool … 4229 … 4147 … 4067 … … |
| Straighten |
2 |
|
2D |
ImageJ |
Software |
… Last modified 10/17/2019 - 11:36 Download Page http://fiji.sc/Straighten... Usage Example Link http://fiji.sc/Straighten... … migration.tool … 4036 … 4155 … … |
| TopoJ |
2 |
|
2D |
ImageJ |
Software |
… Last modified 10/17/2019 - 13:38 Download Page http://fiji.sc/TopoJ Documentation Link http://fiji.sc/TopoJ … migration.tool … 4302 … Hovis David … 4065 … … |
| ImageJFX |
2 |
|
2D, 3D, multi-channel, time-series |
Fiji |
Software |
… Type Collection Author Cyril MONGIS Requires Fiji Execution Platform Linux Mac Windows Implementation Type plugin is compatible with Fiji Supported image dimension 2D 3D multi-channel … |
| Trainable Weka Segmentation |
2 |
|
2D, 3D, multi-channel, time-series |
Fiji |
Software |
… Albert Cardona Verena Kaynig Johannes Schindelin Requires Fiji Execution Platform Linux Mac Windows Implementation Type … GPL Description The Trainable Weka Segmentation is a Fiji plugin that combines a collection of machine learning … … Machine learning … The Trainable Weka Segmentation is a Fiji plugin that combines a collection of machine learning … |
| Kappa |
2 |
|
2D, multi-channel |
Fiji |
Software |
… Type Component Author Kevan Lu Hadrien Mary Requires Fiji Execution Platform Linux Mac Windows Programming … and open source License MIT License Description Kappa is a Fiji plugin for Curvature Analysis. It allows a user to … … Shape features … Digital histology … Kappa is a Fiji plugin for Curvature Analysis. It allows a user to … |
| Manual Tracking ImageJ |
2 |
|
2D, 3D, time-series |
Fiji |
Software |
… Type Component Author Fabrice Cordelieres Requires Fiji Execution Platform Linux Mac Windows Implementation Type … objects by mouse clicking. This plugin is bundled with Fiji. has function Object tracking has topic Live sample … objects by mouse clicking. This plugin is bundled with Fiji. … Manual Tracking ImageJ … |
| Multiple Image Processor |
2 |
|
2D, 3D, multi-channel, time-series |
ImageJ, Fiji |
Software |
… Author Nathaniel Gonzalez Santiago Requires ImageJ Fiji Execution Platform Linux Mac Windows Implementation Type … Last modified 10/15/2019 - 17:34 Download Page http://fiji.sc/Multiple_Image_Processor … migration.tool … Nathaniel … |
| LSM Toolbox (ImageJ) |
2 |
|
3D |
ImageJ |
Software |
… Last modified 03/02/2020 - 22:15 Download Page http://fiji.sc/LSM_Toolbox Documentation Link http://fiji.sc/LSM_Toolbox … migration.tool … 4648 … 4649 … 4549 … … |
| Coloc 2 |
2 |
|
2D |
Fiji |
Software |
… Type Component Author Johannes Schindelin Requires Fiji Execution Platform Linux Mac Windows Implementation Type … I do not know License GPLv3 Description " Coloc 2 is Fiji's plugin for colocalization analysis. It implements and … colocalisation … Bioimage informatics … " Coloc 2 is Fiji's plugin for colocalization analysis. It implements and … |
| Leaf Segmentation using Trainable Weka Segmentation plugin |
2 |
|
2D |
Fiji |
Software |
… Albert Cardona Verena Kaynig Johannes Schindelin Requires Fiji Execution Platform Linux Mac Windows Programming … page of the ImageJ plugin Trainable Weka Segmentation (in Fiji, it's bundled). A segmentation protocol based on machine … page of the ImageJ plugin Trainable Weka Segmentation (in Fiji, it's bundled). A segmentation protocol based on machine … |
| Auto Threshold |
2 |
|
2D |
Fiji |
Software |
… Type Component Author Gabriel Landini Requires Fiji Execution Platform Linux Mac Windows Implementation Type … and open source License GPLv3 Description Bundled with Fiji. "Do all" is the great feature... has function Image … … Image thresholding … Bioimage informatics … Bundled with Fiji. "Do all" is the great feature... … Auto Threshold … |
| Interactive watershed |
2 |
|
2D, 3D |
Fiji |
Software |
… Type Component Author Benoit Lombardot Requires Fiji Execution Platform Linux Mac Windows Implementation Type … source License BSD3 Description The interactive Watershed Fiji plugin provides an interactive way to explore local … … Fluorescence microscopy … The interactive Watershed Fiji plugin provides an interactive way to explore local … |
| SciView |
2 |
|
3D |
ImageJ |
Software |
… "Simplified" License Description SciView is an ImageJ/FIJI plugin for 3D visualization of images and meshes. It … image and mesh data in 3D and interface with the popular Fiji software ecosystem. An update site is available: … … hmbotelho … Image visualisation … SciView is an ImageJ/FIJI plugin for 3D visualization of images and meshes. It … |
| Using the Script Editor |
2 |
|
|
ImageJ |
Software |
… Last modified 10/18/2019 - 16:40 Download Page http://fiji.sc/Using_the_Script_Editor Documentation Link http://fiji.sc/Using_the_Script_Editor … migration.tool … 4972 … … |
| Find Dimension of Raw Image (ImageJ) |
2 |
|
|
ImageJ |
Software |
… Last modified 03/03/2020 - 18:34 Download Page http://fiji.sc/Find_Dimension_of_Raw_Image Documentation Link http://fiji.sc/Find_Dimension_of_Raw_Image … migration.tool … 5044 … … |
| Helmholtz Analysis |
2 |
|
|
ImageJ, Fiji |
Software |
… Author Dougherty Bob Schindelin Johannes Requires ImageJ Fiji Execution Platform Linux Mac Windows Implementation Type … Last modified 05/03/2023 - 12:23 Download Page http://fiji.sc/Helmholtz_Analysis Documentation Link Helmholtz … |
| Linear Stack Alignment with SIFT (ImageJ) |
2 |
|
3D |
ImageJ |
Software |
… Last modified 03/02/2020 - 17:24 Download Page http://fiji.sc/Linear_Stack_Alignment_with_SIFT Documentation Link http://fiji.sc/Linear_Stack_Alignment_with_SIFT … migration.tool … … |
| Granulometric Filtering (ImageJ) |
2 |
|
2D |
ImageJ |
Software |
… Last modified 03/03/2020 - 12:57 Download Page http://fiji.sc/Granulometric_Filtering Documentation Link http://fiji.sc/Granulometric_Filtering … migration.tool … Dimiter … |
| 3D segmentation (reconstruction) and modeling using Free-D |
2 |
|
2D, 3D |
|
Software |
… but there is an exportor to convert this format into fiji readable one * import already generated contours is on … but there is an exportor to convert this format into fiji readable one * import already generated contours is on … |
| Create new TrakEM project in Fiji |
2 |
|
|
|
Software |
… 01/30/2018 - 17:33 … Moritz … Create new TrakEM project in Fiji … |
| DEFCoN-ImageJ |
2 |
|
2D |
Fiji |
Software |
… Component Author Baptiste Ottino Kyle Douglass Requires Fiji Execution Platform Linux Mac Windows Implementation Type … - 12:14 Last modified 04/28/2023 - 15:04 Download Page Fiji update site, add Kmdouglass Documentation Link … |
| ImageJ Feature Extraction |
2 |
|
2D |
ImageJ |
Software |
… Correspondences]. For more details, see the linked page in Fiji wiki. For details about SIFT algorithm, see 2569. For … Last modified 05/03/2023 - 12:10 Download Page http://fiji.sc/Feature_Extraction Reference Publication Link IJCV … Correspondences]. For more details, see the linked page in Fiji wiki. For details about SIFT algorithm, see 2569. For … |
| Arrow |
2 |
|
2D |
ImageJ, ICY Annotation, Arrow |
Software |
… replaces the old Arrow_.class tool that was present in Fiji before. The main changes are the ability to draw the … Last modified 05/02/2023 - 13:10 Download Page http://fiji.sc/Arrow … migration.tool … Jean-Yves Tinevez … 4771 … … replaces the old Arrow_.class tool that was present in Fiji before. The main changes are the ability to draw the … |
| BioImage Model Zoo |
2 |
|
2D, 3D, multi-channel, time-series |
|
Software |
… partners in the AI4Life project is compatible with Fiji ilastik ImJoy DeepImageJ StarDist - ImageJ Supported … AI models to the bioimaging community. Integrated with Fiji, ilastik, ImJoy and more Try model instantly with … AI models to the bioimaging community. Integrated with Fiji, ilastik, ImJoy and more Try model instantly with … |
| BTrackMate |
2 |
|
|
|
Software |
… step creates a CSV file which can then be loaded into the Fiji tracker to do particle tracking with TrackMate … Last modified 01/28/2021 - 14:50 Download Page Update site Fiji MTrack Usage Example Link … step creates a CSV file which can then be loaded into the Fiji tracker to do particle tracking with TrackMate … |
| MTrack2 (ImageJ) |
2 |
|
2D, time-series |
ImageJ |
Software |
… Last modified 03/02/2020 - 16:46 Download Page http://fiji.sc/MTrack2 Documentation Link http://fiji.sc/MTrack2 … migration.tool … 5016 … Nico Stuurman … … |
| Tissue analysis from histological sections |
2 |
|
2D |
Fiji, Trainable Weka Segmentation |
Software |
… Type Workflow Author Sébastien Tosi Requires Fiji Trainable Weka Segmentation Execution Platform Linux Mac … and jpg files) located in a user defined folder by calling Fiji Weka trainable segmentation to classify each pixel, and … and jpg files) located in a user defined folder by calling Fiji Weka trainable segmentation to classify each pixel, and … |
| Sync Windows |
2 |
|
2D, 3D, time-series |
ImageJ |
Software |
… Last modified 10/17/2019 - 12:20 Download Page http://fiji.sc/Sync_Windows Documentation Link http://fiji.sc/Sync_Windows … migration.tool … Kelly Patrick … … |
| Open Virtual stack in Fiji |
2 |
|
|
|
Software |
… … Moritz … Open Virtual stack in Fiji … |
| Spheres and Tubes in 3D |
2 |
|
3D |
ImageJ, 3D Viewer |
Software |
… Last modified 10/16/2019 - 18:52 Download Page http://fiji.sc/ Documentation Link http://fiji.sc/Spheres_and_Tubes_in_3D … migration.tool … 4180 … … |
| Transform Virtual Stack Slices |
2 |
|
3D |
ImageJ |
Software |
… Last modified 10/18/2019 - 16:02 Download Page http://fiji.sc/Transform_Virtual_Stack_Slices Documentation Link http://fiji.sc/Transform_Virtual_Stack_Slices … migration.tool … … |
| Interactive Rigid (ImageJ) |
2 |
|
2D |
ImageJ |
Software |
… Last modified 03/02/2020 - 22:29 Download Page http://fiji.sc/Interactive_Rigid Documentation Link http://fiji.sc/Interactive_Rigid … migration.tool … 4670 … Stephan … |
| 2D and 3D tracking based on global cost function optimization |
2 |
|
2D, 3D, time-series |
ImageJ, MTrackJ, ImageScience.jar, Jama, Tracking2.0 |
Software |
… : Used for visualization of tracks. Preinstalled in Fiji. Imagescience.jar : This library is used by MTrackJ. Use … site to install this plugin. jama.jar . Preinstalled in Fiji. ##Advantages: support blinking (with a parameters … : Used for visualization of tracks. Preinstalled in Fiji. Imagescience.jar : This library is used by MTrackJ. Use … |
| FeatureJ Laplacian |
2 |
|
2D, 3D |
ImageJ |
Software |
… as a part of ImageJ plugin FeatureJ , and included in Fiji. The second URL above is the link to its Javadoc. … for using this class in Jython script is in CMCI Jython/Fiji cookbook: FeatureJ . has function Image feature … as a part of ImageJ plugin FeatureJ , and included in Fiji. The second URL above is the link to its Javadoc. … |
| ContourLines |
2 |
|
2D |
ImageJ, Fiji |
Software |
… Type Component Author Eugene Katrukha Requires ImageJ Fiji Execution Platform Linux Mac Windows Implementation Type … Free and open source License MIT Description ImageJ/FIJI plugin generating contour lines with equal spacing on … … Image feature detection … Bioimage informatics … ImageJ/FIJI plugin generating contour lines with equal spacing on … |
| Landmark Correspondences |
2 |
|
2D |
ImageJ, Fiji |
Software |
… Type Component Author Stephan Saalfeld Requires ImageJ Fiji Execution Platform Linux Mac Windows Implementation Type … Last modified 05/19/2021 - 20:57 Download Page http://fiji.sc/Landmark_Correspondences … migration.tool … Stephan … |
| Parallel Iterative Deconvolution |
2 |
|
2D, 3D |
ImageJ, Huygens, PSF Generator |
Software |
… Last modified 10/16/2019 - 18:10 Download Page http://fiji.sc/Parallel_Iterative_Deconvolution Documentation Link http://fiji.sc/Parallel_Iterative_Deconvolution … migration.tool … … |
| Chess |
2 |
|
|
ImageJ |
Software |
… to make an image interactive. It let you play chess within Fiji! Entry Curator migration Post date 10/11/2013 - 15:08 … Last modified 10/15/2019 - 18:00 Download Page http://fiji.sc/Chess … migration.tool … basic_html … migration … … to make an image interactive. It let you play chess within Fiji! … Chess … |
| ImageJ Auto Crop |
2 |
|
2D |
ImageJ |
Software |
… by cropping as much background as possible. Found in Fiji, under Image> Adjust. In the version labeled with (guess … 23:27 Download Page Source code Documentation Link http://fiji.sc/Auto_Crop … migration.tool … 4526 … 4527 … 4145 … … by cropping as much background as possible. Found in Fiji, under Image> Adjust. In the version labeled with (guess … |
| Multi-Template matching |
2 |
|
2D |
Fiji |
Software |
… orcid.org/0000-0001-7686-3249 Gehrig Jochen Requires Fiji Execution Platform Linux Mac Windows Implementation Type … overlap between detections. The solution is available as a Fiji plugin (Multi-Template Matching AND IJ-OpenCV update … overlap between detections. The solution is available as a Fiji plugin (Multi-Template Matching AND IJ-OpenCV update … |
| TrackMate |
1.993 |
|
2D, 3D, multi-channel, time-series |
Fiji |
Software |
… Type Collection Author Jean-Yves Tinevez Requires Fiji Execution Platform Linux Mac Windows Implementation Type … Last modified 10/17/2019 - 10:27 Download Page http://fiji.sc/TrackMate Documentation Link Documentation Manual … |
| Segmentation and quantification of subcellular structures in fluorescence microscopy images using Squassh |
1.985 |
|
2D, 3D |
ImageJ, Squassh |
Software |
… in fluorescence 2D/3D microscopy images based on a Fiji plugin **Squassh** is described in Rizek et al (2014). … - 19:02 Download Page The paper. Documentation Link Fiji-Squassh colocalization plugin notes by Chong Zhang … in fluorescence 2D/3D microscopy images based on a Fiji plugin **Squassh** is described in Rizek et al (2014). … |
| Variational algorithms to remove stationary noise |
1.946 |
|
2D, 3D |
|
Software |
… Mac Windows Implementation Type plugin is compatible with Fiji MATLAB Python Supported image dimension 2D 3D … th.univ-toulouse.fr/~weiss/Codes/VSNR/Documentation_VSNR_V2_Fiji.p… Reference Publication Link … |
| SPIM Registration Method (ImageJ) |
1.907 |
|
3D |
ImageJ |
Software |
… Last modified 04/27/2023 - 17:10 Download Page http://fiji.sc/SPIM_Registration_Method Documentation Link http://fiji.sc/SPIM_Registration_Method Reference Publication Link … |
| Region Competition |
1 |
|
|
Fiji, MosaicSuite |
Software |
… Grégory Paul Ivo F Sbalzarini Mosaic group Requires Fiji MosaicSuite Execution Platform Linux Mac Windows … |
| VIB Protocol |
1 |
|
3D |
ImageJ, CellProfiler Align |
Software |
… Last modified 10/18/2019 - 14:33 Download Page http://fiji.sc/VIB_Protocol … migration.tool … Mark Longair … … |
| Local Thickness (ImageJ) |
1 |
|
3D |
ImageJ |
Software |
… Last modified 03/02/2020 - 16:54 Download Page http://fiji.sc/Local_Thickness Documentation Link … |
| Bleach Correction |
1 |
|
2D, 3D, time-series |
ImageJ |
Software |
… Last modified 02/16/2021 - 13:57 Download Page http://fiji.sc/Bleach_Correction Reference Publication Link Bleach … |
| White Balance |
1 |
|
|
ImageJ |
Software |
… 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 … |
| Myotracker |
1 |
|
2D |
Fiji |
Software |
… Type Workflow Author Jose Fernandez Requires Fiji Execution Platform Linux Mac Windows Implementation Type … |
| Grayscale granulometry |
1 |
|
|
|
Software |
… License/Openness I do not know Description This imageJ/Fiji plugin provides an analysis of the granulometry inside … operation … Analysis … Microscopy … This imageJ/Fiji plugin provides an analysis of the granulometry inside … |
| Test Java3D |
1 |
|
3D |
ImageJ |
Software |
… Last modified 10/17/2019 - 16:31 Download Page http://fiji.sc/Test_Java3D Documentation Link … |
| Tubeness |
1 |
|
2D, 3D |
ImageJ |
Software |
… otherwise return 0. This plugin is now bundled as part of Fiji. has function Image feature detection has topic Bioimage … otherwise return 0. This plugin is now bundled as part of Fiji. … Tubeness … |
| Nucleus Counter (ImageJ) |
1 |
|
|
ImageJ, Graylevel Watershed for ImageJ |
Software |
… Last modified 03/03/2020 - 10:02 Download Page http://fiji.sc/Nucleus_Counter … migration.tool … basic_html … … |
| Celsius to fahrenheit |
1 |
|
|
|
Software |
… Last modified 03/03/2020 - 18:07 Download Page http://fiji.sc/Celsius_to_fahrenheit … migration.tool … 5041 … 5042 … |
| Microscope autopilot |
1 |
|
2D, 3D, multi-channel, time-series |
|
Software |
… Programming Language Java is compatible with ImageJ Fiji Supported image dimension 2D 3D multi-channel … |
| Multithreaded Image Processing in Javascript |
1 |
|
|
ImageJ |
Software |
… Last modified 10/16/2019 - 17:09 Download Page http://fiji.sc/Multithreaded_Image_Processing_in_Javascript … … |
| HDomeTransform3D |
1 |
|
2D, 3D |
Fiji, MiToBo |
Software |
… Type Component Author Oliver Greß Requires Fiji MiToBo Execution Platform Linux Mac Windows … |
| mamut2r |
1 |
|
|
|
Software |
… to imports data coming from .xml files generated with the Fiji MaMuT plugin for lineage and tracking of biological … to imports data coming from .xml files generated with the Fiji MaMuT plugin for lineage and tracking of biological … |
| NucleusJ |
1 |
|
2D, 3D |
Fiji, MorphoLibJ |
Software |
… Type Collection Author Poulet, Alex Requires Fiji MorphoLibJ Execution Platform Linux Mac Windows … |
| 3D Nuclei Clustering Tool |
1 |
|
3D, multi-channel |
ImageJ |
Software |
… Language ImageJ Macros Jython is compatible with Fiji Supported image dimension 3D multi-channel Interaction … |
| Particle Tracker 2D/3D |
1 |
|
2D, 3D, multi-channel, time-series |
Fiji, MosaicSuite |
Software |
… Ivo Sbalzarini Janicke Cardinale Mosaic group Requires Fiji MosaicSuite Execution Platform Linux Mac Windows … |
| RGB-Gray Merge (ImageJ) |
1 |
|
2D, 3D |
ImageJ |
Software |
… Last modified 03/01/2020 - 18:17 Download Page http://fiji.sc/RGB-Gray_Merge … migration.tool … 4135 … 4155 … … |
| Grid |
1 |
|
2D, 3D |
ImageJ, Grid |
Software |
… Last modified 03/03/2020 - 10:18 Download Page http://fiji.sc/Grid Usage Example Link … |
| Analyzing gels and western blots with ImageJ |
1 |
|
2D |
ImageJ |
Software |
… eb.bioquant.uni-heidelberg.de/image-analysis/ShortTutorials/Fiji_GelAnalyzer.pdf Additional keywords intensity profile … eb.bioquant.uni-heidelberg.de/image-analysis/ShortTutorials/Fiji_GelAnalyzer.pdf … Analyzing gels and western blots with … |
| FISH signals detection |
1 |
|
2D |
Fiji |
Software |
… Type Component Author Sébastien Tosi Requires Fiji Programming Language ImageJ Macros Supported image … |
| 3D affine transformation based on paired points |
1 |
|
3D |
Fiji |
Software |
… Type Component Author Kota Miura Requires Fiji Execution Platform Linux Mac Windows Programming … |
| Graph Cut |
1 |
|
|
ImageJ, Graph Cut |
Software |
… Last modified 03/03/2020 - 11:28 Download Page http://fiji.sc/Graph_Cut Documentation Link … |
| MorphoLibJ |
1 |
|
2D, 3D |
ImageJ |
Software |
… plugin Programming Language Java is compatible with ImageJ Fiji Supported image dimension 2D 3D Interaction Level … |
| RGB Measure Plus |
1 |
|
multi-channel |
ImageJ |
Software |
… Last modified 10/18/2019 - 13:40 Download Page http://fiji.sc/RGB_Measure_Plus … migration.tool … Dimiter Prodanov … |
| IsoData Classifier |
1 |
|
2D |
ImageJ |
Software |
… Last modified 03/01/2020 - 12:33 Download Page http://fiji.sc/IsoData_Classifier … migration.tool … 4977 … 4016 … … |
| BUnwarpJ |
1 |
|
2D |
ImageJ |
Software |
… Last modified 03/02/2020 - 21:19 Download Page http://fiji.sc/BUnwarpJ Documentation Link … |
| MaMuT |
1 |
|
2D, 3D, multi-channel, time-series |
Fiji, BigDataViewer, TrackMate |
Software |
… orcid.org/0000-0002-0998-4718 Pietzsch Tobias Requires Fiji BigDataViewer TrackMate Execution Platform Linux Mac … |
| Stitching 2D/3D |
1 |
|
2D, 3D |
ImageJ |
Software |
… Last modified 10/17/2019 - 13:45 Download Page http://fiji.sc/Stitching_2D/3D Documentation Link … |
| Align Image by line ROI |
1 |
|
2D |
Fiji |
Software |
… Type Component Author Johannes Schindelin Requires Fiji Execution Platform Linux Mac Windows Implementation Type … |
| MiToBo |
1 |
|
2D, 3D |
Fiji |
Software |
… Type Collection Requires Fiji Execution Platform Linux Mac Windows Implementation Type … |
| 3D Viewer |
1 |
|
3D |
ImageJ, 3D Viewer |
Software |
… Last modified 03/01/2020 - 16:03 Download Page http://fiji.sc/3D_Viewer Documentation Link … |
| The NEMO dots assembly: Single-particle tracking and analysis |
1 |
|
|
|
Software |
… This workflow presents single-particle tracking in Fiji using Track-Mate, and track motility analysis in MATLAB … … This workflow presents single-particle tracking in Fiji using Track-Mate, and track motility analysis in MATLAB … |
| Simulate Color Blindness |
1 |
|
|
ImageJ, Fiji |
Software |
… Type Component Author Johannes Schindelin Requires ImageJ Fiji Execution Platform Linux Mac Windows Implementation Type … |
| Watershed Algorithm |
1 |
|
|
ImageJ, Graylevel Watershed for ImageJ |
Software |
… Last modified 09/13/2017 - 12:07 Download Page http://fiji.sc/Watershed_Algorithm_(ImageJ_plugin) … migration.tool … |
| SME |
1 |
|
3D |
|
Software |
… 3D image stacks. We provide a parameter-free ImageJ/Fiji plugin that allows 2D visualization and interpretation … 3D image stacks. We provide a parameter-free ImageJ/Fiji plugin that allows 2D visualization and interpretation … |
| Temporal-Color Code |
1 |
|
3D, time-series |
ImageJ |
Software |
… Last modified 10/17/2019 - 12:25 Download Page http://fiji.sc/Temporal-Color_Code … migration.tool … Miura Kota … … |
| 3D PSF estimator |
1 |
|
3D |
ImageJ, Fiji, MosaicSuite |
Software |
… Author Jannick Cardinale Mosaic group Requires ImageJ Fiji MosaicSuite Execution Platform Linux Mac Windows … |
| SIOX: Simple Interactive Object Extraction |
1 |
|
2D, multi-channel |
ImageJ |
Software |
… Last modified 10/18/2019 - 13:36 Download Page http://fiji.sc/SIOX:_Simple_Interactive_Object_Extraction … … |
| Local Z Projector |
1 |
|
3D, multi-channel, time-series |
ImgLib2, ImageJ 2.x |
Software |
… Local Z Projector is an ImageJ2 plugin, available in Fiji, that can perform local-Z projection of a 3D stack, … … Local Z Projector is an ImageJ2 plugin, available in Fiji, that can perform local-Z projection of a 3D stack, … |
| Microtubules Tool (3D) |
1 |
|
3D, multi-channel |
ImageJ, Fiji, Skeletonize3D, 3D Objects Counter |
Software |
… Type Workflow Author Volker Baecker Requires ImageJ Fiji Skeletonize3D 3D Objects Counter Execution Platform … |
| Tube un-winder |
1 |
|
3D |
Fiji |
Software |
… Type Component Author Sébastien Tosi Requires Fiji Execution Platform Linux Mac Windows Programming … |
| MosaicIA |
1 |
|
3D, time-series |
Fiji, MosaicSuite |
Software |
… Shivanandan, A. Radenovic, and I. F. Sbalzarini Requires Fiji MosaicSuite Execution Platform Linux Mac Windows … |
| List all threads |
1 |
|
|
ImageJ |
Software |
… Last modified 09/13/2017 - 12:02 Download Page http://fiji.sc/List_all_threads … migration.tool … migration … List … |
| Super-Resolution Radial Fluctuations (SRRF) |
1 |
|
2D, time-series |
ImageJ |
Software |
… The SRRF algorithm source code and plugin for ImageJ and Fiji Documentation Link User guide zip file Reference … |
| Trakem2 lens distortion correction |
1 |
|
2D, 3D, multi-channel |
Fiji, TrakEM2 |
Software |
… Saalfeld Stephan orcid.org/0000-0002-4106-1761 Requires Fiji TrakEM2 Execution Platform Linux Mac Windows … |
| Quality metric of 3D SPIM stacks |
1 |
|
|
|
Software |
… Free and open source Description An ImageJ/Fiji macro which measures quality through two stacks of … … iSPIM … basic_html … Light-sheet microscopy … An ImageJ/Fiji macro which measures quality through two stacks of … |
| Minimum cost Z surface projection |
1 |
|
3D |
Fiji |
Software |
… Type Component Author Benoit Lombardot Requires Fiji Execution Platform Linux Mac Windows Implementation Type … |
| Report a Bug |
1 |
|
|
ImageJ |
Software |
… Last modified 10/18/2019 - 13:38 Download Page http://fiji.sc/Report_a_Bug … migration.tool … 4961 … Mark Longair … … |
| 3Dscript |
1 |
|
3D, multi-channel |
ImageJ |
Software |
… BSD 2-Clause License Description 3Dscript is a plugin for Fiji/ImageJ for creating 3D and 4D animations of microscope … … Volume rendering … 3Dscript is a plugin for Fiji/ImageJ for creating 3D and 4D animations of microscope … |
| 3D vessel segmentation of synchrotron phase contrast tomography |
1 |
|
3D |
Fiji, ilastik |
Software |
… Type Workflow Requires Fiji ilastik Execution Platform Linux Mac Windows Supported … |
| Level Sets |
1 |
|
2D |
ImageJ |
Software |
… Last modified 03/01/2020 - 12:43 Download Page http://fiji.sc/Level_Sets … migration.tool … Curtis Rueden … 4004 … … |
| Miniature Faking |
1 |
|
2D |
ImageJ |
Software |
… Last modified 10/16/2019 - 12:19 Download Page http://fiji.sc/Miniature_Faking … migration.tool … 4135 … 4053 … … |
| Interaction Analysis |
1 |
|
|
Fiji, MosaicSuite |
Software |
… Ivo F Sbalzarini Jo A Helmuth Grégory Paul Requires Fiji MosaicSuite Execution Platform Linux Mac Windows … |
| Image Expression Parser |
1 |
|
|
ImageJ |
Software |
… Last modified 03/03/2020 - 12:06 Download Page http://fiji.sc/Image_Expression_Parser … migration.tool … 5037 … … |
| Enhance Local Contrast (CLAHE) |
1 |
|
2D |
ImageJ |
Software |
… Last modified 10/29/2019 - 18:29 Download Page http://fiji.sc/Enhance_Local_Contrast_(CLAHE) … migration.tool … … |
| Correlia |
1 |
|
2D, multi-channel |
ImageJ |
Software |
… GPL 3.0 Description Correlia is an open-source ImageJ/FIJI plug-in for the registration of 2D multi-modal … … Multimodal imaging … Correlia is an open-source ImageJ/FIJI plug-in for the registration of 2D multi-modal … |
| MIJ |
1 |
|
|
ImageJ, MATLAB |
Software |
… source Description A Java package for running ImageJ and Fiji within Matlab. has function Conversion has topic … informatics … A Java package for running ImageJ and Fiji within Matlab. … MIJ … |
| SPIM de-striper |
1 |
|
|
Fiji |
Software |
… Type Component Author Sébastien Tosi Requires Fiji Execution Platform Linux Mac Windows Programming … |
| Image Stitching |
1 |
|
2D, 3D, multi-channel, time-series |
ImageJ, EBImage tile |
Software |
… Last modified 03/03/2020 - 11:16 Download Page http://fiji.sc/Image_Stitching Documentation Link … |
| Auto Local Threshold |
1 |
|
2D |
ImageJ |
Software |
… Last modified 10/29/2019 - 18:14 Download Page http://fiji.sc/Auto_Local_Threshold … migration.tool … Gabriel … |
| Integral Image Filters |
1 |
|
2D |
ImageJ |
Software |
… Last modified 03/01/2020 - 12:10 Download Page http://fiji.sc/Integral_Image_Filters … migration.tool … Stephan … |
| Linear Kuwahara (ImageJ) |
1 |
|
2D |
ImageJ |
Software |
… Last modified 03/02/2020 - 16:36 Download Page http://fiji.sc/Linear_Kuwahara … migration.tool … 4177 … 4155 … Edge … |
| Anisotropic Diffusion 2D |
1 |
|
2D |
Fiji |
Software |
… Vladimir Pilny Jiri Janacek Johannes Schindelin Requires Fiji Execution Platform Linux Mac Windows Implementation Type … |
| Save as animated gif (ImageJ) |
1 |
|
time-series |
ImageJ |
Software |
… Last modified 03/02/2020 - 12:00 Download Page http://fiji.sc/Save_as_animated_gif … migration.tool … Ryan Raz … … |
| StackReg |
1 |
|
3D, time-series |
ImageJ, TurboReg |
Software |
… 03/16/2022 - 07:54 Download Page https://github.com/fiji-BIG/StackReg/blob/master/src/main/java/StackReg_.java … |
| Interactive Stack Rotation (ImageJ) |
1 |
|
3D, multi-channel |
ImageJ |
Software |
… Last modified 03/02/2020 - 22:07 Download Page http://fiji.sc/Interactive_Stack_Rotation … migration.tool … Stephan … |
| Using ImageJ to Analyze the Size, Shape, and Directionality of Networks of Coupled Astrocytes |
1 |
|
3D |
Fiji |
Software |
… Steven Condamine Dorly Verdier Arlette Kolta Requires Fiji Execution Platform Linux Mac Windows Supported image … |
| Background Subtractor |
1 |
|
|
Fiji, MosaicSuite |
Software |
… Component Author Janick Cardinale MOSAIC Group Requires Fiji MosaicSuite Execution Platform Linux Mac Windows … |
| MIA |
1 |
|
2D, 3D, multi-channel, time-series |
Fiji, MorphoLibJ |
Software |
… Type Collection Author Stephen Cross Requires Fiji MorphoLibJ Execution Platform Linux Mac Windows … |
| ImgLib2 |
1 |
|
2D, 3D, multi-channel, time-series |
ImageJ |
Software |
… It is the basis of KNIME, ImageJ2 and a couple of Fiji plugins. has topic Bioimage informatics Entry Curator … It is the basis of KNIME, ImageJ2 and a couple of Fiji plugins. … ImgLib2 … |
| nanoFeatures |
1 |
|
2D, multi-channel |
Matlab Image Processing Toolbox, Matlab Computer Vision System Toolbox, MATLAB |
Software |
… the NIKON and ONI microscopes and from the ThunderSTORM Fiji plugin, then cluster the localizations and filter by … the NIKON and ONI microscopes and from the ThunderSTORM Fiji plugin, then cluster the localizations and filter by … |
| 3D intensity profile |
1 |
|
3D |
Fiji |
Software |
… Type Component Author Kota Miura Requires Fiji Execution Platform Linux Mac Windows Supported image … |
| ImageJ Plugin for Non-Local-Means Filtering |
1 |
|
2D |
ImageJ |
Software |
… blurring but preserves edges and boundaries. Listed in Fiji update sites. ## Algorithm Algorithm description is in … blurring but preserves edges and boundaries. Listed in Fiji update sites. ## Algorithm Algorithm description is in … |
| Analyze Particles |
1 |
|
2D |
ImageJ, Fiji |
Software |
… Type Component Requires ImageJ Fiji Execution Platform Linux Mac Windows Implementation Type … |
| BigDataViewer |
1 |
|
2D, 3D, multi-channel, time-series |
ImgLib2 |
Software |
… microscopy data in mind and integrates well with Fiji's SPIMage processing pipeline. has function Image … microscopy data in mind and integrates well with Fiji's SPIMage processing pipeline. … BigDataViewer … |
| Upload Sample Image |
1 |
|
|
ImageJ |
Software |
… Last modified 05/03/2023 - 16:15 Download Page http://fiji.sc/Upload_Sample_Image … migration.tool … 4972 … 4984 … … |
| Image Stabilizer |
1 |
|
2D, time-series |
ImageJ |
Software |
… Last modified 06/06/2018 - 18:59 Download Page http://fiji.sc/Image_Stabilizer Documentation Link … |
| Find Maxima (Python) |
1 |
|
2D |
SciPy, PIL, Python, Jupyter, Jupyter notebook |
Software |
… implemented in Python recreated from implementation in Fiji(ImageJ) This is a re-implementation of the java plugin … implemented in Python recreated from implementation in Fiji(ImageJ) This is a re-implementation of the java plugin … |
| Otsu Thresholding |
1 |
|
|
ImageJ, Histogram |
Software |
… Last modified 09/13/2017 - 12:05 Download Page http://fiji.sc/Otsu_Thresholding … migration.tool … migration … Otsu … |
| InspectJ |
1 |
|
2D |
ImageJ |
Software |
… Free and open source Description InspectJ is a free ImageJ/FIJI tool to inspect digital image integrity. InspectJ_v2 is … recognition … Image validation … InspectJ is a free ImageJ/FIJI tool to inspect digital image integrity. InspectJ_v2 is … |
| File Import |
1 |
|
|
ImageJ |
Software |
… Last modified 03/10/2019 - 03:45 Download Page http://fiji.sc/File_Import … migration.tool … migration … File Import … |
| MIPs for PSFs |
1 |
|
3D |
ImageJ, Fiji |
Software |
… Author Laurent Gelman Jens Rietdorf Requires ImageJ Fiji Execution Platform Linux Mac Windows Programming … |
| Skeletonize3D |
1 |
|
2D, 3D |
ImageJ |
Software |
… Last modified 04/27/2023 - 12:52 Download Page http://fiji.sc/Skeletonize3D … migration.tool … 4232 … Ignacio … |
| WormScan |
1 |
|
|
Fiji |
Software |
… Mark D. Mathew Neal D. Mathew Paul R. Ebert Requires Fiji Execution Platform Linux Mac Windows Programming … |
| SPIM Bead Registration |
1 |
|
|
ImageJ |
Software |
… Last modified 04/27/2023 - 16:50 Download Page http://fiji.sc/SPIM_Bead_Registration_(deprecated) … migration.tool … |
| Interactive Similarity |
1 |
|
|
ImageJ |
Software |
… Last modified 03/01/2020 - 12:51 Download Page http://fiji.sc/Interactive_Similarity … migration.tool … … |
| CellProfiler Align |
1 |
|
2D |
CellProfiler |
Software |
… might preprocess images using a plugin for that purpose in FIJI/ImageJ. | Supports 2D? | Supports 3D? | Respects masks? … might preprocess images using a plugin for that purpose in FIJI/ImageJ. | Supports 2D? | Supports 3D? | Respects masks? … |
| Shape Index Map |
1 |
|
2D, 3D, multi-channel, time-series |
ImageJ |
Software |
… Last modified 10/16/2019 - 20:00 Download Page http://fiji.sc/ Documentation Link … |
| Moving Least Squares |
1 |
|
|
ImageJ |
Software |
… Last modified 09/13/2017 - 12:09 Download Page http://fiji.sc/Moving_Least_Squares … migration.tool … migration … … |
| MiNA - Mitochondrial Network Analysis |
1 |
|
2D, 3D |
ImageJ |
Software |
… morphology using fluorescence images or 3D stacks in Fiji. The workflow makes use of ImageJ Ops , 3D Viewer , … morphology using fluorescence images or 3D stacks in Fiji. The workflow makes use of ImageJ Ops , 3D Viewer , … |
| ImageJ Binary Operations |
1 |
|
2D |
ImageJ |
Software |
… Mac Windows Implementation Type plugin is compatible with Fiji Supported image dimension 2D Interaction Level Automated … |
| Retinex |
1 |
|
|
ImageJ |
Software |
… Last modified 10/16/2019 - 13:33 Download Page http://fiji.sc/Retinex Documentation Link … |
| ADAPT |
1 |
|
2D, time-series |
ImageJ |
Software |
… of ProTrusions) is a plug-in developed for the ImageJ/Fiji platform to automatically detect and analyse cell … of ProTrusions) is a plug-in developed for the ImageJ/Fiji platform to automatically detect and analyse cell … |
| Adiposoft |
1 |
|
2D |
ImageJ |
Software |
… Download Page IJ wiki: Adiposoft Documentation Link http://fiji.sc/Adiposoft Reference Publication Link Galarraga et. … |
| Distance Analysis (DiAna) |
1 |
|
2D, 3D, multi-channel |
Fiji |
Software |
… Author Jean-Francois Gilles Thomas Boudier Requires Fiji Execution Platform Linux Mac Windows Implementation Type … |
| Diffraction PSF 3D |
1 |
|
3D |
ImageJ |
Software |
… Last modified 03/08/2019 - 02:17 Download Page http://fiji.sc/Diffraction_PSF_3D Documentation Link … |
| CSBDeep a toolbox for Content-aware Image Restoration (CARE) in Knime |
1 |
|
|
KNIME |
Software |
… restoration, with guidelines for training. See also the Fiji plugin. See more CSBDeep in Knime . has function Image … restoration, with guidelines for training. See also the Fiji plugin. See more CSBDeep in Knime . … CSBDeep a toolbox … |
| 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 Implementation Type … |
| shinyHTM |
1 |
|
2D, 3D, multi-channel, time-series |
|
Software |
… statistical significance Image visualization relies on Fiji/ImageJ, along with its wealth of analytical tools. … statistical significance Image visualization relies on Fiji/ImageJ, along with its wealth of analytical tools. … |
| Anaglyph for Red Cyan glasses |
1 |
|
3D |
ImageJ |
Software |
… Last modified 10/15/2019 - 17:50 Download Page http://fiji.sc/Anaglyph_for_Red_Cyan_glasses … migration.tool … 4910 … |
| View5D |
1 |
|
2D, 3D, multi-channel, time-series |
ImageJ |
Software |
… Last modified 10/18/2019 - 16:10 Download Page http://fiji.sc/View5D … migration.tool … Rainer Heintzmann … … |
| StarDist - ImageJ |
1 |
|
2D, 3D |
ImageJ |
Software |
… Free and open source Description This is the ImageJ/Fiji plugin for StarDist , a cell/nuclei detection method for … microscopy … Machine learning … This is the ImageJ/Fiji plugin for StarDist , a cell/nuclei detection method for … |
| A simple MSER based segmentation tool for spot detection in 2/3/4D. |
1 |
|
2D, 3D, time-series |
|
Software |
… Download Page Source: https://github.com/kapoorlab/Fiji-MSER, https://github.com/kapoorlab/Ma… Documentation … |
| Iterative Deconvolve 3D |
1 |
|
2D, 3D |
ImageJ |
Software |
… Last modified 03/01/2020 - 12:41 Download Page http://fiji.sc/Iterative_Deconvolve_3D … migration.tool … 4081 … … |
| Segmentation Editor |
1 |
|
2D, 3D |
ImageJ |
Software |
… Last modified 10/16/2019 - 18:28 Download Page http://fiji.sc/Segmentation_Editor … migration.tool … Johannes … |
| Series Labeler |
1 |
|
2D, 3D, multi-channel, time-series |
ImageJ |
Software |
… Last modified 10/16/2019 - 18:37 Download Page http://fiji.sc/Series_Labeler … migration.tool … 4771 … 4155 … … |
| Interactive Moving Least Squares (ImageJ) |
1 |
|
2D |
ImageJ |
Software |
… Last modified 03/02/2020 - 17:44 Download Page http://fiji.sc/Interactive_Moving_Least_Squares … migration.tool … … |
| 2D spots counting using KNIME |
1 |
|
2D |
KNIME Image Processing and Analysis |
Software |
… for KNIME workflow. Section 2.3 is also available, using Fiji. Sample image: hela -cells.tif (674k x 3) has function … for KNIME workflow. Section 2.3 is also available, using Fiji. Sample image: hela -cells.tif (674k x 3) … 2D spots … |
| RATS: Robust Automatic Threshold Selection |
1 |
|
2D |
ImageJ |
Software |
… Last modified 10/18/2019 - 14:09 Download Page http://fiji.sc/RATS:_Robust_Automatic_Threshold_Selection … |
| MosaicSuite |
1 |
|
2D, 3D, time-series |
Fiji, ImageJ 2.x |
Software |
… Ziegler, Urs Berger, Phillip Koumoutsakos, Petros Requires Fiji ImageJ 2.x Execution Platform Linux Mac Windows … |
| Replace Red with Magenta |
1 |
|
2D |
ImageJ |
Software |
… Last modified 11/12/2019 - 00:13 Download Page http://fiji.sc/Replace_Red_with_Magenta … … Johannes Schindelin … … |
| FFmpeg |
1 |
|
|
|
Software |
… see the listing here ) For handling video files in ImageJ/Fiji, see also here . has function Conversion Additional … see the listing here ) For handling video files in ImageJ/Fiji, see also here . … FFmpeg … |
| Rolling Ball Background Subtraction |
1 |
|
2D |
ImageJ |
Software |
… Last modified 10/29/2019 - 18:07 Download Page http://fiji.sc/Rolling_Ball_Background_Subtraction … migration.tool … |
| NeuroMorph |
1 |
|
3D |
Blender |
Software |
… any 3D image segmentation software, such as ilastik or Fiji . has function Analysis Object classification Image … any 3D image segmentation software, such as ilastik or Fiji . … NeuroMorph … |
| Name Landmarks and Register |
1 |
|
|
ImageJ |
Software |
… Last modified 09/13/2017 - 12:06 Download Page http://fiji.sc/Name_Landmarks_and_Register … migration.tool … … |
| Spots colocalization (ComDet) |
1 |
|
2D, multi-channel |
ImageJ, Jama |
Software |
… - 01:42 Last modified 12/17/2018 - 01:49 Download Page Fiji Update Site Documentation Link Wiki@Github @ImageJ.net … |
| 3View import list |
1 |
|
3D |
ImageJ, TrakEM2 |
Software |
… instruction in the documentation page Documentation Link Fiji wiki: 3View import list … migration.tool … 4497 … 4498 … … |
| DeepImageJ |
1 |
|
|
ImageJ, Tensorflow |
Software |
… variety of pre-trained deep learning models in ImageJ and Fiji . The plugin bridges the gap between deep learning and … variety of pre-trained deep learning models in ImageJ and Fiji . The plugin bridges the gap between deep learning and … |
| Image-classification with deep learning in KNIME |
1 |
|
|
|
Software |
… table generated by the qualitative annotations plugins in Fiji. Workflows for the training of a model AND for the … table generated by the qualitative annotations plugins in Fiji. Workflows for the training of a model AND for the … |
| ImarisXT |
1 |
|
|
ImageJ, Imaris, MATLAB, ImarisCell, ImarisMeasurementPro, ImarisTrack, ImarisFilamentTracer, Python |
Software |
… Documentation Link ImageJ and Fiji Support in ImarisXT … migration.tool … Oxford … |
| Squassh |
1 |
|
2D, 3D |
Fiji, MosaicSuite |
Software |
… Type Collection Author MOSAIC Group Requires Fiji MosaicSuite Execution Platform Linux Mac Windows … |
| Volume Calculator |
1 |
|
3D |
ImageJ, Skeletonize3D |
Software |
… Last modified 10/18/2019 - 14:49 Download Page http://fiji.sc/Volume_Calculator … migration.tool … Peter C. Marks … … |
| Spline Deformation Generator |
1 |
|
2D |
ImageJ |
Software |
… Last modified 10/16/2019 - 20:25 Download Page http://fiji.sc/Spline_Deformation_Generator … migration.tool … 4939 … |
| Blob segmentation |
1 |
|
2D |
Fiji, MorphoLibJ |
Software |
… Type Component Author Ignacio Arganda-Carreras Requires Fiji MorphoLibJ Execution Platform Linux Mac Windows … |
| Time Stamper |
1 |
|
time-series |
ImageJ |
Software |
… Last modified 10/17/2019 - 16:22 Download Page http://fiji.sc/Time_Stamper Documentation Link … |
| Multi Kymograph |
1 |
|
2D, time-series |
ImageJ |
Software |
… Description This macro and plugins suite for ImageJ (and Fiji) serves to measure the velocity of moving structures and … informatics … This macro and plugins suite for ImageJ (and Fiji) serves to measure the velocity of moving structures and … |
| RGB to Montage |
1 |
|
multi-channel |
ImageJ |
Software |
… Last modified 10/18/2019 - 13:33 Download Page http://fiji.sc/RGB_to_Montage … migration.tool … unknown … 4135 … … |
| Blood vessel segmentation and network analysis |
1 |
|
3D |
Fiji |
Software |
… Type Workflow Author Sébastien Tosi Requires Fiji Execution Platform Linux Mac Windows Programming … |
| Correct 3D drift |
1 |
|
2D, 3D, time-series |
|
Software |
… Last modified 03/03/2020 - 12:30 Download Page http://fiji.sc/Correct_3D_drift Reference Publication Link … |
| MultiStackReg |
1 |
|
3D |
Fiji, TurboReg |
Software |
… Type Component Author Brad Busse Requires Fiji TurboReg Execution Platform Linux Mac Windows … |
| RGB Profiler |
1 |
|
multi-channel |
ImageJ |
Software |
… Last modified 10/18/2019 - 13:27 Download Page http://fiji.sc/RGB_Profiler … migration.tool … Christophe … |
| GDSC plugins |
1 |
|
|
Fiji |
Software |
… Type Collection Author Alex Herbert Requires Fiji Execution Platform Linux Mac Windows Implementation Type … |
| HyphaTracker |
1 |
|
2D, time-series |
ImageJ |
Software |
… Language ImageJ Macros is compatible with ImageJ Fiji Supported image dimension 2D time-series Interaction … |
| Stochastic Denoising |
1 |
|
2D |
ImageJ |
Software |
… Last modified 10/17/2019 - 16:18 Download Page http://fiji.sc/Stochastic_Denoising Reference Publication Link … |
| Reconstruct Reader |
1 |
|
|
ImageJ, TrakEM2 |
Software |
… Last modified 10/18/2019 - 13:25 Download Page http://fiji.sc/Reconstruct_Reader … migration.tool … 4972 … Larry … |
| PTA2 |
1 |
|
2D |
Fiji |
Software |
… Type Component Author Yoshiyuki Arai Requires Fiji Execution Platform Linux Mac Windows Implementation Type … |
| Thresholder (ImageJ) |
1 |
|
2D, 3D, time-series |
ImageJ |
Software |
… java file Documentation Link ImageJ Documentation Fiji Documentation (Links to ImageJ documentation) … lascholz … |
| TrakEM2 |
1 |
|
2D, 3D |
ImageJ, 3D Viewer |
Software |
… and image stitching, registration, editing and annotation (Fiji comes with TrakEM2). It supports arbitrary-sized … and image stitching, registration, editing and annotation (Fiji comes with TrakEM2). It supports arbitrary-sized … |
| Image Stitching |
1 |
|
|
|
Software |
… Last modified 09/12/2017 - 11:03 Download Page http://fiji.sc/Image_Stitching … migration.tool … migration … Image … |
| MorphoNet |
1 |
|
2D, 3D, multi-channel, time-series |
|
Software |
… Windows Implementation Type web is compatible with ImageJ Fiji Supported image dimension 2D 3D multi-channel … |
| MultiThresholder (ImageJ) |
1 |
|
2D, 3D |
ImageJ |
Software |
… Last modified 03/02/2020 - 17:42 Download Page http://fiji.sc/MultiThresholder … migration.tool … 4046 … 4155 … … |
| ClearVolume |
0.997 |
|
3D, multi-channel, time-series |
ClearCL, ClearGL |
Software |
… volumes. Moreover, ClearVolume is integrated into the Fiji/ImageJ2/KNIME ecosystem. You can now open your stacks … volumes. Moreover, ClearVolume is integrated into the Fiji/ImageJ2/KNIME ecosystem. You can now open your stacks … |
| Sholl Analysis (ImageJ) |
0.942 |
|
2D, 3D |
ImageJ |
Software |
… Last modified 05/03/2023 - 21:48 Download Page http://fiji.sc/Sholl_Analysis Documentation Link Scholl Analysis … |
| ImageJ Analyze Skeleton |
0.896 |
|
2D, 3D |
ImageJ, Analyze 12.0 |
Software |
… Last modified 04/27/2023 - 14:09 Download Page http://fiji.sc/AnalyzeSkeleton Reference Publication Link … |
| ImageJ Align RGB planes |
0.876 |
|
2D |
ImageJ, EBImage rotate, CellProfiler Align |
Software |
… http://fiji.sc/Align_RGB_planes … migration.tool … 4472 … 4473 … … |
| Quantifying staining in tissue sections |
0.831 |
|
2D |
ImageJ, Colour Deconvolution |
Software |
… 15:10 Last modified 04/29/2023 - 22:32 Documentation Link Fiji colour deconvolution page (same plugin) Reference … |
