All Classes
-
All Classes Interface Summary Class Summary Enum Summary Class Description AboutBox This plugin implements the Help/About ImageJ command by opening the about.jpg in ij.jar, scaling it 400% and adding some text.Analyzer This plugin implements ImageJ's Analyze/Measure and Analyze/Set Measurements commands.Animator This plugin animates stacks.AppearanceOptions This plugin implements the Edit/Options/Appearance command.ArrayUtil Arrow This is an Roi subclass for creating and displaying arrows.ArrowTool ArrowToolOptions This plugin implements the Edit/Options/Arrow Tool command.AutoThresholder Autothresholding methods (limited to 256 bin histograms) from the Auto_Threshold plugin (http://fiji.sc/Auto_Threshold) by G.Landini at bham dot ac dot uk).AutoThresholder.Method AVI_Reader ImageJ Plugin for reading an AVI file into an image stack (one slice per video frame) Restrictions and Notes: - Only few formats supported: - uncompressed 8 bit with palette (=LUT) - uncompressed 8 & 16 bit grayscale - uncompressed 24 & 32 bit RGB (alpha channel ignored) - uncompressed 32 bit AYUV (alpha channel ignored) - various YUV 4:2:2 and 4:2:0 compressed formats (i.e., formats with full luminance resolution, but reduced chroma resolution - png or jpeg-encoded individual frames.AVI_Writer This plugin implements the File/Save As/AVI command.BackgroundSubtracter Implements ImageJ's Subtract Background command.BatchConverter This plugin implements the File/ /Convert command, which converts the images in a folder to a specified format.BatchMeasure This plugin implements the File/Batch/Measure command, which measures all the images in a user-specified folder.BatchProcessor This plugin implements the File/Batch/Macro and File/Batch/Virtual Stack commands.Benchmark Implements the Plugins/Utilities/Run Benchmark command.Binary Implements the Erode, Dilate, Open, Close, Outline, Skeletonize and Fill Holes commands in the Process/Binary submenu.BinaryInterpolator BinaryProcessor This class processes binary images.Binner This plugin implements the Image/Transform/Bin command.BitBuffer A class for reading arbitrary numbers of bits from a byte array.Blitter ImageJ bit blitting classes must implement this interface.BMP_Reader This plugin reads BMP files.BMP_Writer Implements the File/Save As/BMP command.BrowserLauncher This plugin implements the File/Import/URL command and the commands in the Help menu that open web pages.BrushTool This class implements the Paintbrush Tool, which allows the user to draw on an image, or on an Overlay if "Paint on overlay" is enabled.ByteBlitter This class does bit blitting of byte images.ByteProcessor This is an 8-bit image and methods that operate on that image.ByteStatistics 8-bit image statistics, including histogram.Calibration Calibration objects contain an image's spatial and density calibration data.CalibrationBar This plugin implements the Analyze/Tools/Calibration Bar command.Calibrator Implements the Analyze/Calibrate command.CanvasResizer This plugin implements the Image/Adjust/Canvas Size command.ChannelArranger This plugin implements the Image/Colors/Arrange Channels command, which allows the user to change the order of channels.Channels Displays the ImageJ Channels window.ChannelSplitter This plugin implements the Image/Color/Split Channels command.CircularRoiMaker This class implements the Process/FFT/Make Circular Selection command.ClassChecker Checks for duplicate class and JAR files in the plugins folders and deletes older duplicates.Clipboard Copies/pastes images to/from the system clipboard.ColorBlitter This class does bit blitting of RGB images.ColorChooser Displays a dialog that allows the user to select a color using three sliders.ColorPicker Implements the Image/Color/Color Picker command.ColorProcessor This is an 32-bit RGB image and methods that operate on that image..Colors This plugin implements most of the Edit/Options/Colors command.ColorSpaceConverter ColorSpaceConverterColorStatistics RGB image statistics, including histogram.ColorThresholder Selects pixels according to hsb or rgb components.CommandFinder CommandListener Plugins that implement this interface are notified when ImageJ is about to run a menu command.CommandLister This class is used by the Plugins/Shortcuts/List Shortcuts command to display a list keyboard shortcuts.Commands Runs miscellaneous File and Window menu commands.Compiler Compiles and runs plugins using the javac compiler.CompositeConverter This plugin implements the Image/Color/Make Composite command.CompositeImage Concatenator This plugin, which concatenates two or more images or stacks, implements the Image/Stacks/Tools/Concatenate command.ContrastAdjuster This plugin implements the Brightness/Contrast, Window/level and Color Balance commands, all in the Image/Adjust sub-menu.ContrastEnhancer Implements ImageJ's Process/Enhance Contrast command.ControlPanel ControlPanel.Converter Implements the conversion commands in the Image/Type submenu.Convolver This plugin convolves images using user user defined kernels.Coordinates The plugin implements the Image/Adjust/Coordinates command.CurveFitter Curve fitting class based on the Simplex method in the Minimizer class Notes on fitting polynomial functions: (i) The range of x values should not be too far from 0, especially for higher-order polynomials.Debugger DialogListener PlugIns or PlugInFilters that want to listen to changes in a GenericDialog without adding listeners for each dialog field should implementthis method.DICOM This plugin decodes DICOM files.DicomTools DICOM utilitiesDirectoryChooser This class displays a dialog box that allows the user can select a directory.Distribution This plugin implements the Analyze/Distribution command.DownsizeTable A table for easier downsizing by convolution with a kernel.DragAndDrop This class opens images, roi's, luts and text files dragged and dropped on the "ImageJ" window.Duplicater Deprecated. replaced by Duplicator classDuplicator This plugin implements the Image/Duplicate command.Editor This is a simple TextArea based editor for editing and compiling plugins.EDM This plugin implements the Euclidean Distance Map (EDM), Watershed, Ultimate Eroded Points and Voronoi commands in the Process/Binary submenu.EllipseFitter This class fits an ellipse to an ROI.EllipseRoi This class implements the ellipse selection tool.EventListener This plugin implements the Plugins/Utilities/Monitor Events command.Executer Runs ImageJ menu commands in a separate thread.ExtendedPlugInFilter ImageJ plugins that process an image may implement this interface.ExtensionDescriptor FFT This class implements the FFT, Inverse FFT and Redisplay Power Spectrum commands in the Process/FFT submenu.FFTCustomFilter This class implements the Process/FFT/Custom Filter command.FFTFilter This class implements the Process/FFT/Bandpass Filter command.FFTMath The class implements the Process/FFT/Math command.FHT This class contains a Java implementation of the Fast Hartley Transform.FileInfo This class consists of public fields that describe an image file.FileInfoVirtualStack This plugin opens a multi-page TIFF file, or a set of raw images, as a virtual stack.FileOpener Opens or reverts an image specified by a FileInfo object.FileSaver Saves images in tiff, gif, jpeg, raw, zip and text format.Filler This plugin implements ImageJ's Fill, Clear, Clear Outside and Draw commands.Filters This plugin implements the Invert, Smooth, Sharpen, Find Edges, and Add Noise commands.Filters3D FITS_Reader Opens and displays FITS images.FITS_Writer This plugin saves a 16 or 32 bit image in FITS format.Fitter ImageJ plugin that does curve fitting using the modified CurveFitter class.FloatArray This class implements an expandable float array similar to an ArrayList or Vector but more efficient.FloatBlitter This class does bit blitting of 32-bit floating-point images.FloatPolygon Used by the Roi classes to return float coordinate arrays and to determine if a point is inside or outside of spline fitted selections.FloatProcessor This is an 32-bit floating-point image and methods that operate on that image.FloatStatistics 32-bit (float) image statistics, including histogram.FloodFiller This class, which does flood filling, is used by the floodFill() macro function and by the particle analyzer The Wikipedia at "http://en.wikipedia.org/wiki/Flood_fill" has a good description of the algorithm used here as well as examples in C and Java.FolderOpener Implements the File/Import/Image Sequence command, which opens a folder of images as a stack.FontUtil This class contains static utility methods for replacing fonts that are not available on the current system.FractalBoxCounter Calculate the so-called "capacity" fractal dimension.FreehandRoi Freehand region of interest or freehand line of interestFunctionFinder This class implements the text editor's Macros/Find Functions command.Functions This class implements the built-in macro functions.GaussianBlur This plug-in filter uses convolution with a Gaussian function for smoothing.GaussianBlur3D GelAnalyzer This plugin generates gel profile plots that can be analyzed using the wand tool.GenericDialog This class is a customizable modal dialog box.GIF_Reader This plugin opens GIFs and Animated GIFs.GifWriter Saves the active image in GIF format, or as an animated GIF if the image is a stack.Grid This class implements the Analyze/Tools/Grid command.GroupedZProjector This plugin implements the Image/Stacks/Tools/Grouped Z Project command.GUI This class consists of static GUI utility methods.Histogram This plugin implements the Analyze/Histogram command.HistogramWindow This class is an extended ImageWindow that displays histograms.Hotkeys Implements the Plugins/Hotkeys/Create Shortcut and Remove commands.HTMLDialog This is modal or non-modal dialog box that displays HTML formated text.HyperStackConverter Implements the "Stack to HyperStack", "RGB to HyperStack" and "HyperStack to Stack" commands.HyperStackMaker This plugin implements the File/New/Hyperstack command.HyperStackReducer Implements the Image/HyperStacks/Reduce Dimensionality command.IJ This class consists of static utility methods.IJ.ExceptionHandler IJEventListener Plugins that implement this interface are notified when the user changes the foreground color, changes the background color, closes the color picker, closes the Log window or switches to another tool.IJMath ImageCalculator This plugin implements the Process/Image Calculator command.ImageCanvas This is a Canvas used to display images in a Window.ImageConverter This class converts an ImagePlus object to a different type.ImageInfo This plugin implements the Image/Show Info command.ImageJ This frame is the main ImageJ class.ImageJ_Updater This plugin implements the Help/Update ImageJ command.ImageJApplet Runs ImageJ as an applet and optionally opens up to nine images using URLs passed as a parameters.ImageLayout This is a custom layout manager that supports resizing of zoomed images.ImageListener Plugins that implement this interface are notified when an image is opened, closed or updated.ImageMath This plugin implements ImageJ's Process/Math submenu.ImagePanel This class is used by GenericDialog to add images to dialogs.ImagePlus An ImagePlus contain an ImageProcessor (2D image) or an ImageStack (3D, 4D or 5D image).ImageProcessor This abstract class is the superclass for classes that process the four data types (byte, short, float and RGB) supported by ImageJ.ImageProperties ImageReader Reads raw 8-bit, 16-bit or 32-bit (float or RGB) images from a stream or URL.ImageRoi An ImageRoi is an Roi that overlays an image.ImageStack This class represents an expandable array of images.ImageStatistics Statistics, including the histogram, of an image or selection.ImagesToStack Implements the Image/Stacks/Images to Stack" command.ImageWindow A frame for displaying images.ImageWriter Writes a raw image described by a FileInfo object to an OutputStream.ImportDialog This is a dialog box used to imports raw 8, 16, 24 and 32-bit images.Info Deprecated. replaced by ij.plugin.ImageInfoInterpreter This is the recursive descent parser/interpreter for the ImageJ macro language.Java2 This class contains static methods that use the Java 2 API.JavaProperties Displays the Java system properties in a text window.JavaScriptEvaluator Implements the text editor's Macros/Run command, and the IJ.runMacroFile() method, when the file name ends with ".js".JpegWriter The File/Save As/Jpeg command (FileSaver.saveAsJpeg() method) uses this plugin to save images in JPEG format.Line This class represents a straight line selection.Line.PointIterator Dedicated point iterator for thin lines.LineGraphAnalyzer Implements ImageJ's Analyze/Tools/Analyze Line Graph command.LineWidthAdjuster Adjusts the width of line selections.ListVirtualStack This plugin opens images specified by list of file paths as a virtual stack.LogStream This class provides the functionality to divert output sent to the System.out and System.err streams to ImageJ's log console.LookUpTable This class represents a color look-up table.LUT This is an indexed color model that allows an lower and upper bound to be specified.LUT_Editor LutApplier This plugin implements the Image/Lookup Tables/Apply LUT command.LutLoader Opens NIH Image look-up tables (LUTs), 768 byte binary LUTs (256 reds, 256 greens and 256 blues), LUTs in text format, or generates the LUT specified by the string argument passed to the run() method.LutViewer Displays the active image's look-up table.Macro The class contains static methods that perform macro operations.Macro_Runner This class runs macros and scripts installed in the Plugins menu as well as macros and scripts opened using the Plugins/Macros/Run command.MacroConstants MacroExtension MacroInstaller This plugin implements the Plugins/Macros/Install Macros command.MacroRunner This class runs macros in a separate thread.MacroToolRunner MaximumFinder This ImageJ plug-in filter finds the maxima (or minima) of an image.Measurements MeasurementsWriter Saves a table as a csv or tab-delimited text file.MedianCut Converts an RGB image to 8-bit index color using Heckbert's median-cut color quantization algorithm.Memory This plugin implements the Edit/Options/Memory command.MemoryMonitor This plugin continuously plots ImageJ's memory utilization.Menus This class installs and updates ImageJ's menus.MessageDialog A modal dialog box that displays information.Minimizer Minimizer based on Nelder-Mead simplex method (also known as polytope method), including the 'outside contraction' as described in: J.C.MontageMaker Implements the Image/Stacks/Make Montage command.MultiLineLabel Custom component for displaying multiple lines.NewImage New image dialog box plus several static utility methods for creating images.NewPlugin This class creates a new macro or the Java source for a new plugin.NextImageOpener NonBlockingGenericDialog This is an extension of GenericDialog that is non-modal.OpenDialog This class displays a dialog window from which the user can select an input file.Opener Opens tiff (and tiff stacks), dicom, fits, pgm, jpeg, bmp or gif images, and look-up tables, using a file open dialog or a path.Options This plugin implements most of the commands in the Edit/Options sub-menu.Orthogonal_Views This plugin projects dynamically orthogonal XZ and YZ views of a stack.OtherInstance OvalRoi Oval region of interestOverlay An Overlay is a list of ROIs that can be drawn non-destructively on an Image.OverlayBrushTool OverlayCommands This plugin implements the commands in the Image/Overlay menu.OverlayLabels This plugin implements the Image/Overlay/Labels command.ParticleAnalyzer Implements ImageJ's Analyze Particles command.PasteController Implements ImageJ's Paste Control window.PGM_Reader This plugin opens PxM format images.PixelInspectionTool This plugin continuously displays the pixel values of the cursor and its surroundings.Plot This class creates an image that line graphs, scatter plots and plots of vector fields (arrows) can be drawn on and displayed.PlotCanvas This subclass of ImageCanvas has special provisions for plots: - Zooming: sets the plot range - Scrolling: moves data area This behavior is suppressed if the plot is frozenPlotContentsDialog This class implements the Plot Window's Data>"Add from Plot", "Add form Table", "Add Fit" and "More>Contents Style" dialogsPlotDialog PlotMaker Plugins that generate "Live" profile plots (Profiler and ZAxisProfiler) displayed in PlotWindows implement this interface.PlotVirtualStack This is a virtual stack of frozen plots.PlotWindow This class implements the Analyze/Plot Profile command.PlugIn Plugins that acquire images or display windows should implement this interface.PluginClassLoader ImageJ uses this class loader to load plugins and resources from the plugins directory and immediate subdirectories.PlugInDialog This is a non-modal dialog that plugins can extend.PlugInFilter ImageJ plugins that process an image should implement this interface.PlugInFilterRunner PlugInFrame This is a closeable window that plugins can extend.PluginInstaller Installs plugins dragged and dropped on the "ImageJ" window, or plugins, macros or scripts opened using the Plugins/Install command.PlugInInterpreter Plugins that run scripts (e.g., BeanShell, Jython) extend this class.PlugInTool PNG_Writer Saves in PNG format using the ImageIO classes.PNM_Writer PointRoi This class represents a collection of points that can be associated with counters.PointToolOptions This plugin implements the Edit/Options/Point Tool command.PolygonFiller This class fills polygons using the scan-line filling algorithm described at "http://www.cs.rit.edu/~icss571/filling/".PolygonRoi This class represents a polygon region of interest or polyline of interest.Prefs This class contains the ImageJ preferences, which are loaded from the "IJ_Props.txt" and "IJ_Prefs.txt" files.Printer This plugin implements the File/Page Setup and File/Print commands.ProfilePlot Creates a density profile plot of a rectangular selection or line selection.Profiler Implements the Analyze/Plot Profile and Edit/Options/Profile Plot Options commands.Program An object of this type is a tokenized macro file and the associated symbol table.ProgressBar This is the progress bar that is displayed in the lower right hand corner of the ImageJ window.Projector This plugin creates a sequence of projections of a rotating volume (stack of slices) onto a plane using nearest-point (surface), brightest-point, or mean-value projection or a weighted combination of nearest- point projection with either of the other two methods (partial opacity).ProxySettings This plugin implements the Plugins/Utilities/Proxy Settings command.RandomAccessStream This class uses a memory cache to allow seeking within an InputStream.RankFilters This plugin implements the Mean, Minimum, Maximum, Variance, Median, Open Maxima, Close Maxima, Remove Outliers, Remove NaNs and Despeckle commands.Raw This plugin implements the File/Import/Raw command.RecentOpener Opens, in a separate thread, files selected from the File/Open Recent submenu.Recorder This is ImageJ's macro recorder.RectToolOptions This plugin implements the rounded rectangle tool dialog box.Resizer This plugin implements the Edit/Crop and Image/Adjust/Size commands.ResultsTable This is a table for storing measurement results and strings as columns of values.ResultsTableMacros This class implements the Apply Macro command in tables.RGBStackConverter Converts a 2 or 3 slice stack, or a hyperstack, to RGB.RGBStackMerge This plugin implements the Image/Color/Merge Channels command.RGBStackSplitter Deprecated; replaced by ij.plugin.ChannelSplitter.Roi A rectangular region of interest and superclass for the other ROI classes.RoiDecoder This class decodes an ImageJ .roi file.RoiEncoder Saves an ROI to a file or stream.RoiEnlarger This plugin, which enlarges or shrinks selections, implements the Edit/Selection/Enlarge command.RoiInterpolator This class interpolates between ROIs in the ROI Manager.RoiListener Plugins that implement this interface are notified when an ROI is created, modified or deleted.RoiManager This plugin implements the Analyze/Tools/ROI Manager command.RoiProperties Displays a dialog that allows the user to specify ROI properties such as color and line width.RoiReader Opens ImageJ, NIH Image and Scion Image for windows ROI outlines.RoiRotationTool RoiRotator This plugin implements the Edit/Selection/Rotate command.RoiScaler This plugin implements the Edit/Selection/Scale command.RoiWriter Saves the current ROI outline to a file.RotatedRectRoi This class implements the rotated rectangle selection tool.Rotator This plugin implements the Image/Rotate/Arbitrarily command.SaltAndPepper Implements ImageJ's Process/Noise/Salt and Pepper command.SaveChangesDialog A modal dialog box with a one line message and "Don't Save", "Cancel" and "Save" buttons.SaveDialog This class displays a dialog window from which the user can save a file.ScaleBar This plugin implements the Analyze/Tools/Draw Scale Bar command.ScaleDialog Implements the Analyze/Set Scale command.Scaler This plugin implements the Image/Scale command.ScreenGrabber This plugin implements the Plugins/Utilities/Capture Screen and Plugins/Utilities/Capture Image commands.ScrollbarWithLabel This class, based on Joachim Walter's Image5D package, adds "c", "z" labels and play-pause icons (T) to the stack and hyperstacks dimension sliders.Selection This plugin implements the commands in the Edit/Selection submenu.Shadows Implements the commands in the Process/Shadows submenu.ShapeRoi A subclass ofij.gui.Roi(2D Regions Of Interest) implemented in terms of java.awt.Shape.ShortBlitter This class does bit blitting of 16-bit images.ShortProcessor ShortProcessors contain a 16-bit unsigned image and methods that operate on that image.ShortStatistics 16-bit image statistics, including histogram.SimpleCommands This plugin implements the Plugins/Utilities/Unlock, Image/Rename and Plugins/Utilities/Search commands.Slicer Implements the Image/Stacks/Reslice command.SpecifyROI This plugin implements the Edit/Selection/Specify command.SplineFitter This class fits a spline function to a set of points.Stack_Statistics This plugin implements the Image/Stacks/Statistics command.StackCombiner This plugin implements the Image/Stacks/Combine command.StackConverter This class does stack type conversions.StackEditor Implements the AddSlice, DeleteSlice and "Stack to Images" commands.StackInserter This plugin, which implements the Image/Stacks/Tools/Insert command, inserts an image or stack into another image or stack.StackLabeler This plugin implements the Image/Stacks/Label command.StackMaker The plugin implements the Image/Stacks/Tools/Montage to Stack command.StackPlotter StackProcessor This class processes stacks.StackReducer This plugin implements the Image/Stacks/Tools/Reduce command.StackReverser This plugin implements the Image/Transform/Flip Z and Image/Stacks/Tools/Reverse commands.StackStatistics Statistics, including the histogram, of a stack.StackWindow This class is an extended ImageWindow that displays stacks and hyperstacks.StackWriter This plugin, which saves the images in a stack as separate files, implements the File/Save As/Image Sequence command.Startup This plugin implements the Edit/Options/Startup command.StartupRunner Runs the RunAtStartup (created by Edit/Options/Startup) and AutoRun (in StartupMacros) macros.Straightener This plugin implements the Edit/Selection/Straighten command.StringSorter A simple QuickSort for String arrays.SubHyperstackMaker This plugin is used by the Image/Stacks/Tools/Make Substack command to create substacks of hyperstacks.SubstackMaker This plugin implements the Image/Stacks/Tools/Make Substack command.SurfacePlotter Symbol Objects of this class are used as entries in the macro language symbol table.SyncWindows This class "synchronizes" mouse input in multiple windows.Text This plugin implements the Edit/Options/Fonts command and the dialog displayed when you double click on the text tool.TextEncoder Saves an image described by an ImageProcessor object as a tab-delimited text file.TextFileReader This plugin displays the contents of a text file in a window.TextPanel This is an unlimited size text panel with tab-delimited, labeled and resizable columns.TextReader This plugin opens a tab or comma delimeted text file as an image.TextRoi This class is a rectangular ROI containing text.TextWindow Uses a TextPanel to displays text in a window.TextWriter This plugin implements the File/Save As/Text command, which saves the contents of Editor windows and TextWindows (e.g., "Log" and "Results").ThreadLister Displays thread information in a text window.ThreadUtil ThresholdAdjuster Adjusts the lower and upper threshold levels of the active image.Thresholder This plugin implements the Process/Binary/Make Binary and Convert to Mask commands.ThresholdToSelection TiffDecoder Decodes single and multi-image TIFF files.TiffEncoder Saves an image described by a FileInfo object as an uncompressed, big-endian TIFF file.Tokenizer This class converts an imageJ macro file file into a token stream.Toolbar The ImageJ toolbar.Tools This class contains static utility methods.Transformer Implements the Flip and Rotate commands in the Image/Transform submenu.Translator This plugin implements the Image/Translate command.TrimmedButton This is an extended Button class used to reduce the width of the HUGE buttons on Mac OS X.TypeConverter This class converts an ImageProcessor to another data type.Undo This class consists of static methods and fields that implement ImageJ's Undo command.UnsharpMask This plugin-filter implements ImageJ's Unsharp Mask command.URLOpener Opens TIFFs, ZIP compressed TIFFs, DICOMs, GIFs and JPEGs using a URL.UserFunction A plugin should implement this interface for minimizing a single-valued function or fitting a curve with a custom fit function.Variable VirtualStack This class represents an array of disk-resident images.WaitForUserDialog This is a non-modal dialog box used to ask the user to perform some task while a macro or plugin is running.Wand This class implements ImageJ's wand (tracing) tool.WandToolOptions This plugin implements the Edit/Options/Wand Tool command.WildcardMatch This class allows for simple wildcard pattern matching.WindowManager This class consists of static methods used to manage ImageJ's windows.WindowOrganizer This class implements the Window menu's "Show All", "Main Window", "Cascade" and "Tile" commands.Writer Deprecated. XY_Reader This plugin implements the File/Import/XY Coordinates command.XYCoordinates Writes the XY coordinates and pixel values of all non-background pixels to a tab-delimited text file.XYWriter Saves the XY coordinates of the current ROI boundary.YesNoCancelDialog A modal dialog box with a one line message and "Yes", "No" and "Cancel" buttons.ZAxisProfiler Implements the Image/Stacks/Plot Z-axis Profile command, which plots the selection mean gray value versus slice number.Zoom This plugin implements the commands in the Image/Zoom submenu.ZProjector This plugin performs a z-projection of the input stack.