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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
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)

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