Plugin Grid

3D Objects Counter	Analyze Skeleton 2D time series	AnalyzeSkeleton
Analyze Stripes	AplimTools	Automatic detection of neuronal labeling in histological image series
BAR	BioVoxxel Toolbox	Cell Counter
DiameterJ	Directionality	Distance Analysis
FAST	FijiRelax	Find Peaks
Granulometric Filtering	Hough Circle Transform	Interaction Analysis
Manual Tracking	MorphoLibJ	MOSAICsuite
MyofibrilJ	Nucleus Counter	Particle Tracker
PillarTracker	Point Picker	Sholl Analysis
SME Projection	Spot Intensity Analysis	SpotCounter
SpotTracker	Strahler Analysis	TreeJ

3D Binary Filters

Distance Transform 3D

LungJ

Coloc 2	Colocalization by Cross Correlation	Colocalization Test
Colocalization Threshold	Colocalize	Distance Analysis
Interaction Analysis	LUMoS Spectral Unmixing	MOSAICsuite

Automated workflow for parallel Multiview Reconstruction	Diffraction PSF 3D	Iterative Deconvolve 3D
MOSAICsuite	Multiview-Reconstruction	Parallel Iterative Deconvolution
Parallel Spectral Deconvolution	Region Competition	Squassh

Anisotropic Diffusion 2D	Background Subtractor	BAR
Biomat	Enhance Local Contrast (CLAHE)	Integral Image Filters
Kalman Stack Filter	LungJ	Miniature Faking
MorphoLibJ	MOSAICsuite	PillarTracker
Rolling Ball Background Subtraction	Sigma Filter	Temporal Median

Align Image by line ROI	Atlas Toolkit	Automated workflow for parallel Multiview Reconstruction
BigWarp	BUnwarpJ	Correct 3D Drift
DS4H Image Alignment	Elastic Alignment and Montage	Feature Extraction
Fijiyama	Grid/Collection Stitching Plugin	Image Stabilizer
Image Stitching	Landmark Correspondences	Linear Stack Alignment with SIFT
Manual drift correction plugin	Microscope Measurement Tools	Multiview-Reconstruction
Register Virtual Stack Slices	SPIM Bead Registration (deprecated)	SPIM Registration
SPIM Registration Method	SPIM Registration on cluster (deprecated)	StackReg
Stitching 2D/3D	TrakEM2 align sections tutorial	TrakEM2

Anaglyph for Red Cyan glasses	Analyze Skeleton 2D time series	BAR
Blend two images	Celsius to fahrenheit	Delayed Snapshot
Dynamic ROI Profiler	Fiji Logo 3D	Find Dimension of Raw Image
Find Peaks	List all threads	Make Screencast
MyofibrilJ	Same Slice in Multiple Images	Scripting TrackMate
Using TrackMate from MATLAB	TrakEM2 Scripting	Scripting the Trainable Weka Segmentation

Auto Local Threshold	Auto Threshold	Automatic optimal filament segmentation
Balloon	BAR	Classic Watershed
Distance Transform Watershed	Dithering	FAST
Graph Cut	Gray Morphology	Interactive Marker-controlled Watershed
Interactive Watershed	IsoData Classifier	Lasso and Blow Tool
LungJ	Marker-controlled Watershed	Maximum Entropy Threshold
Mixture Modeling Thresholding	MorphoLibJ	Morphological Segmentation
MOSAICsuite	Multi Otsu Threshold	MultiThresholder
Public data sets	RATS › Robust Automatic Threshold Selection	Region Competition
Segment blob in 3D Viewer	Segmentation Editor	Snakuscule
SNT	SNT › Tubular Geodesics	Squassh
Statistical Region Merging	TrackMate	Trainable Segmentation Plugin Implementation
Trainable Segmentation Plugin (deprecated)	TrakEM2	TrakEM2 segmentation modes tutorial
TrakEM2 semi-automatic segmentation tutorial	Trainable Weka Segmentation - How to compare classifiers	Trainable Weka Segmentation - How to install new classifiers
Trainable Weka Segmentation	Minimum Splits and Mergers Warping error	Minimum Splits and Mergers Warping error
Rand error	Scripting the Trainable Weka Segmentation	Topology preserving warping error

Manual Tracking	MTrack2	MTrackJ
Particle Tracker	PhotoBend	PillarTracker
Public data sets	SpotTracker	Temporal Median
ToAST	Analyzing TrackMate results with MATLAB	TrackMate

Align Image by line ROI	Analyze Stripes	Auto Crop
Cover Maker	DS4H Image Alignment	Extended Depth of Field
Graph Cut	Importing Image Files	Linear Kuwahara
Low Light Tracking Tool	Make Fiji Package	Example mamut.properties file
Miji	Moving Least Squares	Advanced mode(MTrack)
Read more on microtubule polarity and (+) end vs. (-) end tracking	Read more about MSER parameters	Read more about Preprocessing
Read more about the RANSAC parameters	Read more on RANSAC models	MSER as the segmentation method
Watershedding and Hough transform parameters	Watershed followed by MSER	PhotoBend
Point Analysis	RATS › Robust Automatic Threshold Selection	Replace Red with Magenta
Retinex	Simple Neurite Tracer › Basic Instructions	Simple Neurite Tracer › "Export to SWC" Tutorial
Simple Neurite Tracer › Preprocessing Data for Better Results	Simple Neurite Tracer › Selecting paths	Simple Neurite Tracer › Sholl analysis
Simple Neurite Tracer › Step-By-Step Instructions	Testing Procedure for Simple Neurite Tracer	Simple Neurite Tracer › Using MIP Overlays
SNT › Manual	SNT › Modeling	SNT › Scripting
SNT › Step-By-Step Instructions	Spirals	Statistical Region Merging
Stochastic Denoise	TopoJ	Analyzing TrackMate results with MATLAB
How to write custom actions for TrackMate	How to write your own detection algorithm for TrackMate	How to write your own edge feature analyzer algorithm for TrackMate
How to write your own particle-linking algorithm for TrackMate	How to write your own spot feature analyzer algorithm for TrackMate	How to write your own track feature analyzer algorithm for TrackMate
How to write your own viewer for TrackMate	Getting started with TrackMate	TrackMate
Manual editing of tracks using TrackMate	Manual tracking with TrackMate	TrackScheme
Trainable Segmentation Plugin Implementation	Trainable Segmentation Plugin (deprecated)	TrakEM2 add more sections/layers tutorial
TrakEM2 align sections tutorial	TrakEM2 basics tutorial	TrakEM2 measurements tutorial
TrakEM2 saving project tutorial	TrakEM2 segmentation modes tutorial	TrakEM2 semi-automatic segmentation tutorial
TrakEM2 tutorials	Trainable Weka Segmentation - How to compare classifiers	Trainable Weka Segmentation - How to install new classifiers

3D Viewer	3Dscript	ActogramJ
BigDataViewer	BigWarp	ClearVolume
Image5D	PillarTracker	Quiver Plot
View5D	Volume Viewer	VTEA

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