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Plugins

    2010-06-14 - Fiji "Heidelberg" is out

    2011-03-16 - Elastic aligment and montaging

    3D Objects Counter

    3D Surface Plot

    3D Viewer

    3Dscript

    3View import list

    ActogramJ

    Align Image by line ROI

    Align RGB planes

    Anaglyph for Red Cyan glasses

    AnalyzeSkeleton

    Analyze Skeleton 2D time series

    Analyze Stripes

    Anisotropic Diffusion 2D

    AplimTools

    Arrow

    Atlas Toolkit

    Auto Crop

    Auto Local Threshold

    Auto Threshold

    Automatic detection of neuronal labeling in histological image series

    Automatic optimal filament segmentation

    BAR

    BUnwarpJ

    Background Subtractor

    Balloon

    BigWarp

    Biomat

    Bleach Correction

    Blend two images

    Block Matching

    Cell Counter

    Celsius to fahrenheit

    Chess

    Classic Watershed

    ClearVolume

    Coloc 2

    Colocalization Test

    Colocalization Threshold

    Colocalization by Cross Correlation

    Colocalize

    Color Histogram

    Color Inspector 3D

    Colorizer Overlay

    Colour Deconvolution

    Colour merge

    Copy Pixel Size

    Correct 3D Drift

    Cover Maker

    Crop (3D)

    DHM Utilities

    DHM Utilities/Phase Unwrapping

    DHM Utilities/Reconstruction

    DICOM open

    DS4H Image Alignment

    Deep Zoom

    Delaunay Voronoi

    Delayed Snapshot

    Descriptor based registration

    DiameterJ

    Dichromacy

    Differentials

    Diffraction PSF 3D

    Directionality

    Distance Analysis

    Distance Transform Watershed

    Distortion Correction

    Dithering

    Dynamic ROI Profiler

    Dynamic Reslice

    Elastic Alignment and Montage

    Enhance Local Contrast (CLAHE)

    Extended Depth of Field

    Extract Images From PDF...

    FS Align TrakEM2

    FeatureJ

    Feature Extraction

    FijiArchipelago

    Fiji Developer

    Fiji Logo 3D

    Fiji/Menu

    Fiji Plugins

    Fiji/Z-Spacing Correction

    Fijiyama

    Find Dimension of Raw Image

    Find Peaks

    FlowJ

    Fourier Ring Correlation Plugin

    Frames

    Gabriel Graph

    Gnu Plot

    Granulometric Filtering

    Graph Cut

    Gray Morphology

    Grid

    Helmholtz Analysis

    Hill Shade

    IJ Robot

    Image5D

    Image Expression Parser

    Image Stabilizer

    Image Stitching

    Importing Image Files

    Integral Image Filters

    Interaction Analysis

    Interactive Affine

    Interactive Fitting

    Interactive Marker-controlled Watershed

    Interactive Moving Least Squares

    Interactive Perspective

    Interactive Rigid

    Interactive Similarity

    Interactive Stack Rotation

    Interactive Watershed

    IsoData Classifier

    Iterative Deconvolve 3D

    JFilament

    Kalman Stack Filter

    Kuwahara Filter

    KymoResliceWide

    LSM Toolbox

    LUMoS Spectral Unmixing

    Landmark Correspondences

    Lasso and Blow Tool

    Level Sets

    Linear Distance

    Linear Kuwahara

    Linear Stack Alignment with SIFT

    List all threads

    Local Thickness

    LungJ

    MOSAICsuite

    MTrack2

    MTrackJ

    M I P

    MaMuT

    Make Fiji Package

    Manual Tracking

    Manual drift correction plugin

    Marker-controlled Watershed

    Max Inscribed Circles

    Maximum Entropy Threshold

    MiToBo

    Microscope Measurement Tools

    Miniature Faking

    Minimum Cost Z surface Projection

    Mixture Modeling Thresholding

    MorphoLibJ

    Morphological Segmentation

    MosaicIA

    MosaicJ

    Moving Least Squares

    Multi-Template Matching

    MultiThresholder

    Multi Kymograph

    Multi Otsu Threshold

    Multi Stack Montage

    Multiple Image Processor

    Multithreaded Image Processing in Clojure

    Multithreaded Image Processing in JavaScript

    Multiview-Reconstruction

    MyofibrilJ

    Name Landmarks and Register

    NeuronJ

    NoiSee

    Nucleus Counter

    OMEVisual

    OlympusImageJPlugin

    PIV analyser

    PQCT

    Panorama

    Parallel Iterative Deconvolution

    Parallel Spectral Deconvolution

    Particle Tracker

    PhotoBend

    PillarTracker

    PlugIn Design Guidelines

    PointPicker

    Point Analysis

    Point Picker

    RATS › Robust Automatic Threshold Selection

    RGB-Gray Merge

    RGB Measure Plus

    RGB Profiler

    RGB to Montage

    ROI Picker

    RandomJ

    Read and Write Excel

    Reconstruct Reader

    Region Competition

    Register Virtual Stack Slices

    Replace Red with Magenta

    Report a Bug

    Retinex

    Roi 1-click tools

    Rolling Ball Background Subtraction

    SIMcheck

    SIOX › Simple Interactive Object Extraction

    SLIM Curve

    SME Projection

    SNT

    SNT › Tubular Geodesics

    SPIM Bead Registration (deprecated)

    SPIM Opener

    SPIM Registration

    SPIM Registration Method

    Saim

    Same Slice in Multiple Images

    Samples

    Save as animated gif

    Segment blob in 3D Viewer

    Segmentation Editor

    Shape Index Map

    Shepp-Logan Phantom

    Sholl Analysis

    Show Color Surfaces

    Sigma Filter

    Simulate Color Blindness

    Skeletonize3D

    Slice Labeler

    Snakuscule

    Spheres and Tubes in 3D

    Spline Deformation Generator

    SpotCounter

    SpotTracker

    Spot Intensity Analysis

    Spots colocalization (ComDet)

    Squassh

    StackReg

    Stack Manipulation

    StarDist

    Statistical Region Merging

    StereoMate

    Stitching 2D/3D

    Stochastic Denoise

    Strahler Analysis

    Straighten...

    Sync Windows

    Temporal-Color Code

    Temporal Median

    Test Java3D

    Thread Killer

    Time Lapse

    Time Stamper

    ToAST

    TopoJ

    TrackMate

    Trainable Segmentation Plugin Implementation

    Trainable Segmentation Plugin (deprecated)

    Trainable Weka Segmentation

    TrakEM2

    TrakEM2 Archipelago

    TransformJ

    Transform Virtual Stack Slices

    TreeJ

    Tubeness

    TurboReg

    Tutorial Maker

    UnwarpJ

    Updater

    Upload Sample Image

    User ›Freetrashbox/DiameterJ

    Using the Script Editor

    VIB Protocol

    VTEA

    Vaa3d Reader

    Vaa3d Writer

    Video Editing

    View5D

    Volume Calculator

    Volume Viewer

    Watershed Algorithm (ImageJ plugin)

    Wavelet Denoise

    Xlib

    Example 1

    Example 2

    Example 3

    Example 4

    Example 5

    Howto - Authoring a page

    Math test