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Fiji

Login: fiji

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Blog: https://fiji.sc/

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3D_Blob_Segmentation: null
3D_Objects_Counter: null
3D_Viewer: null
Analyze_Reader_Writer: OBSOLETE - Merged into https://github.com/fiji/IO
AnalyzeSkeleton: ImageJ/Fiji plugin to analyze 2D and 3D skeleton images
Anisotropic_Diffusion_2D: null
Archipelago_Plugins: null
Arrow: null
Auto_Local_Threshold: null
Auto_Threshold: null
BalloonSegmentation: null
BeanShell_Interpreter: OBSOLETE; see https://github.com/scijava/script-editor
bij: Bio-medical imaging in Java
blockmatching: null
Bug_Submitter: null
bUnwarpJ: ImageJ/Fiji plugin for consistent elastic registration of 2D images
Calculator_Plus: null
Cell_Counter: null
CLI: OBSOLETE
Clojure_Interpreter: OBSOLETE; see https://github.com/scijava/script-editor
Colocalisation_Analysis: Fiji's plugin for colocalization analysis
Color_Histogram: null
Color_Inspector_3D: null
Colour_Deconvolution: null
cookbook: Plugins collated for the Fiji Cookbook
Correct_3D_Drift: null
CorrectBleach: null
CPU_Meter: null
Cross_Fader: An ImageJ 1.x plugin that takes a two-slice stack and copies part of the second slice into the current one.
Descriptor_based_registration: null
Dichromacy: null
Directionality: A Fiji plugin for inferring the main orientation of structures in an image.
dockerfiles: Fiji Dockerfiles for Docker builds.
dotfiles: Configuration files for Fiji resources
fake: OBSOLETE; see: https://github.com/scijava/minimaven
Feature_Detection: null
fiji: A "batteries-included" distribution of ImageJ :battery:
Fiji_Archipelago: null
fiji-compat: null
Fiji_Developer: null
fiji.github.io: Website
fiji-historical: Fiji history prior to the root commit of fiji/fiji
fiji-javadoc: An aggregator for Fiji Javadocs
fiji-lib: null
Fiji_Package_Maker: null
Fiji_Plugins: null
fiji-scripting: OBSOLETE; see https://github.com/scijava/script-editor
Fiji_Updater: OBSOLETE; see https://github.com/imagej/imagej-updater
FlowJ: null
FS_Align_TrakEM2: null
Graph_Cut: null
Gray_Morphology: null
H5J_Loader_Plugin: H5J Reader Plugin for Fiji project.
HDF5_Vibez: HDF5 plugin for ImageJ and Fiji.
Helmholtz_Analysis: null
IJ_Robot: This plugin calls the Robot Java class. The purpose of the plugin is to allow the macro language to control other programs via clicking and key presses.
Image_5D: A plugin to extend image stacks to 5 dimensions: x, y, channel (color), slice (z), frame (t).
Image_Expression_Parser: null
Interactive_3D_Surface_Plot: null
IO: null
IsoData_Classifier: null
iterativedeconv: Mirror of Parallel Iterative Deconvolution project
ivussnakes: A Git-CVS clone of the 'ivussnakes' module of http://ivussnakes.cvs.sourceforge.net/viewvc/ivussnakes/
Jama: OBSOLETE; see http://central.maven.org/maven2/gov/nist/math/jama/1.0.3/
java6-linux32: Fiji's version of OpenJDK6 + Java 3D 1.5 for 32-bit Linux
java6-linux64: Fiji's version of OpenJDK6 + Java 3D 1.5 for 64-bit Linux
java6-macosx: Fiji's version of Java 3D 1.5 (sans OpenJDK6) for Mac OS X
java6-win32: Fiji's version of OpenJDK6 + Java 3D 1.5 for 32-bit Windows
java6-win64: Fiji's version of OpenJDK6 + Java 3D 1.5 for 64-bit Windows
javac: OBSOLETE
Javascript: OBSOLETE; see https://github.com/scijava/script-editor
JMathLib: Mirror of JMathLib project
JRuby_Interpreter: OBSOLETE; see https://github.com/scijava/script-editor
Jython_Interpreter: OBSOLETE; see https://github.com/scijava/script-editor
Kuwahara_Filter: null
KymographBuilder: KymographBuilder is Yet Another Kymograph Fiji plugin.
Lasso_and_Blow_Tool: null
legacy-imglib1: OBSOLETE; see https://github.com/imglib/imglib2
level_sets: null
Linear_Kuwahara: null
Live_Wire: A Git-CVS clone of the 'livewire' module of http://ivussnakes.cvs.sourceforge.net/viewvc/ivussnakes/
LocalThickness: null
LSM_Reader: null
LSM_Toolbox: null
MaMuT: The fiji plugin for Massive Annotation
Manual_Tracking: null
microscope-image-quality: TensorFlow-based classifier for microscope image focus quality.
M_I_P: null
MTrack2: null
Multi_Kymograph: null
pal-optimization: null
panorama: null
PIV_analyser: null
pom-fiji: OBSOLETE - Use https://github.com/scijava/pom-scijava instead!
pQCT: Fiji plugins for pQCT image analysis.
profilers: A bunch of useful profilers based on Javassist [UNMAINTAINED]
QuickPALM: null
RATS: RATS: Robust Automatic Threshold Selection
Reconstruct_Reader: null
Refresh_Javas: OBSOLETE
register_virtual_stack_slices: Fiji package for registering and transforming arbitrarily large sequences of images
registration_3d: null
Samples: null
Scala_Interpreter: OBSOLETE; see https://github.com/scijava/script-editor
Script_Launcher: OBSOLETE
Series_Labeler: null
Simple_Neurite_Tracer: The ImageJ framework for semi-automated tracing of neurons and tubular structures
Siox_Segmentation: Fiji plugin based on the SIOX project to segment color images
Skeletonize3D: ImageJ/Fiji plugin to skeletonize binary images
spectraldeconv: Mirror of Parallel Spectral Deconvolution project
SPIM_Opener: null
SPIM_Registration: Deprecated, instead check out: https://github.com/preibischLab/multiview-reconstruction & https://github.com/PreibischLab/BigStitcher
SplineDeformationGenerator: null
Stack_Manipulation: null
Statistical_Region_Merging: null
Stitching: Fiji's Stitching plugins reconstruct big images from tiled input images.
Stitching_Tests: Regression tests for the ImageJ Stitching plugin
Stochastic_Denoise: null
Sync_Win: null
Thread_Killer: null
Threshold_Colour: OBSOLETE; included with https://github.com/imagej/imagej1
Time_Lapse: A set of tools intended to help with time-lapse data
Time_Stamper: null
ToAST: null
TopoJ: null
TrackMate: TrackMate is your buddy for your everyday tracking.
TrackMate3: This is the prototype code for the 3rd version of TrackMate, planned for mid 2017.
trackmate-core: Core library for TrackMate applications. Ship basic data structures and algorithms.
TrackMate-examples: A simple repository that shows how to extend TrackMate with your own modules.
Trainable_Segmentation: Fiji library to perform image segmentation based on the Weka learning schemes
TrakEM2_Archipelago: null
TurboReg2: An adaptation of the ImageJ TurboReg plugin to ImageJ2 [UNMAINTAINED]
Updater_Fix: null
Vaa3d_Reader: null
Vaa3d_Writer: Vaa3d writer plugin for ImageJ 1.x
VIB: null
vib-historical: Virtual Insect Brain (VIB) history prior to Fiji integration
VIB-lib: null
Video_Editing: null
View5D: null
Volume_Calculator: null
Volume_Viewer: null
weave_jy2java: A framework for inlining java code in an otherwise interpreted programming language running on the JVM, such as jython. See https://github.com/fiji/fiji/issues/161
winrun4j: WinRun4J Java Application Launcher
Yawi_2D: Mirror of Yawi2D project
Yawi_3D: Mirror of Yawi3D project

This work is supported by the National Institutes of Health's National Center for Advancing Translational Sciences, Grant Number U24TR002306. This work is solely the responsibility of the creators and does not necessarily represent the official views of the National Institutes of Health.