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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)
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, 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) 2ff7e9595c
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