Plugins

Contents
    Acquisition
    Analysis
    Collections
    Color
    Filters
    Graphics
    Input/Output
    Programming Examples
    Stacks
    Utilities
    More Sites with Plugins

Acquisition [top]
     Hamamatsu Orca 12-bit Camera
     Shading Corrector
     QuickTime Capture
     TWAIN
     JTwain
     SensiCam Long Exposure Camera
     Video Capture Macro Tool (Video for Windows via VirtualDub)
     Capturing plugin (Captures images on Windows using JMF)

     www.scioncorp.com: Scion Frame Grabbers and Firewire Cameras
     www.qimaging.com: QImaging Firewire Cameras
     ScionFGAkiz: Scion full-frame-rate capture
     FWCamAkiz: Mac OS X Firewire Cameras
     www.pixelsmart.com: PixelSmart Frame Grabbers
     www.bruxton.com: Andor, Cooke, Hamamatsu, PCO, Princeton Instruments,
        Photometrics, Red Shirt Imaging and SciMeasure Cameras
     www.aas2.com: Ann Arbor Sensor Systems AXT100
        Thermal Imaging Camera
     www.pco.de: Cooke PCO, Sensicam and Pixelfly Cameras
     mbl.edu: CamAcqJ plugin for QImaging Retiga cameras (Windows only)
     www.fclab.com: FCLab FC1000/2000 USB 2.0 Cameras (Windows only)
     micro-manager.org (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
     xlimaging.us: XLi megapixel USB 2.0 cameras (Windows only)
     PHASE GmbH: Firewire 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)

Analysis [top]
     Autocorrelation
     MRI t2 calculations
     Line Analyzer
     Image Correlator
     Particle Remover
     Circularity
     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
     Colocalization
     Granulometry
     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 Co-localization 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)

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
     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.)

Filters [top]
     Real Convolver
     FFT
     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
     De-interlace
     2D Gaussian Filter
     Kalman Filter
     Dual-Energy Algorithm
     Anisotropic Diffusion (edge-preserving noise reduction)
     Mixture Modeling Thresholding
     Otsu Thresholding
     Watershed Segmentation
     Grayscale Morphology
     Maximum Entropy Thresholding
     2D Hybrid Median Filter
     3D Hybrid Median Filter
     Spectral Unmixing
     Haar Wavelet Filter and Adaptive Median Filter
     'A trous' Wavelet Filter
     MultiThresholder (Isodata, Entropy, Otsu, Mixture Modeling)
     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 (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)

Graphics [top]
     Arrow
     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
     Image Layering Toolbox
     Contour Plotter
     Animated Sine Wave
     Dynamic Profiler
     Z-Axis Profiler
     Dotted and Dashed Lines
     Radial Grid
     Interactive 3D Surface Plots
     Fractal Generator
     Diffusion Limited Aggregate Models
     Fractal Growth Models
     Polar Transformer (convert to polar coordinates)

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
     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)

Programming Examples [top]
     Primes
     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)
     Tool Demo (install and use tools)
     Calculate 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
Stacks [top]
     Object Tracker
     Stack Reverser
     Group_ZProjector
     Concatenator
     Stack Combiner
     Stack Histogram
     Stack Maker
     Slice Remover
     MultiTracker
     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
     Image5D
     3D Object Counter
     Stack Builder
     Concatenate Images or Stacks
     Time Series Analyzer

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
     Benchmarks
     Stitch BLISS Tile Images
     Command Line Macros
     Anaglyph (creates stereo images)
     Convert Images to 16-bit Signed
     Cairn Optosplit Image Splitter
     Action Bar (a customizable tool bar)
     ROI Brush Tool
     ROI Adjust Tool
     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

More Sites with Plugins [top]
     Michael Abramoff
       VolumeJ, FlowJ, Flow3J, SurfaceJ, Register ROI,
       PCA (Principal Component Analysis)
     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,
       StereoJ (height maps from stereo pair)
     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, MicroArray Profile, Label Image
     Per Christian Henden
       Fractal Count, Map Fractal Count, Susan Filtering,
       Extrude Map, Gaussian Noise
     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)
     Tony Parker
       Dispose All Windows, Interfile Encoder/Decoder, Lookup Tables
       Align Stacks, Orthogonal Views (axial, coronal, and sagital)
     Dimiter Prodanov
       Grayscale Morphology, Grayscale Covariogram (and variogram)
       Grayscale Granulometry
     Jerek 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
     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)
     LOCI Bio-Formats library (Reads microscopy file formats)
       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
       DICOM, PNG, GIF, BMP, EPS, OME-XML, OME-TIFF, ABD TIFF
     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
     Image Differentials (gradient, Laplacian, and Hessian)
     Point Picker
     TurboReg (image registration)
     Neuron Morphology
     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
     3D Editing
     Extended Depth of Field (in focus images from 3D objects)
     Yawi3D (Yet Another Wand for ImageJ 3D)
     UnwarpJ (registration 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)
     MultiStackReg (multi-stack alignment)
     3D Deconvolution in Optical Microscopy
     PixFRET (FRET calculations)
     LargeMontage (creates a montage from image files)
     Power and log transforms, contrast stretching, spatial filtering
     SpotTracker (particle tracking over noisy image sequences)
     Visible Human Preprocessing Toolkit
     Multiple Image Processor (batch process images)
     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 (bidirectional elastic registration of images)
     IJStage and IJSerial (microscope stage control and serial I/O)
     Scrollable StackWindow (mouse wheel support for stacks)
     IJUpdate (updates ImageJ to stable or test releases)
     LSMToolbox (open Zeiss confocal microscope images)
     Open and z-project PerkinElmer Ultraview ERS RAW-files
     ParticleTracker (particle detection and tracking from digital videos)
     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)
     RoiPushTool (edit area selections using circular brush)
     WindowLevelTool (adjust window/level by dragging the mouse)
     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)
     MosaicJ (build a mosaic from overlapping partial images)
     OpenMIMS (Multi Isotope Mass Spectrometry)
     Iterative Deconvolution 2D (deblurring using MRNSD, CGLS or HyBR)
     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)