Contents
Acquisition
Analysis
Collections
Color
Filters
Segmentation
Graphics
Input/Output
Programming Examples
Scripting
Stacks
Tools
Toolsets
Utilities
Links to External Sites
Acquisition [top]
Hamamatsu Orca 12-bit Camera
Shading Corrector
QuickTime Capture (Capture images using QuickTime)
TWAIN
JTwain
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)
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 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]
Autocorrelation
MRI t2 calculations
Line Analyzer
Image Correlator (image correlation)
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 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)
Waveness/Roughness
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
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)
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)
Grayscale Morphology
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
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)
Canny Edge Detector
Plane Brightness Adjustment (enhances CLSM images)
Polynomial Surface Fit (fits polynomial surface to an image)
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]
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 (binning)
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)
Point Cloud (creates a point cloud from CT scans)
OpenGL 5D Visualizer (MIP and DVR reconstruction)
Custom Montage (enhanced Make Montage)
Image Montage Macro
Image Slice Macro
Example Plots (log-log, semi-log, vector, error bar)
Dynamic Z and T Axis Profiler
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]
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)
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]
JavaScript (examples)
BeanShell
Python (examples)
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
nd Stack Builder (imports Metamorph nd and ROI files)
Concatenate Images or Stacks
Time Series Analyzer
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 ToolMacro Tools (65 macro tools on the ImageJ website)
Macro Tool DocumentationToolsets [top]
Multi-Channels Image and Stack Helper
ROI Manager Tools
Toolsets Folder on ImageJ websiteUtilities [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
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
Quadrant Picking (divides an image into 4 quadrants)
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 (FFT), 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
ImageCanvasWithOverlay,
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
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
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)
Adjustable Watershed (Watershed segmentation based on the Euclidian Distance Map)