Programming Examples
    Links to External Sites

Acquisition [top]
     Hamamatsu Orca 12-bit Camera
     Shading Corrector
     QuickTime Capture (Capture images using QuickTime)
     Twain Scan
     SensiCam Long Exposure Camera
     Video Capture Macro Tool (Video for Windows via VirtualDub)
     Capturing plugin (Captures images on Windows using JMF)
     Webcam Capture (Video capture on OS X, Linux and Windows) QImaging Firewire Cameras
     ScionFGAkiz: Scion full-frame-rate capture
     FWCamAkiz: Mac OS X Firewire Cameras PixelSmart Frame Grabbers Andor, Cooke, Hamamatsu, PCO, Princeton Instruments,
        Photometrics, Red Shirt Imaging and SciMeasure Cameras Ann Arbor Sensor Systems AXT100
        Thermal Imaging Camera Cooke PCO, Sensicam and Pixelfly Cameras CamAcqJ plugin for QImaging Retiga cameras (Windows only) FCLab FC1000/2000 USB 2.0 Cameras (Windows only) (μManager): Open source, multi-platform, extendable;
        stage, filter wheel and shutter control; serial I/O; Zeiss and Nikon
        microscopes; Hamamatsu, Andor, PVCAM, DVC and IIDC Firewire cameras;
        Shutters, stages, etc. by Vincent (Uniblitz), Ludl, Prior, ASI and Sutter
     PHASE GmbH: Firewire and GigE Vision camera control software (Windows only)
     CivilCapture: Capture images using the LTI-Civil Java library
     Lumenera: Infinity USB 2.0 cameras (Mac only)
     Dage-MTI: Plugin for XLV, XL16 and XLM cameras (Windows only)
     Jenoptik: Mac and Windows plugins for ProgRes microscope cameras
     AVerMedia: Plugins for DarkCrystal HD Capture cards (Windows only)
     iSight Capture: Webcam video capture using JavaCV and OpenCV
     Videoscan: Plugin for Videoscan camera (Windows only)
     HF_IDS_Cam: High Frequency IDS Camera Capture (Linux and Windows only)

Analysis [top]
     MRI t2 calculations
     Line Analyzer
     Image Correlator (image correlation)
     Particle Remover
     Modulation Transfer Function
     Specify ROI
     Specify Line Selection
     Comment Writer
     16-bit Histogram
     Results and Text
     Draw line or point grids
     Moment Calculator
     Batch Statistics
     Cell Counter
     Oval Profile Plot
     Color Comparison
     Radial Profile Plot
     Microscope Scale
     MRI Analysis Calculator
     Sync Measure 3D
     Hough Circles
     Convex Hull, Circularity, Roundness
     Fractal Dimension and Lacunarity
     Measure And Label
     Texture Analysis
     Named Measurements
     Cell Outliner
     Grid Cycloid Arc
     RGB Profiler
     Colocalization Finder
     Spectrum Extractor
     Contact Angle
     RG2B Colocalization
     Color Profiler
     Hull and Circle
     MR Urography
     Template Matching
     Extract IMT from ultrasound images
     ITCN (Image-based Tool for Counting Nuclei)
     Multi Cell Outliner
     FRETcalc - FRET by acceptor photobleaching
     JACoP (Just Another Colocalization Plugin)
     FRET and Colocalization Analyzer
     CASA (Computer Assisted Sperm Analyzer)
     Radial Profile Plot Extended
     Concentric Circles (non-destructive overlay)
     Azimuthal Average
     Slanted Edge Modulation Transfer Function
     Calculate 3D Noise
     FWHM (analyze photon detector pinhole images)
     SSIM_index (calculate structural similarity index)
     Image Moments (image moments of n-th rank)
     MS_SSIM_index (multi-scale structural similarity index )
     Colony Counter (count colonies in agar plates)
     Levan (chromosome morphology)
     EXTRAX (electron diffraction intensity extraction)
     Fractal Surface Measurement
     Foci Picker3D (finds local maxima in 2D and 3D images)
     Diameter (measures the diameter of a blood vessels)
     Graph Demo (creates particle adjacency lists)
     Asymmetry Analysis (HR-TEM image conditions)
     2D NMR Analysis (integrates peaks in 2D NMR spectra)
     MetaData and Intracellular Calcium Line Scan Analysis
     GHT (General Hough Transformation object recognition)
     IntraCell (nanoparticle colocalization within cells)
     Lemos Asymmetry Analysis (dental panoramic radiographs)
     Merz Grid Macro (semicircular lines and points in overlay)
     Stress Granule Counter (counts SGs in eucaryotic cells)
     Vamp 2D/3D (isolate puncta in 2D and 3D images)
     Sampling Window (unbiased sampling window)
     Map Bone Microstructure (histomorphometry parameters)
     Immunohistochemistry (IHC) Image Analysis Toolbox
     GaussFit_OnSpot (gaussian spot fitting)
     simFRAP (calculates diffusion coefficients from FRAP series)
     TTorg (transverse tubular system regularity analysis)
     VesselJ (quantify blood and lymphatic vessels in murine corneal flat-mounts)
     AxonJ (counts and segments whole-nerve axons)
     ReadPlate (macros that measures multi-well plates of up to 96 wells)
     COELI (COvariancE of Lucky Images)
     Neuron Morpho (Neuron Morphology)

Collections [top]
     UCSD Confocal Microscopy Plugins
     MBF ImageJ for Microscopy Collection by Tony Collins

Color [top]
     RGB Stack Splitter
     RGB Stack Merge
     HSB Stack Splitter
     RGB Recolor
     LUT Lister
     Color Counter [Updated]
     Color Picker
     RGB Gray Stack Merge
     Color Chooser
     LUT Panel
     Color Histogram
     RGB Measure
     LUT Editor
     3D Color Inspector/Color Histogram
     RGB Measure Plus
     Color Space Converter
     Color Transformer (Luv, Lab, HSI, HSV, HSL, etc.)
     RGB to CMYK (converts RGB to 32-bit CMYK stack) [new]

Filters [top]
     Real Convolver
     LoG Filtering
     Background Subtraction and Normalization
     Contrast Enhancer
     Background Correction
     Byte Swapper
     Discrete Cosine Transform (DCT)
     FFT Filter
     FFTJ and DeconvolutionJ
     Unpack 12-bit Images
     2D Gaussian Filter
     Kalman Filter
     Dual-Energy Algorithm
     Anisotropic Diffusion (edge-preserving noise reduction)
     Grayscale Morphology [Updated]
     2D Hybrid Median Filter
     3D Hybrid Median Filter
     Spectral Unmixing
     Haar Wavelet Filter and Adaptive Median Filter
     'A trous' Wavelet Filter
     Kuwahara Filter
     Granulometric Filtering
     Windowed-Sinc Filter (low pass time series filter)
     Anisotropic Diffusion 2D (edge-preserving noise reduction)
     Auto Gamma (gamma correction)
     Linearize Gel Data
     Radon Transform (CT back projection, sinogram)
     Correct X Shift of Confocal Images
     Multi Otsu Threshold
     Spectral Unmixing of Bioluminescence Signals
     Lipschitz Filter
     Float Morphology (erode, dilate, open, close)
     X_Shifter (correct pixel mismatch of confocal images)
     Sigma Filter (edge-preserving noise reduction)
     Rolling Ball Background Subtraction
     Mean Shift Filter (edge-preserving smoothing)
     Accurate Gaussian Blur
     Add Poisson Noise [Updated]
     CLAHE (enhances local contrast)
     Floyd Steinberg Dithering
     Polar Transformer (corrects radial and angular distortions)
     Gaussian Blur 3D
     Image Rotator (rotates image around ROI center of mass)
     Mexican Hat (2D Laplacian of Gaussian) [new]
     Canny Edge Detector [new]
     Plane Brightness Adjustment (enhances CLSM images) [new]
     Polynomial Surface Fit (fits polynomial surface to an image) [new]

Segmentation [top]
     Mixture Modeling Thresholding
     Otsu Thresholding
     Watershed Segmentation Maximum Entropy Thresholding
     MultiThresholder (IsoData, MaxEntropy, Otsu, etc.)
     Multi Otsu Threshold
     SIOX (Simple Interactive Object Extraction)
     RATS (Robust Automatic Threshold Selection)
     Densitometry 1 (1-channel color segmentation)
     Densitometry 3 (3-channel color segmentation)
     Blob Labeler (labels connected blobs of pixels)
     RetFM-J (segments and quantitates retina cell nuclei)

Graphics [top]
     Text Demo
     QuickTime Movie Player
     3D Surface Plotter
     Paint Brush
     Resize Canvas
     Example Plot
     Morph one image to another
     Random Ovals
     3D Text Demo using Java 2D
     Reduce size using averaging (binning)
     Image Layering Toolbox
     Contour Plotter
     Animated Sine Wave
     Dynamic Profiler
     Z-Axis Profiler
     Dotted and Dashed Lines [Updated]
     Radial Grid
     Interactive 3D Surface Plots
     Fractal Generator
     Diffusion Limited Aggregate Models
     Fractal Growth Models
     Polar Transformer (convert to polar coordinates)
     Point Cloud (creates a point cloud from CT scans) [new]
     OpenGL 5D Visualizer (MIP and DVR reconstruction) [new]
     Custom Montage (enhanced Make Montage) [new]
     Image Montage Macro [new]
     Image Slice Macro [new]
     Example Plots (log-log, semi-log, vector, error bar) [new]
     Dynamic Z and T Axis Profiler [new]

Input/Output [top]
     Open and save Analyze format images
     Open and save ASCII header format images
     Open and save SPE Images
     Open and save PNG, PICT, Targa, etc. using Jimi
     Open Biorad Z-Series
     Open Leica SP multi-channel stacks
     Batch Converter
     Open QuickTime Movies
     Save stack as QuickTime movie
     Open Multiple Images
     Import Multiple Raw Images
     Jimi Stack Writer
     AVI Writer
     JMF Movie Reader
     Open Images Using a File List
     Animated Gif Reader
     Leica SP Splitter
     Open PDS Images
     Import polygon ROI from a text file
     Import LUT from a text file
     Save evenly spaced ROI coordinates
     Save stacks as animated gifs
     AVI Reader
     LSM Reader (Zeiss LSM 510 confocal microscopes)
     Save in BMP format
     Import DICOM Sequences
     Quess RAW
     Image Viewer
     Handle Extra File Types
     IPLab Reader
     DICOM Rewriter (Anonymizer)
     Excel Writer
     Multi FDF and VFF Opener
     OpenSIF (opens Andor SIF files)
     QuickTime Still Extractor
     PNG Writer
     EXIF Reader
     JMF Movie Player
     DICOM Sort
     Import Bruker NMR Files
     AVI Splitter
     DICOM Directory Analyser
     Zeiss ZVI Reader
     Import Digital Elevation Model from text file
     Open/save ISAC images (e.g., Fuji BAS scanners)
     Gatan DM3 Reader
     Deltavision Opener
     Open Molecular Imaging and Nanoscope AFM files
     NIfTI Input/Output
     Packard InstantImager Reader
     Open and Save UNC format images
     QuickTime Stack Writer
     PDF Writer
     Open Leica SP2 TIFF Sequence
     PGM/PPM/PNM Writer
     EPS (Encapsulated PostScript) Writer
     PerkinElmer Reader
     Nikon ND2 Reader (Windows only)
     TIA Reader (FEI/Emispec .ser files)
     TIFF Dumper (displays TIFF tags of current image)
     TIFF Tags (displays TIFF tags in Results window)
     Open Heyex Raw Files (imports Heidelberg Spectralis images)
     CINE File Reader (opens Phantom High Speed Camera files)
     Watch Dir (watches for new images in a directory)
     MRI File Manager (reads Bruker MRI spectrometer files)
     AVI Analyzer (analyzes the structure of RIFF (AVI) files)

Programming Examples [top]
     Step Maker
     Display Updater
     Mouse Listener
     Image Processing Demo
     Key Listener
     Field of View Calculator
     Gear Math
     Circle Test
     Image Window with Panel
     Examples from the Tutorial
     Image Inverter
     Window Focus Bouncer
     Escape (aborting a filter)
     Custom Particle Analyzer
     Using Packages for Utility Classes
     Command Line Example
     Non-destructive Graphic Overlay
     Load images, text and macros from a JAR file
     Add grid of numeric fields to a dialog
     Package plugins in a JAR file
     Save/Restore User Preferences
     Link ImageJ to MySQL
     Image Listener
     Create signed 16-bit image from array
     Display text in an editor window
     Add values to the Results Table
     JCalc (an example PlugInFrame)
     Calculate ROI Mean (using selection masks)
     Blend Images using toFloat(i,fp) and setPixels(i,fp)
     Get and set image properties using macros
     Image5D Macro Language Extensions
     RSS Feed Reader
     Multiple LUT Stack
     Binary erosion using EDM, with "Preview" and "Help"
     Event Listener (listen for color or tool changes)
     MacBook Position (use JNI to read Sudden Motion Sensor)
     MultiColumnDialog (create dialogs with multiple columns)
     Find 3D Max (compare pixel access methods)
     Image and text overlay with transparent background
     Apply formula to all pixels in an image or stack
     Interactively set the position and size of a selection
     Add radio buttons to dialogs and handle events
     Cross Fader (use slider to move one image over another)
     Roi Iterator Demo (process pixels contained in a selection)

Scripting [top] [new]
     JavaScript (examples)
     Python (examples)

Stacks [top]
     Object Tracker
     Stack Reverser
     Stack Combiner
     Stack Histogram
Stack Maker
     Slice Remover
     Click Forward
     Stack Splitter
     Time Stamper
     Stack Builder
     Hypervolume (4D Stack) Shuffler
     Stack Inserter
     Voxel Counter
     Stack Normalizer
     Stack Focuser (extended depth of field)
     HyperVolume (4D Stack) Browser
     Substack Maker
     Hypervolume Opener
     Virtual Stack Opener
     Slice Labeler
     RGB Zprojector
     Manual Tracking
     Substack Select
     Volume Viewer/3D-Slicer
     3D Object Counter
     nd Stack Builder (imports Metamorph nd and ROI files)
     Concatenate Images or Stacks
     Time Series Analyzer [Updated]
     3D Viewer
     Radial Reslice (orthogonal reconstructions)
     RC Montage (enhanced Image>Stacks>Make Montage)
     StackSlicer (dynamic orthoganal views)
     Smart Projector (optimizes projections of time-lapse stacks)
     Measure Track (measures ROIs from Tracker output)
     Make Isotropic (rescales along z-axis)
     Untilt Stack (removes tilt from a stack of images)
     Stack Reducer (makes stacks smaller)
     Demontager (opposite of Image>Stacks>Make Montage)
     Depth From Focus (improves focal depth)
     3D Convex Hull (3D shape descriptors, solidity and convexity)
     LC_Pro (automated ROI analysis of image sequences)
     Stack Contrast Adjustment (enhances CLSM stacks)
     Virtual Test Stack (creates test stacks of any size and type)
     Pointing Cell Tracking (fork of Manual Tracking)

Tools [top]
     Tool Demo (create and install a custom tool)
     Eight Tools (install multiple custom tools)
     ROI Brush Tool
     Window Level Tool
     Arrow Tool
     Lasso Selection Tool
     Pixel Inspection Tool
     Overlay Brush Tool
     Bezier Curve Tool (line selection from bezier curves)
     N Digits Tool (displays cursor location in status bar)
     CC (Common Commands) Menu Tool
     Action Bar (a customizable tool bar)
     Command Bar (adds toolbar with 19 commands)
     Versatile Wand Tool

     Macro Tools (65 macro tools on the ImageJ website)
     Macro Tool Documentation

Toolsets [top]
     Multi-Channels Image and Stack Helper
     ROI Manager Tools
     Toolsets Folder on ImageJ website

Utilities [top]
     Background Task
     Plugins Control Panel
     Straighten Curved Objects
     "Plasma" Benchmark
     Window Closer
     Copy/Paste to System Clipboard
     Thumbnail Maker
     Sync Windows
     Image Calculator Plus
     JavaScript Editor
     Drag and Drop
     Combine Images to Create Mosaic
     Adjust Window and Level
     Joel Time Stamper
     Query DICOM Header
     Calculate Fura-2 (calcium) Ratios
     Stitch BLISS Tile Images
     Command Line Macros
     Two Shot Anaglyph (creates stereo images)
     Convert Images to 16-bit Signed
     Cairn Optosplit Image Splitter
     ImageJ Updater (updates to latest ij.jar)
     Calculate SNR of CCD Cameras
     Calculate TIRF Penetration Depth
     Calculate CCD Readout Noise
     Thread Killer (aborts plugins)
     Calculate Lens Objective Parameters
     CT Window Level (specify W&L in Hounsfield units)
     Anonymize IJ DICOM
     Iterative Radial Voting (inference of structural saliency)
     Plugin Installer (installs plugins using drag and drop)
     ANKAphase (X-ray inline phase-contrast radiographs)
     nVidia Fix (works around buggy nVidia display drivers)
     Anaglyph (red/green anaglyph or output for Sharp LL-1513d)
     Results Importer (copy contents of text windows to Results)
     TRSI (Translation, Rotation, and Scale Invariant Character Recognition)
     Image Pyramid (creates image pyramids using a box filter)
     MREJ (MRE elasticity reconstruction)
     SPICE-CT Package for Computed Tomography QC [new]
     Quadrant Picking (divides an image into 4 quadrants) [new]

Links to External Sites [top]
     Michael Abramoff
       VolumeJ, FlowJ, Flow3J, SurfaceJ, Register ROI,
       PCA (Principal Component Analysis)
     Noël Bonnet
       Anisotropic diffusion, Shading correction, Contrast enhancement,
       Regularized image gradient (Shen-Castan), Manual segmentation,
       Multivariate Statistical Analysis (MSA), Principal Component Analysis (PCA),
       Correspondence Analysis (CA), Fuzzy Segmentation, N-component
       segmentation, Watershed segmentation, Stackscope
     Thomas Boudier
       Active Contours (Snakes), Canny-Deriche Filter,
       Shape Analysis by Fourier Descriptors
     Wilhelm Burger and Mark Burge
       53 plugins, including Alpha Blending, Histogram Equalization,
       Gamma Correction, UnsharpMask, Harris Corner Detector,
       Hough Linear Transform, Region Labeling, Trace Contours,
       Median Cut Quantization, DFT 2D, DCT 2D, Affine Mapping,
       Twirl, Ripple and Sphere Mapping, Bicubic Interpolation
     Gary Chinga
       Surface roughness statistics, Dynamic (adaptive) threshold,
       Shape descriptors, Image correlation, Stack plots,
     Ulf Dittmer
       Expression (applies formulas to images), HPGL Reader, Warp,
       OpenGL Example, PxM Reader (imports PBM, PGM and PPM),
       Pixellate, Seam Carving, Animated PNG (APNG) Writer
     Bob Dougherty
       Ellipse ROI, Live Histogram, Measure Stack, Multi Measure,
       NTSC DV2Float, QuickTime Grab, Layers, Stack Sorter, Measure
       ROI, Polynomial Fit, PLOT3D I/O, Polar Gradient, 3D Fast Hartley
       Transform (FHT, FFT), 2D and 3D Deconvolution, Diffraction PSF 3D
       3D Local Thickness (3D Distance Map), MicroArray Profile, Label Image
     Jeff Hardin
       QuickTime Movie Player, Concatenate Movies, QT4D Player,
       QT4D Writer, Acquire4D, Rename Perkin-Elmer Files
     Per Christian Henden
       Orientation Measurement, Fractal Estimation, Susan Smoothing
       (2D&3D), Isolated Pixel Removal (2D&3D), Small Region Removal,
       Adaptive 3D Threshold, Semi Band-threshold, 3D Otsu Thresholding,
       3D Discrete Distance Tranform, Extrude Map, Gaussian Noise
     Frederick Hessman
       Anaglyph, Astronomy Plugin Package, Directory Watcher,
       Figure Calibration, Image Padder, Paint by Number,
       RGB Composer, Telescope Tracking Package, SVD Analysis
     Gregory Jefferis
       Biorad Reader, BioRad Writer, Amira Reader
       Amira Writer, IGS Raw Reader (gzip)
     Gabriel Landini
       Convolution filters, game of life, contour lines , morphological
       operators, dilation, erosion, 4- and 8-connected particle analysis
       color thresholding, color deconvolution (stain separation)
     Mark Longair
       Simple Neurite Tracer, Three Pane Crop, Unpack To PNG,
       Quantile Based Normalization, Find Connected Regions,
       Mask Of Nearby Points, "Tubeness" (useful for tracing
       neurons or blood vessels)
     Peter Sebastian Masny
       Census (identify, count, and process objects),
       XYZ_MaxProject (max projection along all three axis)
     Tony Parker
       Dispose All Windows, Interfile Encoder/Decoder, Lookup Tables
       Align Stacks, Orthogonal Views (axial, coronal, and sagital)
     Sean Parsons
       FFT Box, Phase Space, ROI Group Manager and Tight Montage
     Stephan Preibisch
       Stitching, Gaussian Convolution, FFT Transform, Principal
       Curvature and Sobel Filter (plugins work in both 2D and 3D)
     Jarek Sacha
       Image IO (uses JAI to open addition image types)
       Clustering, Texture Synthesus, 3D Toolkit, Half-Median
       RGB to CIE L*a*b*, Multiband Sobel edges, VTK Examples
       DCRaw (digital camera raw images), ImageJ for Zaurus PDA
       Groovy Console (edit and run Groovy scripts)
     Martin Schlueter
       Geometric Mappings, Color transforms,
       Delaunay Triangulation and Interpolation
     Nico Stuurman
       MultiTracker2, RGB Stack Merge2, ICS Opener, Optical Insights
       Running Z Projector, Binner, QED Swap
     TransformJ (Geometric Transformations up to 4D)
       Affine, Crop, Embed, Mirror, Rotate, Scale, Shift, Turn

     FeatureJ (Image Feature Extraction)
       Canny edges, derivatives, Hessian, Laplacian, eigenvalues, statistics

     RandomJ (Image Randomization)
       Binomial, Exponential, Gamma, Gaussian, Poisson, Uniform

     NeuronJ (Neurite Tracing and Quantification)
     OME Bio-Formats library and plugin (loci-tools.jar)
       PIC, MetaMorph STK, LSM, FluoView, IPLab, Deltavision, Leica LEI,
       ABD, GEL, Imaris, Openlab LIFF and RAW, DM3, PerkinElmer,
       Image-Pro Sequence, NEF, PICT, IPW, PGM, OIB
       AxioVision ZVI, Image Cytometry Standard ICS and IDS, UltraView ERS

     ImageJ Documentation Wiki
       Align_4, Align_RGB_planes, Align_Slice
       Fourier Shape Analysis
       Threshold_Colour, Colour_Deconvolution, Lut_Panel
       Canny-Deriche Edge Detection, Fit Polynomial
       Tudor DICOM Toolkit, LSM_Reader, SIMS_Toolbox
       Morphological Operators, 3D binary morphological filters
       Active contour (Snake), LiveWire, Bezier Curve ROI
       Quadratic Curve ROI, HyperVolume_Browser, Surface Blur
       TrakEM2, Image5D, Thresholding by connection
       Cell Image Analyzer, IJUpdate, LSMToolbox, Action Bar
       Nonuniform Background Removal, 3D Filters, Wait For User
       Pixel Inspecter
     University of Sussex (download)
       Find Peaks, Find Peaks (Frame), Find Peaks Optimiser,
       Stack Threshold, Colocalisation Threshold, Confined
       Displacement Algorithm (CDA), Stack Correlation Analyser,
       Stack Colocalisation Analyser, Threshold, Contrast Enhancer,
       GaussianFit Loader, Difference of Gaussians
     Image Differentials (gradient, Laplacian, and Hessian)
     Point Picker
     TurboReg (image registration [alignment])
     Cubic Spline Resizing
     Segmenting Assistant
     NucMed Collection (PET/SPECT imaging)
     Jython, FFT, Lecture Notes (German)
     Install and use Jython with ImageJ
     Fractional Splines and Wavelets
     DICOM Import and Export (uses dcm4che library)
     Watershed Algorithm
     Extended Depth of Field (in focus images from 3D objects)
     Yawi3D (Yet Another Wand for ImageJ 3D)
     UnwarpJ (registration [alignment] using warping)
     Save in Biorad PIC format
     Find Colocalized Pixels in RGB Channels
     Measure Total Above Thresholded Area in a Stack
     StackReg (recursive alignment [registration] of stacks)
     3D Deconvolution in Optical Microscopy
     PixFRET (FRET calculations)
     Power and log transforms, contrast stretching, spatial filtering
     SpotTracker (particle tracking over noisy image sequences)
     DStretch (digital enhancement of pictographs)
     SplineSnake (segmentation using active contour)
     MIJ (interfacing ImageJ and Matlab)
     DropSnake and LB_ADSA (contact angle measurement)
     Read, write and display Amira files
     LOCI 4D Data Browser
     QA-Distri (plugins for QA in digital radiology)
     bUnwarpJ (elastic registration [alignment] of images)
     IJStage and IJSerial (microscope stage control and serial I/O)
     IJUpdate (updates ImageJ to stable or test releases)
     LSMToolbox (open Zeiss confocal microscope images)
     Open and z-project PerkinElmer Ultraview ERS RAW-files
     MTrackJ (track and analyze moving objects in image sequences)
     IJProxy (proxy server settings for ImageJ)
     Inhomogen Isotropic Diffusion 2D Filter
     Install and use Ruby to write an ImageJ plugin
     Introduction to Astronomical Image Processing using ImageJ
     Chemotaxis and Migration Tool
     View5D (interactively display datasets with up to 5 dimensions)
     SplineDeformationGenerator (cubic B-spline deformations)
     Azimuthal Average
     MAI Simulator (generates simulated DNA microarray images)
     SparkMaster (calcium spark analysis)
     Spectral Deconvolution (2D and 3D Tikhonov and TSVD deblurring)
     Iterative Deconvolution 2D (deblurring using MRNSD, CGLS or HyBR)
     HRRT Deconvolution (motion correction of PET brain images)
     MosaicJ (build a mosaic from overlapping partial images)
     OpenMIMS (Multi Isotope Mass Spectrometry)
     Image Stabilizer (stabilizes jittery stacks using Lucas-Kanade method)
     Multiple Stack Viewer (opens multiples stacks in a window)
     Mathematical Morphology (25 plugins that use structuring elements)
     MovieIO (library for reading and writing video files frame-by-frame)
     Turning CDMAM (moves the discs inside CDMAM phantoms)
     MR Urography (kidney assessment)
     AccPbFRET (analyze acceptor photobleaching FRET images)
     Volumest (volume estimation using stereological method)
     Delaunay_Voronoi (Delaunay/Voronoi diagrams from point selections)
     3D Viewer (hardware-accelerated 3D volume and surface visualization)
     Scan Calculator (calculate 3D data from 2D laserscanner data)
     ImageFlow (node-based macro editing)
     Advanced Sholl Analysis (2D Sholl analysis on segmented/traced neurons)
     EdgeFitter (fits a line selection to edges of an object)
     IJ ED (jEdit-based code editor)
     SheppLogan (generates a sampled version of the Shepp-Logan phantom)
     RiFRET (analyze intensity-based ratiometric FRET images)
     ObjectJ (non-destructive markers and linked results)
     Parallel Super-Resolution
     PDF Macro Ext (adds PDF creation functions to the macro language)
     Droplet (drag and drop file processor that uses customizable macros)
     ImageJ SURF (feature detection and image comparison)
     Mouse X (crop and rotate an image, similar to Edit>Selection>Straighten)
     Savitzky-Golay noise reduction filters
     CDA (Confined Displacement Algorithm for Colocalization)
     QuickPALM (PALM/STORM particle detection and reconstruction)
     Serial Macro Extensions (enables macro access to serial devices)
     Colocalization Colormap (quantification/visualization of fluorescent signals)
     JFilament (segment and track 2D and 3D filaments)
     Heatmap From Stack
     HeatMap Histogram
     Export EPS (saves images in Encapsulated PostScript format)
     Template matching and alignment using OpenCV library
     CBF Reader (reads miniCBF files from DECTRIS PILATUS detectors)
     Octane (super-resolution imaging and single molecule tracking)
     Read and write Esri ASCII grid files
     PIV (iterative particle image velocimetry analysis)
     Beth Israel plugins (PET/SPECT and CT/MRI fusion)
     SmartRoot (semi-automated analysis of root systems)
     Speckle TrackerJ (track particles through time)
     ImagePlot (explore patterns in large image collections)
     IJ-Scala (use Scala language to write scripts using ImageJ API)
     Save as Movie (save stacks in avi, mov, wmv or mp4 format)
     jClustering (general framework for dynamic imaging clustering)
     ijblob (library to detect and analyse connected components [blobs] in binary images)
     Okolab Data Import (imports data acquired by Okolab incubators)
     FigureJ (creates image figures for scientific publications)
     Video Encoder (encodes live image streams into .mp4, .flv, .mov and .webm)
     ScientiFig (create, format or reformat scientific figures)
     FRETTY (calculate FRET with spectral unmixing)
     BoneJ (trabecular geometry and whole bone shape analysis)
     Dynamic Pixel Inspector (dynamic time-axis profile plotting)
     Invadopodia tracker (analyze invadopodia dynamics in time-lapse movies)
     xySpark (detection and analysis of Ca2+ sparks in confocal stacks)
     Cell Magic Wand Tool (click on a cell to outline it)
     Color Transformer 2 (extended Color Transformer)
     ThunderSTORM (PALM and STORM analysis and super-resolution imaging)
     Local Gaussian Filter and Adaptive Morphology Operation
     Orthanc (import 2D/3D DICOM images from Orthanc servers)
     Dendritic Filopodia Motility Analyser (evaluation of live cell dendritic protrusions)
     NetCDF (opens Unidata Network Common Data Form files)
     HDF5 Plugin for ImageJ
     CANDLE-J (Enhanced Denoising under Low-light Excitation)
     DiameterJ (nanofiber diameter characterization)
     ActogramJ (analysis and visualization of chronobiological data)
     MouseMove (semi-automated analysis of movement in rodents)
     HyperStackReg (multi-channel hyperstack registration)
     DRIQ (QC measurements in radiography and mammography)
     MJ2 Opener (opens MJ2 files; requires Java 8 and Windows)
     SarcOptiM (high frequency online sarcomere length measurement)
     TTorg (transverse tubular system regularity analysis)
     NucleusJ (nuclear shape and chromatin organization)
     TANGO (high-throughput processing and analysis of 3D fluorescence images)
     SarConfoCal (Simultaneous Ca fluorescence and sarcomeres length from LSCM images)
     Barcode_Codec (1D/2D barcode encoder/decoder)
     QR Decoder for ImageJ (decodes QR barcodes)
     HoloJ (reconstruct and analyze phase and amplitude images from holograms)