Template:ComponentTable:sc.fiji:fiji


Name Description Repository Artifact License Team
SciJava Common SciJava Common is a shared library for SciJava software. It provides a plugin framework, with an extensible mechanism for service discovery, backed by its own annotation processor, so that plugins can be loaded dynamically. It is used by downstream projects in the SciJava ecosystem, such as ImageJ and SCIFIO. on GitHub scijava-common BSD-2 Curtis Rueden
SciJava Configuration SciJava Configuration is a shared collection of files for SciJava software. It provides configuration files for common SciJava dependencies, such as logback and slf4j. on GitHub scijava-config BSD-2 Curtis Rueden
Logback Classic Module logback-classic module logback-classic Eclipse Public License - v 1.0, GNU Lesser General Public License ceki, hixi
SCIFIO-Bio-Formats Compatibility Format Compatibility layer for using un-converted Bio-Formats readers in SCIFIO applications. on GitHub scifio-bf-compat BSD-2 Curtis Rueden
SCIFIO HDF5 SCIFIO plugins for HDF5-based formats. on GitHub scifio-hdf5 BSD-2 Henry Pinkard, Curtis Rueden
SCIFIO Life Sciences Extension Provides SCIFIO support for proprietary life science formats. on GitHub scifio-lifesci GPLv2 Curtis Rueden
SCIFIO OME-XML Extension SCIFIO support for the OME data model, including OME-XML and OME-TIFF. on GitHub scifio-ome-xml BSD-2 Curtis Rueden
ImageJ ImageJ is an open source Java image processing program inspired by NIH Image for the Macintosh. on GitHub imagej BSD-2 Curtis Rueden
ImageJ Legacy Bridge The legacy component enables backward compatibility with the legacy version of ImageJ (1.x). It contains the code necessary to translate ImageJ images into ImageJ1 format and back, so that legacy plugins can be executed faithfully. on GitHub imagej-legacy BSD-2 Curtis Rueden
Op Finder Interactive UI component for browsing and running available Ops. on GitHub op-finder GPLv3 Curtis Rueden
3D Blob Segmentation 3D Blob Segmentation plugin for Fiji. on GitHub 3D_Blob_Segmentation GPLv3 Curtis Rueden
3D Objects Counter 3D Objects Counter plugin for Fiji. on GitHub 3D_Objects_Counter GPLv3 Daniel James White, Curtis Rueden
3D Viewer 3D Viewer for visualizing image stacks three-dimensionally. on GitHub 3D_Viewer GPLv3 Curtis Rueden
Analyze Skeleton Analysis of 2D and 3D skeleton images. on GitHub AnalyzeSkeleton_ GPLv3 Ignacio Arganda-Carreras, Curtis Rueden
Anisotropic Diffusion 2D Anisotropic Diffusion 2D plugin for Fiji. on GitHub Anisotropic_Diffusion_2D GPLv3 Curtis Rueden
Archipelago Plugins Archipelago Plugins plugin for Fiji. on GitHub Archipelago_Plugins GPLv3 Larry Lindsey, Curtis Rueden
Arrow Arrow plugin for Fiji. on GitHub Arrow_ GPLv3 Jean-Yves Tinevez, Curtis Rueden
Auto Threshold Auto Threshold plugin for Fiji. on GitHub Auto_Threshold GPLv3 Gabriel Landini, Curtis Rueden
Balloon Segmentation Balloon Segmentation plugin for Fiji. on GitHub BalloonSegmentation_ GPLv2 Curtis Rueden
Bug Submitter Bug Submitter plugin for Fiji. on GitHub Bug_Submitter GPLv3 Curtis Rueden
CPU Meter CPU Meter plugin for Fiji. on GitHub CPU_Meter GPLv3 Curtis Rueden
Calculator Plus Calculator Plus plugin for Fiji. on GitHub Calculator_Plus GPLv3 Curtis Rueden
Cell Counter Cell Counter plugin for ImageJ. on GitHub Cell_Counter GPLv3 Curtis Rueden
Coloc 2 Fiji's plugin for colocalization analysis. on GitHub Colocalisation_Analysis GPLv3 Daniel James White, Tom Kazimiers, Ellen Arena, Curtis Rueden
Color Histogram Color Histogram plugin for Fiji. on GitHub Color_Histogram GPLv3 Curtis Rueden
Color Inspector 3D Color Inspector 3D plugin for Fiji. on GitHub Color_Inspector_3D GPLv3 Curtis Rueden
Colour Deconvolution Colour Deconvolution plugin for Fiji. on GitHub Colour_Deconvolution GPLv3 Gabriel Landini, Curtis Rueden
CorrectBleach CorrectBleach plugin for Fiji. on GitHub CorrectBleach_ GPLv3 Kota Miura, Curtis Rueden
Correct 3D Drift Script to register time frames (stacks) to each other. on GitHub Correct_3D_Drift GPLv3 Christian Tischer, Curtis Rueden
Descriptor based registration Descriptor based registration plugin for Fiji. on GitHub Descriptor_based_registration GPLv3 Stephan Preibisch, Curtis Rueden
Dichromacy Dichromacy plugin for Fiji. on GitHub Dichromacy_ GPLv3 Gabriel Landini, Curtis Rueden
Directionality Directionality plugin for Fiji. on GitHub Directionality_ GPLv3 Jean-Yves Tinevez, Curtis Rueden
FS Align TrakEM2 FS Align TrakEM2 plugin for Fiji. on GitHub FS_Align_TrakEM2 GPLv3 Larry Lindsey, Curtis Rueden
Feature Detection Feature Detection plugin for Fiji. on GitHub Feature_Detection GPLv3 Curtis Rueden
Fiji Archipelago Fiji Archipelago plugin for Fiji. on GitHub Fiji_Archipelago GPLv2 Larry Lindsey, Curtis Rueden
Fiji Developer Fiji Developer plugin for Fiji. on GitHub Fiji_Developer GPLv3 Curtis Rueden
Fiji Package Maker Fiji Package Maker plugin for Fiji. on GitHub Fiji_Package_Maker GPLv3 Curtis Rueden
Fiji Plugins Fiji Plugins plugin for Fiji. on GitHub Fiji_Plugins GPLv2 Curtis Rueden
FlowJ FlowJ plugin for Fiji. on GitHub FlowJ_ GPLv3 Jean-Yves Tinevez, Curtis Rueden
Graph Cut Graph Cut plugin for Fiji. on GitHub Graph_Cut GPLv3 Jan Funke, Curtis Rueden
Gray Morphology Gray Morphology plugin for Fiji. on GitHub Gray_Morphology GPLv3 Dimiter Prodanov, Curtis Rueden
Helmholtz Analysis Helmholtz Analysis plugin for Fiji. on GitHub Helmholtz_Analysis GPLv3 Curtis Rueden
IJ Robot IJ Robot plugin for Fiji. on GitHub IJ_Robot GPLv3 Gabriel Landini, Curtis Rueden
IO IO plugin for Fiji. on GitHub IO_ GPLv3 Gregory Jefferis, Curtis Rueden
Image5D The Image5D plugins extend image stacks to 5 dimensions: x, y, channel (color), slice (z), frame (t). on GitHub Image_5D BSD-2 Curtis Rueden
Image Expression Parser Image Expression Parser plugin for Fiji. on GitHub Image_Expression_Parser GPLv3 Jean-Yves Tinevez, Curtis Rueden
plugins/Interactive_3D_Surface_Plot.jar on GitHub Interactive_3D_Surface_Plot GPLv3 Johannes Schindelin, Curtis Rueden, Mark Hiner
IsoData Classifier IsoData Classifier plugin for Fiji. on GitHub IsoData_Classifier GPLv3 Curtis Rueden
Kuwahara Filter Kuwahara Filter plugin for Fiji. on GitHub Kuwahara_Filter GPLv3 Wayne Rasband, Curtis Rueden
LSM Reader LSM Reader plugin for Fiji. on GitHub LSM_Reader GPLv2 Curtis Rueden
LSM Toolbox LSM Toolbox plugin for Fiji. on GitHub LSM_Toolbox GPLv2 Jean-Yves Tinevez, Curtis Rueden
Lasso and Blow Tool Lasso and Blow Tool plugin for Fiji. on GitHub Lasso_and_Blow_Tool GPLv3 Curtis Rueden
Linear Kuwahara Linear Kuwahara plugin for Fiji. on GitHub Linear_Kuwahara GPLv3 Christian Tischer, Curtis Rueden
LocalThickness Local Thickness is used to compute the local thickness of a 3D image stack. on GitHub LocalThickness_ GPLv3 Curtis Rueden
MTrack2 MTrack2 plugin for Fiji. on GitHub MTrack2_ GPLv3 Daniel James White, Curtis Rueden
M I P M I P plugin for Fiji. on GitHub M_I_P GPLv3 Curtis Rueden
Manual Tracking Manual Tracking plugin for Fiji. on GitHub Manual_Tracking GPLv3 Curtis Rueden
Multi Kymograph Measure velocities of moving structures in an image time series. on GitHub Multi_Kymograph GPLv3 Curtis Rueden
PIV analyser PIV analyser plugin for Fiji. on GitHub PIV_analyser GPLv3 Jean-Yves Tinevez, Curtis Rueden
QuickPALM QuickPALM plugin for Fiji. on GitHub QuickPALM_ GPLv3 Ricardo Henriques, Daniel James White, Curtis Rueden
RATS RATS plugin for Fiji. on GitHub RATS_ GPLv3 Curtis Rueden
Reconstruct Reader Reconstruct Reader plugin for Fiji. on GitHub Reconstruct_Reader GPLv3 Larry Lindsey, Curtis Rueden
SPIM Opener SPIM Opener plugin for Fiji. on GitHub SPIM_Opener GPLv3 Curtis Rueden
SPIM Registration Software for the reconstruction of multi-view microscopic acquisitions like Selective Plane Illumination Microscopy (SPIM) Data. on GitHub SPIM_Registration GPLv2 Stephan Preibisch, Curtis Rueden
Samples Samples plugin for Fiji. on GitHub Samples_ GPLv3 Curtis Rueden
Series Labeler Series Labeler plugin for Fiji. on GitHub Series_Labeler GPLv3 Daniel James White, Curtis Rueden
Simple Neurite Tracer The ImageJ framework for semi-automated tracing of neurons and other tube-like structures. on GitHub Simple_Neurite_Tracer GPLv3 Tiago Ferreira, Curtis Rueden
Siox Segmentation Siox Segmentation plugin for Fiji. on GitHub Siox_Segmentation Apache Software License, Version 2.0 Ignacio Arganda-Carreras, Curtis Rueden
Skeletonize3D Skeletonize3D plugin for Fiji. on GitHub Skeletonize3D_ GPLv3 Ignacio Arganda-Carreras, Curtis Rueden
SplineDeformationGenerator SplineDeformationGenerator plugin for Fiji. on GitHub SplineDeformationGenerator_ GPLv3 Ignacio Arganda-Carreras, Curtis Rueden
Stack Manipulation Stack Manipulation plugin for Fiji. on GitHub Stack_Manipulation GPLv3 Jean-Yves Tinevez, Curtis Rueden
Statistical Region Merging Statistical Region Merging plugin for Fiji. on GitHub Statistical_Region_Merging BSD-2 Curtis Rueden
Stitching A plugin for reconstructing big images/stacks from an arbitrary number of tiled input images/stacks. on GitHub Stitching_ GPLv2 Stephan Preibisch, Curtis Rueden
Sync Win Sync Win plugin for Fiji. on GitHub Sync_Win GPLv3 Curtis Rueden
Thread Killer Thread Killer plugin for Fiji. on GitHub Thread_Killer GPLv3 Curtis Rueden
Time Lapse Time Lapse tools written in conjunction with the work for "A Doppler effect in embryonic pattern formation", Soroldoni et al, Science 11 July 2014: Vol. 345 no. 6193 pp. 222-225, DOI: 10.1126/science.1253089 on GitHub Time_Lapse GPLv3 Curtis Rueden
Time Stamper Time Stamper plugin for Fiji. on GitHub Time_Stamper GPLv3 Daniel James White, Curtis Rueden
ToAST ToAST plugin for Fiji. on GitHub ToAST_ GPLv3 Curtis Rueden
TopoJ TopoJ plugin for Fiji. on GitHub TopoJ_ GPLv3 Curtis Rueden
TrackMate TrackMate plugin for Fiji. on GitHub TrackMate_ GPLv3 Jean-Yves Tinevez, Curtis Rueden
TrakEM2 Archipelago TrakEM2 Support for Fiji Archipelago on GitHub TrakEM2_Archipelago GPLv2 Larry Lindsey, Curtis Rueden
Trainable Segmentation Trainable Segmentation plugin for Fiji. on GitHub Trainable_Segmentation GPLv3 Ignacio Arganda-Carreras, Curtis Rueden
VIB-lib Support library for all the VIB stuff. on GitHub VIB-lib GPLv3 Curtis Rueden
VIB VIB plugin for Fiji. on GitHub VIB_ GPLv3 Curtis Rueden
Vaa3d Reader Custom reader for Vaa3D application 3D volume file formats .v3draw and .v3dpbd. on GitHub Vaa3d_Reader GPLv3 Christopher M. Bruns, Curtis Rueden
Vaa3d Writer Plugin to write .v3draw files readable by Vaa3d. on GitHub Vaa3d_Writer GPLv3 Brian Long, Curtis Rueden
Video Editing Video Editing plugin for Fiji. on GitHub Video_Editing GPLv3 Curtis Rueden
View5D View5D plugin for Fiji. on GitHub View5D_ GPLv2 Jean-Yves Tinevez, Curtis Rueden
Volume Calculator The Volume Calculator plugin is designed to let users measure the volumes of arbitrary segments of blood vessels by selecting them directly from a 3D image. Although Volume Calculator was developed for quantification in a mouse hindlimb ischemia experiment, it should be useful for the volume measurement of any network. This possibility is determined by the following requirement: the plugin is configured to work best with images that can be read and analyzed by the Skeleton 3D and Analyze 3D plugins. Hence, it is suggested that users first check their images with these two plugins. on GitHub Volume_Calculator GPLv3 Curtis Rueden
Volume Viewer Volume Viewer plugin for Fiji. on GitHub Volume_Viewer GPLv3 Kai Uwe Barthel, Curtis Rueden
bUnwarpJ bUnwarpJ plugin for Fiji. on GitHub bUnwarpJ_ GPLv3 Ignacio Arganda-Carreras, Curtis Rueden
Block Matching Block Matching plugin for Fiji. on GitHub blockmatching_ GPLv3 Stephan Saalfeld, Curtis Rueden
fiji-compat Old compatibility layer for Fiji. on GitHub fiji-compat GPLv3 Curtis Rueden
jars/fiji-lib.jar Utility classes for Fiji-based projects. on GitHub fiji-lib GPLv3 Curtis Rueden
plugins/H5J_Loader_Plugin.jar A Maven project implementing an ImageJ plugin on GitHub H5J_Loader_Plugin Janelia Farm Research Campus Software Copyright 1.1 Les Foster
Legacy ImgLib1 This project serves purely for phasing out ImgLib1 in favor of ImgLib2. on GitHub legacy-imglib1 BSD-2, GPLv2 Stephan Preibisch, Stephan Saalfeld, Curtis Rueden
Level Sets Level Sets plugin for Fiji. on GitHub level_sets GPLv3 Curtis Rueden
pal-optimization PAL: Phylogenetic Analysis Library on GitHub pal-optimization GNU Lesser General Public License v3+ Curtis Rueden
panorama panorama plugin for Fiji. on GitHub panorama_ GPLv3 Stephan Saalfeld, Curtis Rueden
Register Virtual Stack Slices Registers image slices from a sequence of image slices stored in a folder. on GitHub register_virtual_stack_slices GPLv3 Ignacio Arganda-Carreras, Curtis Rueden
registration 3d registration 3d plugin for Fiji. on GitHub registration_3d GPLv3 Stephan Preibisch, Curtis Rueden
Sholl Analysis An ImageJ 1.x plugin that uses automated Sholl to perform neuronal morphometry directly from segmented images and traces from Simple Neurite Tracer on GitHub Sholl_Analysis GPLv3 Tiago Ferreira
JavaITK thin plate spline A java port of the ITK thin plate spline implementation. on GitHub jitk-tps Apache Software License, Version 2.0 John Bogovic, Stephan Saalfeld
plugins/mpicbg_.jar mpicbg_ GPLv3 Johannes Schindelin, Curtis Rueden, Mark Hiner
Bio-Formats Plugins for ImageJ A collection of plugins for ImageJ, including the Bio-Formats Importer, Bio-Formats Exporter, Bio-Formats Macro Extensions, Data Browser and Stack Slicer. bio-formats_plugins GPLv2 curtis, melissa
BigWarp plugin for Fiji A tool for manual pointwise deformable registration using bigdataviewer. on GitHub bigwarp_fiji GPLv2 John Bogovic, Stephan Saalfeld
TrakEM2 thin plate splines Thin plate splines in TrakEM2. on GitHub trakem2_tps GPLv2 John Bogovic, Stephan Saalfeld
BigDataViewer Core BigDataViewer core classes with minimal dependencies. on GitHub bigdataviewer-core BSD-2 Tobias Pietzsch, Curtis Rueden
BigDataViewer Visualization Tools Helpers to use BigDataViewer as quick visualization in other projects on GitHub bigdataviewer-vistools BSD-2 Tobias Pietzsch, Curtis Rueden
BigDataViewer Fiji Fiji plugins for starting BigDataViewer and exporting data. on GitHub bigdataviewer_fiji GPLv3 Tobias Pietzsch, Curtis Rueden
SPIM Data representation of multi-angle, multi-channel (etc.) SPIM images and their registration on GitHub spim_data BSD 2-Clause License Tobias Pietzsch, Stephan Preibisch
T2-NIT T2-NIT component of TrakEM2 suite. on GitHub T2-NIT GPLv3 Albert Cardona, Stephan Saalfeld, Curtis Rueden
T2-TreelineGraph T2-TreelineGraph component of TrakEM2 suite. on GitHub T2-TreelineGraph GPLv3 Albert Cardona, Stephan Saalfeld, Curtis Rueden
TrakEM2 TrakEM2 plugin for ImageJ. on GitHub TrakEM2_ GPLv3 Albert Cardona, Stephan Saalfeld, Curtis Rueden
VectorString VectorString component of TrakEM2 suite. on GitHub VectorString GPLv3 Albert Cardona, Stephan Saalfeld, Curtis Rueden
trakem2-transform trakem2-transform component of TrakEM2 suite. on GitHub trakem2-transform GPLv3 Albert Cardona, Stephan Saalfeld, Curtis Rueden
Joda-Time Date and time library to replace JDK date handling on GitHub joda-time Apache jodastephen, broneill