List of Extensions

Categories filter

Save as animated gif
Import-Export
Bio-Formats
Import-Export, SciJava, OME
DICOM
Import-Export
FIBSEM importer
Import-Export
Formats
Import-Export
LSM Toolbox
Import-Export
LuraWave
Import-Export
OlympusImageJPlugin
Import-Export
Extract Images From PDF...
Import-Export
QuickTime
Import-Export, Development
TIFF
Import-Export, Development
Vaa3d Reader
Import-Export
Vaa3d Writer
Import-Export
Video
Import-Export
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, Scripting
3View import list
TrakEM2
4d Tools
Import-Export, Stacks
Live Kymographer
Kymograph
AccPbFRET
Analysis
ActionBar
Development
ActogramJ
Visualization
Adaptive Median Filter
Uncategorized
Adelson's Squares
Uncategorized
AdipoQ
Automation, Analysis, Particle Analysis, Segmentation, Object Detection, Colocalization
Adiposoft
Uncategorized
Adjustable Watershed
Segmentation
Align Image by line ROI
Registration
Align RGB planes
Color Processing
AMPT
Annotation, Interactive, Photogrammetry
Anaglyph for Red Cyan glasses
Scripting, Unmaintained
AnalyzeSkeleton
Skeleton, Analysis, Neuroanatomy
Analyze Stripes
Analysis, Tutorials
Anisotropic Diffusion 2D
Filtering
AnnotatorJ
Annotation, Image Annotation, Deep Learning, Import-Export, Segmentation, Object Detection, Classification, Interactive
Anomalous Diffusion Filters
Filtering
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
Machine Learning
Background Subtractor
Filtering
Balloon segmentation
Segmentation
BAR
Analysis, Filtering, Image Annotation, Scripting, Segmentation
Batch Composite
Automation, Color Processing, Import-Export, Stacks
Batch Processor
Automation
BigDataViewer
Visualization
BigDataServer
Visualization, Transform
BigDataProcessor2
Uncategorized
BigDataProcessor
Uncategorized
BigStitcher
ImgLib, Registration, Stitching
BigTrace
Visualization, Analysis, Curve Tracing
BigWarp
Visualization, Transform, Registration
Biomat
Filtering, Mathematical Morphology
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, Skeleton
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
CiliaQ
Automation, 3D, Analysis, Particle Analysis, Segmentation, Object Detection, Colocalization, Tracking, Cilia
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
ColonyArea
Segmentation, Registration
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, 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
Import-Export
DeepClas4Bio
Uncategorized
DeformationTracker
Uncategorized
Deforming Mesh 3D
Uncategorized
Delaunay Voronoi
Image Annotation
Delayed Snapshot
Scripting
Dendritic Spine Counter
Annotation, Segmentation, Feature Extraction
DenoiSeg
Machine Learning, 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
Draw 3D ROI
3D, 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-HIPPOS
Analysis
FAST
Analysis, Segmentation
Fast4DReg
Registration, Channel alignment
Feature Extraction
Registration, Feature Extraction
Feature Finder
Feature Extraction
FeatureJ
ImageScience
Import/Export movie using FFmpeg
Import-Export
FigureJ
Visualization
Fiji Developer
Uncategorized
Fiji Logo 3D
Scripting
Fiji Plugins
Uncategorized
Fiji Z-Spacing Correction
TrakEM2, Transform
FijiArchipelago
TrakEM2
FijiRelax
Analysis
FijiWings
Analysis, Segmentation
Fijiyama
Registration
FilamentDetector
Object Detection, Tracking
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
Foci Analyzer
Analysis
FOCUST
Analysis, Segmentation
Fourier Ring Correlation Plugin
Uncategorized
Fpbioimage
Uncategorized
Frames
Import-Export
Frangi
Uncategorized
FRAP Tools
Analysis
FreQ
Automation, Analysis, Cilia, Fast Fourier Transformation, Frequency Analysis
FS Align TrakEM2
Uncategorized
Fuzzy Set Intensity Transformations
Uncategorized
Gabriel Graph
Uncategorized
GDSC-SMLM2
Uncategorized
Get dSpace
Uncategorized
Get Meta
Uncategorized
GIFT
Analysis
Glasbey
Color Processing
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
High Pass
Filtering
Hill Shade
Visualization
Hough Circle Transform
Analysis, Feature Extraction
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
Microscopy, Import-Export
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
Microscopy
IsletJ2
Uncategorized
IsoData Classifier
Segmentation
Iterative Deconvolve 3D
Deconvolution
JaCoP
Analysis, Colocalization
JavaCV Installer
Development, Utilities
JFilament
Uncategorized
Java Image Processing Pipeline (JIPipe)
Scripting
Kalman Stack Filter
Filtering
Kappa
Analysis, Curvature
Kuwahara Filter
Uncategorized
KymographBuilder › Yet Another Kymograph Fiji plugin
Kymograph
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
Tracking
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, Tutorials
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
Mastodon
Segmentation, Tracking
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
MotiQ
Automation, Analysis, Particle Analysis, Segmentation, Object Detection, Neuron, Tracking, Skeleton
Moving Least Squares
Tutorials
MRI Perfusion
Perfusion, MRI
MS-ECS-2D update site
Uncategorized
MSER parameters
Uncategorized
MTrack
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
Analysis
Non Local Means Denoise
Denoising
Nscale_segmentation
Segmentation
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
Import Maps from PFE-CalcImage and perform measurements
Import, Microscopy, Electron Microprobe
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
Puncta Process
Particle Analysis
Pub Montage
Uncategorized
Public data sets
Example Data, Segmentation, Tracking
Qualitative Annotations
Image Annotation
Quantile Based Normalization
Uncategorized
QuickFigures
Visualization, User Interface
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
Filtering
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
RootSystemTracker
Analysis
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
Serial Macro Extensions
Utilities, Macro, MacroExtensions
Series Labeler
Image Annotation
ImageJ Server
Uncategorized
Shape Filter
Uncategorized
Shape Index Map
Uncategorized
Shape Smoothing
Uncategorized
Shepp-Logan Phantom
Uncategorized
SNT › Sholl Analysis
Analysis, Neuroanatomy
Show Color Surfaces
Uncategorized
Sigma Filter
Filtering
SIMcheck
Uncategorized
Simulate Color Blindness
Color Processing
SIMworks
Particle Analysis, Segmentation, Microscopy
SIOX: Simple Interactive Object Extraction
Uncategorized
Skeletonize3D
Skeleton
Slice Labeler
Image Annotation
SlideJ
Uncategorized
SLIM Curve
Analysis, Lifetime
SME Projection
Analysis
Snakuscule
Segmentation
SNT
Segmentation, Neuroanatomy
SNT › Sholl Analysis
Analysis, Neuroanatomy
SNT › Strahler Analysis (From Images)
Skeleton, Analysis, Neuroanatomy
Spatial Pathology Plugin
Uncategorized
SpermQ
Automation, Analysis, Segmentation, Cilia, Kymograph
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
Spot Spine
Analysis, Neuroanatomy
SpotCounter
Particle Analysis
Spots colocalization (ComDet)
Colocalization
SpotTracker
Particle Analysis, Tracking
Sprout Morphology
Uncategorized
Squassh
Segmentation, Colocalization, Deconvolution
Stack Fitter
Analysis, Stacks
Stack Manipulation
Uncategorized
StackObjectCombiner
Uncategorized
StackReg
Transform, Registration
StarDist
Machine Learning, Segmentation
Statistical Region Merging
Tutorials, Segmentation
StereoMate
Uncategorized
Stereoscopic 3D Projection
Uncategorized
Stitching 2D/3D
Registration, Stitching
Stitching data acquisition
Uncategorized
Stochastic Denoise
Denoising
SNT › Strahler Analysis (From Images)
Skeleton, Analysis, Neuroanatomy
Straighten...
Uncategorized
Surfaceness
Uncategorized
SynActJ
Uncategorized
Sync Windows
User Interface
Hue Colors
Segmentation
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
Thresholded Blur
Filtering
Time Lapse
Uncategorized
Time Stamper
Image Annotation
Timebar
Image Annotation
ToAST
Tracking
TopoJ
Tutorials
Branch hierarchy analysis
Track analysis
Close gaps in tracks by introducing new spots
Segmentation, Tracking, Benchmark
TrackMate Actions
Segmentation, Tracking
Export tracking results in the cell tracking challenge format
Segmentation, Tracking, Benchmark
TrackMate-ExTrack
Tracking
TrackMate DoG detector
Segmentation, Tracking
TrackMate-Cellpose-Advanced
Segmentation, Tracking, Machine Learning
TrackMate-Cellpose-SAM
Segmentation, Tracking, Machine Learning
TrackMate-Cellpose
Segmentation, Tracking, Machine Learning
TrackMate-Ilastik
Segmentation, Tracking, Machine Learning
TrackMate-Label-Image-Detector
Segmentation, Tracking
TrackMate-Lacss
Segmentation, Tracking, Deep Learning, Machine Learning
TrackMate Mask detector
Segmentation, Tracking
TrackMate-MorphoLibJ
Segmentation, Tracking
TrackMate-Omnipose-Advanced
Segmentation, Tracking, Machine Learning
TrackMate-Omnipose
Segmentation, Tracking, Machine Learning
TrackMate-StarDist
Segmentation, Tracking, Machine Learning
TrackMate-Thresholding-Detector
Segmentation, Tracking
TrackMate v7 detectors
Tracking, Segmentation
TrackMate-Weka
Segmentation, Tracking, Machine Learning
Extending TrackMate
Segmentation, Tracking
TrackMate-Helper
Segmentation, Tracking, Benchmark
TrackMate Kymograph
Tracking, Kymograph
TrackMate-Oneat
Tracking
TrackMate
Segmentation, Tracking
TrackMate FAQ
Tracking, Segmentation
Scripting TrackMate
Tracking, Segmentation
Setting keys for TrackMate detectors and trackers
Tracking, Segmentation, Scripting
Using TrackMate from MATLAB
Segmentation, Tracking
TrackMate Accuracy
Segmentation, Tracking
TrackMate Trackastra
Tracking, Machine Learning
Configuring TrackMate conda path
Tracking, Segmentation
Manual editing of tracks using TrackMate
Segmentation, Tracking
Manual tracking with TrackMate
Segmentation, Tracking
Shortcuts for editing and navigating the main view of TrackMate
Segmentation, Tracking
Editing object shape in TrackMate
Segmentation, Tracking
TrackMate display settings
Tracking, Segmentation
TrackScheme
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
Annotation, Analysis
Tubeness
Uncategorized
TurboReg
Registration
Tutorial Maker
Uncategorized
Trainable Weka Segmentation
Segmentation, Machine Learning
Large-scale cell tracking under segmentation uncertainty
Tracking
UnwarpJ
Registration
Updater
ImageJ2
Upload Sample Image
Uncategorized
Vessel Analysis
Analysis
VHPro
Uncategorized
Virtual Insect Brain (VIB) Protocol
Registration
Video Editing
Uncategorized
View5D
Visualization
VisBio Ortho Stack
Visualization
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
Projection, Segmentation
ZFBONE
Uncategorized
FunImageJ
Development, Scripting
Neuroanatomy update site
Analysis, Neuroanatomy

ImageJ Docs

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List of Extensions