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List of Extensions
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TrakEM2
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Uncategorized
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plugin
Save as animated gif
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Import-Export, SciJava, OME
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QuickTime
Import-Export, Development
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Import-Export, Development
Vaa3d Reader
Import-Export
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2D Histogram
Uncategorized
3D Binary Filters
3D, Binary
3D Blob Segmentation
3D, Segmentation
3D cyclorama
3D, Digital Volume Unrolling, Digital Volume Flattening
3D ImageJ Suite
3D, Analysis, Filtering, Segmentation, Mathematical Morphology
3D Objects Counter
3D, Particle Analysis
3D Segmentation
3D, Segmentation
3D Surface Plot
3D, Visualization
3D Viewer
3D, Visualization
3Dscript
Visualization
3View import list
TrakEM2
AccPbFRET
Analysis
ActionBar
Development
ActogramJ
Visualization
Adaptive Median Filter
Uncategorized
Adelson's Squares
Uncategorized
Adiposoft
Uncategorized
Align Image by line ROI
Tutorials, Registration
Align RGB planes
Color Processing
AMPT
Annotation, Image analysis, Interactive, Photogrammetry, plugin
Anaglyph for Red Cyan glasses
Scripting, Unmaintained
AnalyzeSkeleton
Skeleton, Analysis, Neuroanatomy
Analyze Stripes
Analysis, Tutorials
Anisotropic Diffusion 2D
Filtering
Anomalous Diffusion Filters
Uncategorized
AplimTools
Analysis
Archipelago Plugins
Uncategorized
Arrow
Image Annotation
Atlas Toolkit
Registration
Auto Crop
Tutorials
Auto Local Threshold
Segmentation
Auto Threshold
Segmentation
Automated workflow for parallel Multiview Reconstruction
Transform, Registration, Deconvolution
Automatic detection of neuronal labeling in histological image series
Analysis
Automatic optimal filament segmentation
Segmentation
Average Images
Uncategorized
AxoNet
Uncategorized
Background Subtractor
Filtering
Balloon segmentation
Segmentation
BAR
Analysis, Filtering, Image Annotation, Scripting, Segmentation
Batch Composite
Automation, Color Processing, Import-Export, Stacks
Batch Processor
Uncategorized
BigDataViewer
Visualization
BigDataServer
Visualization, Transform
BigDataProcessor2
Uncategorized
BigDataProcessor
Uncategorized
BigStitcher
ImgLib, Registration, Stitching
BigWarp
Visualization, Transform, Registration
Biomat
Filtering
BIOP Lookup Tables
Uncategorized
BioVoxxel Toolbox
Particle Analysis, Segmentation
Bleach Correction
Uncategorized
Blend two images
Scripting
Blind Analysis Tools
Uncategorized
Block Matching
Uncategorized
BoneJ
Analysis, Mathematical Morphology, Particle Analysis
BoneJ1
Uncategorized
Tissue Branch Tracker
Tracking, Tissue, Skeletonization
bUnwarpJ
Registration
BioVoxxel 3D Box
Particle Analysis, Segmentation
CElegansBeadsAnalysis plugin
Uncategorized
Calc dSpace
Uncategorized
Calculator Plus
Uncategorized
CAMDU
Uncategorized
CARE
Uncategorized
CATS
Uncategorized
Cell Counter
Particle Analysis
Cell detector
Uncategorized
Celsius to fahrenheit
Scripting, Unmaintained
CIP
Uncategorized
CIPMM plugins
Uncategorized
Enhance Local Contrast (CLAHE)
Filtering
Classic Watershed
Segmentation, Mathematical Morphology
ClearVolume
Visualization
CLIJ
Uncategorized
Cluster Analysis
Uncategorized
CMP-BIA tools
Segmentation
Coloc 2
Colocalization, Color Processing
Colocalization by Cross Correlation
Colocalization
Colocalization Image Creator
Uncategorized
Colocalization Object Counter
Uncategorized
Colocalization Test
Colocalization, Color Processing
Colocalization Threshold
Colocalization, Color Processing
Colocalize
Colocalization
Color Histogram
Uncategorized
Color Inspector 3D
Uncategorized
Colorizer Overlay
Image Annotation
Colour Deconvolution
Color Processing
Colour merge
Color Processing
Compute Curvatures
Uncategorized
ComsystanJ
Complexity, Fractal dimension, Entropy, Image analysis, Time signal analysis
Contour Lines
Uncategorized
Copy Pixel Size
Image Annotation
Correct 3D Drift
Registration
Cover Maker
Tutorials
CPU Meter
Uncategorized
Crop (3D)
Uncategorized
Cross Sectional Analyzer
Uncategorized
CSBDeep
Uncategorized
CSIMLab
Filtering, Noise
Deep Zoom
Unmaintained
DeepClas4Bio
Uncategorized
DeformationTracker
Uncategorized
Deforming Mesh 3D
Uncategorized
Delaunay Voronoi
Uncategorized
Delayed Snapshot
Scripting
Dendritic Spine Counter
Annotation, Segmentation, Feature Extraction
DenoiSeg
DeepLearning, Denoising, Segmentation
Descriptor-based registration (2d/3d)
Uncategorized
Descriptor based registration
Uncategorized
Detrendr
Uncategorized
DHM Utilities
Uncategorized
DiameterJ
Analysis
Dichromacy
Uncategorized
DICOM open
Import-Export
Differentials
Uncategorized
Diffraction PSF 3D
Deconvolution
Directionality
Analysis
Distance Analysis
Analysis, Colocalization
Distance Transform 3D
Binary, Unmaintained
Distance Transform Watershed
Segmentation, Mathematical Morphology
Distortion Correction
Transform
Dithering
Segmentation
DS4H Image Alignment
Tutorials, Registration
Dynamic Kymograph
Uncategorized
Dynamic Reslice
Uncategorized
Dynamic ROI Profiler
Scripting, Image Annotation, Unmaintained
Edge and symmetry filter
Uncategorized
Elastic Alignment and Montage
Registration, TrakEM2
Elastix
Uncategorized
Ellipse split
Uncategorized
EpiGraph
Uncategorized
Extended Depth of Field
Tutorials
FAST
Analysis, Segmentation
Feature Extraction
Registration, Feature Extraction
FeatureJ
ImageScience
FigureJ
Uncategorized
Fiji Developer
Uncategorized
Fiji Logo 3D
Scripting
Fiji Plugins
Uncategorized
Fiji/Z-Spacing Correction
TrakEM2, Transform
FijiArchipelago
TrakEM2
FijiRelax
Analysis
FijiWings
Uncategorized
Fijiyama
Registration
FilamentDetector
Uncategorized
FiloQuant
Analysis, Segmentation, Object Detection
Find Connected Regions
Uncategorized
Find Dimension of Raw Image
Scripting
Find Peaks
Scripting, Analysis
FITS Analysis
Uncategorized
FLIMJ
Analysis, Lifetime
FlowJ
Optic Flow
Fourier Ring Correlation Plugin
Uncategorized
Fpbioimage
Uncategorized
Frames
Import-Export
Frangi
Uncategorized
FS Align TrakEM2
Uncategorized
Fuzzy Set Intensity Transformations
Uncategorized
Gabriel Graph
Uncategorized
GDSC-SMLM2
Uncategorized
Get dSpace
Uncategorized
Get Meta
Uncategorized
Glasbey
Uncategorized
Gnu Plot
Plotting
Granulometric Filtering
Particle Analysis
Graph Cut
Segmentation, Tutorials
Gray Morphology
Segmentation, Mathematical Morphology
Grid/Collection Stitching Plugin
Registration, Stitching
Grid
Image Annotation, Unmaintained
Gut Analysis Toolbox
Analysis, Segmentation, Neuron, Gut
HDF5 Vibez
Import-Export
Helmholtz Analysis
Uncategorized
Help on Menu Item
Help
Hill Shade
Uncategorized
Hough Circle Transform
Analysis
HPC Workflow Manager
Scripting
IJ Blob
Uncategorized
IJ Robot
Uncategorized
IJMMD
Uncategorized
Image Annotation
Uncategorized
Image Expression Parser
Uncategorized
Image Stabilizer
Registration
Image Stitching
Registration, Stitching, Cookbook
Image Synthesizer
Uncategorized
Image5D
Visualization
IMBalENce
Uncategorized
Importing Image Files
Cookbook, Tutorials, Import-Export
Plugins
Uncategorized
Integral Image Filters
Filtering, Integral Image
Intensity Profile Tools
Feature Extraction
Interaction Analysis
Particle Analysis, Colocalization
Interaction Factor
Uncategorized
Interactive Affine
Transform
Interactive Fitting
Plotting
Interactive Marker-controlled Watershed
Segmentation, Mathematical Morphology
Interactive Moving Least Squares
Transform
Interactive Perspective
Transform
Interactive Rigid
Transform
Interactive Similarity
Transform
Interactive Stack Rotation
Transform, Interactive
Interactive Watershed
Segmentation
Invasion assay
Uncategorized
IsletJ
Uncategorized
IsletJ2
Uncategorized
IsoData Classifier
Segmentation
Iterative Deconvolve 3D
Deconvolution
JaCoP
Analysis, Colocalization
JFilament
Uncategorized
Java Image Processing Pipeline (JIPipe)
Scripting
Kalman Stack Filter
Filtering
Kappa
Uncategorized
Kuwahara Filter
Uncategorized
KymographBuilder › Yet Another Kymograph Fiji plugin
Uncategorized
KymoResliceWide
Stacks
Labkit - Intuitive Pixel Classification in Fiji
Classification, Machine Learning
Landmark Correspondences
Transform, Registration
Lasso and Blow Tool
Segmentation
Level Sets
Uncategorized
LimeSeg
Segmentation
LinearDistance
Uncategorized
Linear Kuwahara
Tutorials
Linear Stack Alignment with SIFT
Registration
List all threads
Scripting, Unmaintained
Local Thickness
Uncategorized
Low Light Tracking Tool
Tutorials
LSM Worker
Uncategorized
LUMoS Spectral Unmixing
Color Processing, Colocalization
LungJ
Segmentation, Binary, Filtering, Image Annotation
M I P
Uncategorized
Make Fiji Package
Tutorials
Make Screencast
Scripting
Malaria Sporozoites (9.2MB)
Uncategorized
Getting started with MaMuT
Tracking, Tutorial
MaMuT
Tracking
Manual drift correction plugin
Registration
Manual Tracking
Particle Analysis, Tracking
Marker-controlled Watershed
Segmentation, Mathematical Morphology
Mask Of Nearby Points
Uncategorized
Mask(s) from ROI(s)
Image Annotation, Segmentation
Max Inscribed Circles
Segmentation, Feature Extraction
Maximum Entropy Threshold
Segmentation
Microscope Focus Quality
Uncategorized
Microscope Measurement Tools
Registration
Miji
Tutorials, MATLAB
MiNA - Mitochondrial Network Analysis
Uncategorized
Miniature Faking
Filtering, Interactive, Integral Image, Photography
Minimum Cost Z surface Projection
Projection
Minimum/Maximum/Median
Uncategorized
MiToBo
SciJava
Mixture Modeling Thresholding
Segmentation
MoBIE
Uncategorized
ModularImageAnalysis (MIA)
Analysis, Automation, Scripting
MorphoLibJ
Analysis, Filtering, Segmentation, Mathematical Morphology
Morphological Segmentation
Segmentation, Mathematical Morphology
MosaicJ
Uncategorized
MOSAICsuite
Particle Analysis, Filtering, Colocalization, Deconvolution, Segmentation
Moving Least Squares
Tutorials
MRI Perfusion
Perfusion
MS-ECS-2D update site
Uncategorized
MSER parameters
Uncategorized
MicrotubuleTracker
Tracking, Microtubules
MTrack2
Tracking
MTrackJ
Tracking, ImageScience
Multi Kymograph
Uncategorized
Multi Otsu Threshold
Segmentation
Multi Stack Montage
Stacks, Montage, Visualization
Multi-Template Matching
Feature Extraction, Object Detection
Multi-View Deconvolution
Uncategorized
Multi-View Fusion
Uncategorized
Multifrac
Analysis, Feature Extraction, ImageJ2, Mathematical Morphology, Stacks
Multiple Image Processor
Uncategorized
MultiStackReg
Registration
MultiThresholder
Segmentation
Multiview-Reconstruction
Transform, Registration, Deconvolution, ImgLib, Integral Image
MVR-DefineDataset
Uncategorized
MVR-FusionDeconvolution
Uncategorized
MVR-ResaveDataset
Uncategorized
MyofibrilJ
Scripting, Analysis
N2V
Uncategorized
Name Landmarks and Register
Uncategorized
NanoTrackJ
Uncategorized
NeuronDetector
Uncategorized
NeuronJ
ImageScience, Neuroanatomy
Noise Generator
Noise
NoiSee
Uncategorized
Non Local Means Denoise
Denoising
Nucleus Counter
Particle Analysis
OMEVisual
OME
Op Finder
Ops
OpenMPI Plugin Extensions
Scripting
OtoRing
Uncategorized
Panorama
Uncategorized
Parallel Iterative Deconvolution
Deconvolution
Parallel Spectral Deconvolution
Deconvolution
Particle Tracker
Particle Analysis, Tracking
ParticleSizer
Uncategorized
Pendent Drop
Uncategorized
PerfusionMRI
Uncategorized
PhotoBend
Tracking
PhotonImaging
Uncategorized
PillarTracker GUI
Uncategorized
PillarTracker
Tracking, Visualization, Analysis, Filtering
PIV analyser
Optic Flow
PixFRET
Uncategorized
Point Analysis
Tutorials
Point Picker
Particle Analysis
PQCT
Uncategorized
Pub Montage
Uncategorized
Public data sets
Example Data, Segmentation, Tracking
Qualitative Annotations
Image Annotation
Quantile Based Normalization
Uncategorized
QuickPALM
Super-resolution
Quiver Plot
Visualization
Radial Symmetry
Uncategorized
RandomJ
ImageScience
RATS: Robust Automatic Threshold Selection
Segmentation, Tutorials
Read and Write Excel
Import-Export
Reconstruct Reader
TrakEM2
Region Competition
Segmentation, Deconvolution
Register Virtual Stack Slices
Registration, TrakEM2
Replace Red with Magenta
Tutorials
RETINA Analysis Toolkit
Uncategorized
Retinex
Tutorials
RGB-Gray Merge
Color Processing
RGB Measure Plus
Color Processing
RGB Profiler
Color Processing
RGB to Montage
Color Processing
Ridge Detection
Uncategorized
RiFRET
Analysis
Robust clump splitting
Uncategorized
Roi 1-click tools
Image Annotation
ROI Conversions
Uncategorized
Roi-group table
Image Annotation
ROI Picker
Uncategorized
Rolling Ball Background Subtraction
Filtering
RunImageJScript
CellProfiler
Saim
Analysis, Microscopy
Same Slice in Multiple Images
Scripting, Unmaintained
SampEn2D
Pattern Recognition
Samples
Uncategorized
sciview
3D, Visualization
Segment blob in 3D Viewer
Segmentation
Segmentation Editor
Segmentation
SEM FEI metadata scale
Uncategorized
SEM JOEL Scale
Uncategorized
Series Labeler
Image Annotation
ImageJ Server
Uncategorized
Shape Filter
Uncategorized
Shape Index Map
Uncategorized
Shape Smoothing
Uncategorized
Shepp-Logan Phantom
Uncategorized
Sholl Analysis
Analysis, Neuroanatomy
Show Color Surfaces
Uncategorized
Sigma Filter
Filtering
SIMcheck
Uncategorized
Simple Neurite Tracer
Uncategorized
Simulate Color Blindness
Fiji, Color Processing
SIOX: Simple Interactive Object Extraction
Uncategorized
Skeletonize3D
Skeleton
Slice Labeler
Image Annotation
SlideJ
Uncategorized
SLIM Curve
Uncategorized
SME Projection
Analysis
Snakuscule
Segmentation
SNT
Segmentation, Neuroanatomy
Spheres and Tubes in 3D
Unmaintained
SPIM Bead Registration (deprecated)
Registration
SPIM Bead Registration
Uncategorized
SPIM Opener
Uncategorized
SPIM Registration
Registration
SPIM Registration on cluster (deprecated)
Registration
SPIM Workflow Manager For HPC
Transform, Registration, Deconvolution
SPIMage processing course
Uncategorized
Spirals
Tutorials
Spline Deformation Generator
Transform
Spot Intensity Analysis
Particle Analysis
SpotCounter
Particle Analysis
Spots colocalization (ComDet)
Colocalization
SpotTracker
Particle Analysis, Tracking
Sprout Morphology
Uncategorized
Squassh
Segmentation, Colocalization, Deconvolution
Stack Manipulation
Uncategorized
StackObjectCombiner
Uncategorized
StackReg
Transform, Registration
StarDist
Uncategorized
Statistical Region Merging
Tutorials, Segmentation
StereoMate
Uncategorized
Stereoscopic 3D Projection
Uncategorized
Stitching 2D/3D
Registration, Stitching
Stitching data acquisition
Uncategorized
Stochastic Denoise
Denoising
Strahler Analysis
Skeleton, Analysis, Neuroanatomy
Straighten...
Uncategorized
Surfaceness
Uncategorized
SynActJ
plugin
Sync Windows
User Interface
TAPAS
Automation, Analysis, Filtering, Segmentation
TEM suite
Uncategorized
Temporal-Color Code
Color Processing
Temporal Median
Tracking, Filtering
Test Block Matching Parameters
Uncategorized
Test Java3D
Uncategorized
Thread Killer
Uncategorized
Time Lapse
Uncategorized
Time Stamper
Image Annotation
Timebar
Image Annotation
ToAST
Tracking
TopoJ
Tutorials
TrackMate actions
Segmentation, Tracking
Export tracking results in the cell tracking challenge format
Segmentation, Tracking, Benchmark
TrackMate-Helper
Segmentation, Tracking, Benchmark
TrackMate FAQ
Tracking, Segmentation
TrackMate
Segmentation, Tracking
Manual editing of tracks using TrackMate
Segmentation, Tracking
Manual tracking with TrackMate
Segmentation, Tracking
Scripting TrackMate
Tracking, Segmentation
TrackMate-Cellpose
Segmentation, Tracking
Setting keys for TrackMate detectors and trackers
Tracking, Segmentation, Scripting
TrackMate display settings
Tracking, Segmentation
TrackMate-Ilastik
Segmentation, Tracking, Machine Learning
TrackMate-Label-Image-Detector
Segmentation, Tracking
TrackMate Mask detector
Segmentation, Tracking
TrackMate-MorphoLibJ
Segmentation, Tracking
TrackMate-Oneat
Tracking
TrackMate-StarDist
Segmentation, Tracking, Deep-Learning
TrackMate-Thresholding-Detector
Segmentation, Tracking
TrackMate v7 detectors
Tracking, Segmentation
TrackMate-Weka
Segmentation, Tracking, Machine Learning
TrackScheme
Tracking
Using TrackMate from MATLAB
Segmentation, Tracking
Trainable Segmentation Plugin (deprecated)
Segmentation
TraJClassifier
Uncategorized
TrakEM2 Archipelago
Uncategorized
TrakEM2
Registration, Segmentation, TrakEM2, Image Annotation, Neuroanatomy
Transform Virtual Stack Slices
Uncategorized
TransformJ
ImageScience
TreeJ
Analysis
Tubeness
Uncategorized
TurboReg
Uncategorized
Tutorial Maker
Uncategorized
Trainable Weka Segmentation
Segmentation, Machine Learning
UnwarpJ
Uncategorized
Updater
ImageJ2
Upload Sample Image
Uncategorized
Vessel Analysis
Uncategorized
VHPro
Uncategorized
Virtual Insect Brain (VIB) Protocol
Registration
Video Editing
Uncategorized
View5D
Visualization
VisBio Fiji plugin
Uncategorized
Void Whizzard
Uncategorized
Volume Calculator
3D, Analysis
Volume Viewer
3D, Visualization
VTEA › Volumetric Tissue Exploration and Analysis
Segmentation, Visualization
Watershed Algorithm (ImageJ plugin)
Uncategorized
Wavelet Denoise
Filtering
Xlib
Analysis, Filtering, MATLAB, Particle Analysis, Segmentation, Skeleton
ZedMate
Uncategorized
Zellige tutorial
Projection, Segmentation
ZFBONE
Uncategorized
FunImageJ
Lisp
Neuroanatomy
Uncategorized
Forum
Twitter
GitHub
Design:
HTML5 UP
ImageJ Docs
Download
Learn
ImageJ Basics
Tutorials
User Guides
Keyboard Shortcuts
Tips and Tricks
Troubleshooting
Frequently Asked Questions
Supported Platforms
Windows
MacOS
Linux
Raspberry Pi
Android
File Formats
Bio-Formats
Video formats
QuickTime
TIFF
PDF
DICOM
Zeiss LSM
Olympus VSI
Opera Flex
FIB-SEM
Scientific Imaging
Principles of Scientific Imaging
Annotating Images
Colocalization
Color Image Processing
Deconvolution
Image Intensity Processing
Particle Analysis
Registration
Segmentation
Stack-slice Manipulations
T-functions
Tracking
Visualization
Z-functions
Extend
List of Extensions
Update Sites
List of Update Sites
Following an Update Site
Creating an Update Site
Terms of Service
Automatic Upload
Uploading to Core Sites
Update Sites FAQ
Statistics
Scripting
Batch Processing
Scripting Basics
Script Editor
Using Javadoc
User Input
Auto Import
Templates
Running Headlessly
Scripting Comparisons
Toolbox
Languages
BeanShell Scripting
Groovy Scripting
ImageJ Macro
JavaScript
Batch Processing
Lisp (Clojure)
MATLAB
Python
R (Renjin)
Ruby (JRuby)
Scala Scripting
Development
Philosophy
Architecture
Source code
Project management
Coding style
Debugging
Wish list
Tools
GitHub
Maven
CI/CD
Dotfiles
IDEs
Eclipse
NetBeans
IntelliJ IDEA
Command Line
Guides
Writing plugins
Contributing to a plugin
Development lifecycle
Building a POM
Hands-on debugging
Adding new ops
Adding new formats
Using native libraries
Tips for developers
Tips for C++ developers
ImageJ 1.x plugins
Versioning
Logging
Uber-JARs
Git
Git in Eclipse (EGit)
Git mini howto
Git workshop
Git conflicts
Git topic branches
Git notes
Git reflogs
Git submodules
How to pinpoint regressions
How to publish a git repository
How to extract a subproject
Contribute
Citing
Contributors
Organizations
Governance
Funding
Contributing to Fiji
Licensing
Open Source
Apache
BSD
EPL
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