Descriptions and downloads for ImageJ plugins stored here. There are many more plugins in the ImageJ website.

• ImageJVI

• Align_4
• Align_RGB_planes
• Align_Slice
• bUnwarpJ: consistent and elastic registration
• Image Stabilizer

• AATAP
• Analyze Skeleton (2D/3D)
• Automatic detection of neuronal labeling in histological image series
• Bitmap Sholl Analysis
• Chamfer Distances and Geodesic Diameters
• ClonalTools (analysis of mosaic images)
• Colocalization Finder
• Confined Displacement Algorithm Determines True and Random Colocalization (CDA)
• Distance Analysis (DiAna)
• Feature Finder (Template matching)
• Frap_Norm (FRAP measurement and normalization)
• FRAP Analysis (analysis of FRAP experiments)
• Fourier Shape Analysis
• Green and Red Puncta Colocalization
• HeatMap Histogram
• Intravoxel Incoherent Motion (IVIM) Analysis and ADC analysis
• JACoP (Just Another Co-localization Plugin)
• Lipid Droplet (or any other spots) Counter
• Lemos Asymmetry Analysis (asymmetry measurements from dental panoramic radiograph images)
• PoissonNMF: Linear unmixing without reference spectra
• ShapeLogic categorizer: Machine learning or rule based
• MSCS (Micropatterned Single Cell Sorting)
• 3D Object Counter
• 3D Roi Manager
• 3D Analysis
• 3D Mereotopology
• 2D/3D Spatial statistics
• MetroloJ
• OpenMIMS (open, process and analyze images captured with NanoSIMS 50 & 50L secondary ion mass spectrometers)
• Radial thickness measure
• SarConfoCal (Simultaneous Fluorescence and Sarcomere Length Measurements from LSCM Images)
• SarcOptiM (High Frequency Online Sarcomere Length Measurement)
• Time gated phasor
• Three-way PCA
• TTorg (Transverse tubular system regularity analysis)
• Wand Tracker (track objects by selecting them with the magic wand)
• Microscope Image Correlation Spectroscopy
• Neurite-J, Sholl analysis for organotypic cultures
• Find minimum and maximum
• FLEYE, ommatidia analysis
• 3D tissue organisation

• MiToBo - a microscope image analysis toolbox (basic image processing tools, active contours, cell/nuclei/neurite segmentation, scratch assay analysis, ...)

• Chart White Balance
• Colour Deconvolution
• Color Pixel Counter
• Lut Panel
• Threshold Colour
• Color Deconvolution: Optimizing handling of 3D unitary optical density vectors with polar coordinates
• Channel Merger
• Conversions between RGB color space and Lab color space
• Set minimum and maximum values for LUT

• Digital Darkfield Decomposition
• Edge Detection
• Expression
• Fast Filters
• Fit_Polynomial
• Highpass filter
• Hill Shade
• MRI Processor
• Nonuniform Background Removal
• Periodic_Boundary_Blur
• Surface Blur
• Thresholded Blur
• 3D Filters
• 3D Fast Filters with JNI
• Differential contrast enhancement
• Line Lab selective median filtering
• Lab non-local mean with same pixel luminance neighborhood

• Animated PNG Writer
• Bio-Formats
• CBF Reader
• DICOM_open
• HPGL_Reader
• LSM_Reader
• LSMToolbox
• Metamorph nd & ROI files importer (nd stack builder)
• Okolab Data Import
• Perkin Elmer Reader
• PGM 16 bit exporter
• SIMS_Toolbox
• TomoJ
• The Tudor DICOM Toolkit
• Pt3Reader, a Picoquant .pt3 files importer

• Morphological Operators for ImageJ
• Non binary Morphological Operators for ImageJ
• Fast Morphological Filters
• Mitochondrial Morphology
• 2D/3D Skeletonization
• 3D Mathematical Morphology
• Euclidean minimum spanning tree
• Apoptosis Macro

• Active Mask Segmentation (2D)
• Active contour (Snake)
• Adjustable Watershed
• Hysteresis thresholding
• LiveWire Plugin
• Morphological Segmentation (2D/3D)
• Simple Image Pixel Editor
• Spectral Phasor
• Thresholding by connection
• Threshold_Colour
• Versatile Wand
• Yawi 2D (Wand)
• 3D Segmentation
• Chow and Kaneko binarization
• jSLIC superpixels

• Attenuation Correction
• Frame Projector
• HeatMap From Stack
• HyperVolume_Browser
• Image5D
• Image Stabilizer
• Image Stack Merger Plus
• MicroSCoBioJ
• Multiple Image Stack Operator
• Nonuniform Background Removal
• Computing a normal map from a 3D surface and several lightings (Polynomial Texture Mapping)
• NucleusJ
• Perkin Elmer Reader
• Plot stack points
• Stack Fitter
• 3D Filters
• 3D Tools
• 3D ImageJ Suite

• Fractal3D
• TrakEM2
• PhantomaJ

• Action Bar
• Alpha Channel
• Annotation ROI 3D
• Bezier Curve ROI
• Cairn Image Splitter
• ContMensili (update 05 mar 2011)
• DICOM_explode
• Droplet: a Drag and Drop image processor
• FigureJ: easy article figures
• IJ Ed (jEdit for ImageJ)
• Imageflow
• IJUpdate
• IJProxy
• Live Macro (experiment with a webcam and macro language)
• LSM Toolbox
• MidiJ - Midi Plugin for ImageJ
• MRI Cell Image Analyzer
• MVFG - Multi-format Video Frame Grabber
• Multi Undo
• NeuronPersistentJ
• PDF macro extension
• Pixel_Inspector
• Python DM3 Reader
• Quadratic Curve ROI
• Save All
• Seam Carving
• Serial Macro extensions
• SynapCountJ
• TAPAS
• Wait_For_User