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 (Capture images using QuickTime)
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
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)
Jenoptik: Mac and Windows plugins for ProgRes microscope cameras
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)
SSIM_index (calculate structural similarity index)
Image Moments (image moments of n-th rank)
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)
Accurate Gaussian Blur
Add Poisson Noise
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 ReaderStacks [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
3D Viewer
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,
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)
Stephan Preibisch
Stitching, Gaussian Convolution, FFT Transform, Principal
Curvature and Sobel Filter (plugins work in both 2D and 3D)
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)
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)