All Classes

This plugin implements the Help/About ImageJ command by opening about.jpg in ij.jar, scaling it 600% and adding text to an overlay.

This plugin animates stacks.

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).

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.

Implements ImageJ's Subtract Background command.

This plugin implements the File/Batch/Measure command, which measures all the images in a user-specified folder.

Implements the Plugins/Utilities/Run Benchmark command.

Implements the Erode, Dilate, Open, Close, Outline, Skeletonize and Fill Holes commands in the Process/Binary submenu.

This class processes binary images.

A class for reading arbitrary numbers of bits from a byte array.

This plugin reads BMP files.

This plugin implements the File/Import/URL command and the commands in the Help menu that open web pages.

This class does bit blitting of byte images.

8-bit image statistics, including histogram.

This plugin implements the Analyze/Tools/Calibration Bar command.

This plugin implements the Image/Adjust/Canvas Size command.

Displays the ImageJ "Channels" dialog.

This class implements the Process/FFT/Make Circular Selection command.

Copies/pastes images to/from the system clipboard.

Displays a dialog that allows the user to select a color using three sliders.

This is an 32-bit RGB image and methods that operate on that image..

ColorSpaceConverter

Selects pixels according to hsb or rgb components.

Plugins that implement this interface are notified when ImageJ is about to run a menu command.

Runs miscellaneous File and Window menu commands.

Compiles and runs plugins using the javac compiler.

This plugin implements the Brightness/Contrast, Window/level and Color Balance commands, all in the Image/Adjust sub-menu.

ControlPanel.

This plugin convolves images using user user defined kernels.

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.

PlugIns or PlugInFilters that want to listen to changes in a GenericDialog without adding listeners for each dialog field should implementthis method.

DICOM utilities

This plugin implements the Analyze/Distribution command.

This class opens images, roi's, luts and text files dragged and dropped on the "ImageJ" window.

This is a simple TextArea based editor for editing and compiling plugins.

This class fits an ellipse to an ROI.

This plugin implements the Plugins/Utilities/Monitor Events command.

ImageJ plugins that process an image may implement this interface.

This class implements the FFT, Inverse FFT and Redisplay Power Spectrum commands in the Process/FFT submenu.

This class implements the Process/FFT/Bandpass Filter command.

This class contains a Java implementation of the Fast Hartley Transform.

This plugin opens a multi-page TIFF file, or a set of raw images, as a virtual stack.

Saves images in tiff, gif, jpeg, raw, zip and text format.

This plugin implements the Invert, Smooth, Sharpen, Find Edges, and Add Noise commands.

Opens and displays FITS images.

ImageJ plugin that does curve fitting using the modified CurveFitter class.

This class does bit blitting of 32-bit floating-point images.

This is an 32-bit floating-point image and methods that operate on that image.

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.

This class contains static utility methods for replacing fonts that are not available on the current system.

Freehand region of interest or freehand line of interest

This class implements the built-in macro functions.

This class is a customizable modal dialog box.

Saves the active image in GIF format, or as an animated GIF if the image is a stack.

Implements the Image/Stacks/Tools/Grouped Z Project command.

This plugin implements the Analyze/Histogram command.

This class is an extended ImageWindow that displays histograms.

This is modal or non-modal dialog box that displays HTML formated text.

This plugin implements the File/New/Hyperstack command.

This class consists of static utility methods.

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.

This plugin implements the Process/Image Calculator command.

This class converts an ImagePlus object to a different type.

This frame is the main ImageJ class.

Handles exceptions on the EDT.

This is a custom layout manager that supports resizing of zoomed images.

This plugin implements ImageJ's Process/Math submenu.

An ImagePlus contain an ImageProcessor (2D image) or an ImageStack (3D, 4D or 5D image).

An ImageRoi is an Roi that overlays an image.

Statistics, including the histogram, of an image or selection.

A frame for displaying images.

This is a dialog box used to imports raw 8, 16, 24 and 32-bit images.

This is the recursive descent parser/interpreter for the ImageJ macro language.

This class contains static methods that use the Java 2 API.

Implements the text editor's Macros/Run command, and the IJ.runMacroFile() method, when the file name ends with ".js".

This class represents a straight line selection.

Implements ImageJ's Analyze/Tools/Analyze Line Graph command.

This plugin opens images specified by list of file paths as a virtual stack.

This class represents a color look-up table.

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.

The class contains static methods that perform macro operations.

This plugin implements the Plugins/Macros/Install Macros command.

Converts an RGB image to 8-bit index color using Heckbert's median-cut color quantization algorithm.

This plugin continuously plots ImageJ's memory utilization.

A modal dialog box that displays information.

Implements the Image/Stacks/Make Montage command.

New image dialog box plus several static utility methods for creating images.

This class displays a dialog window from which the user can select an input file.

This plugin implements most of the commands in the Edit/Options sub-menu.

An Overlay is a list of ROIs that can be drawn non-destructively on an Image.

This plugin implements the commands in the Image/Overlay menu.

Implements ImageJ's Analyze Particles command.

This plugin opens PxM format images.

This class creates an image that line graphs, scatter plots and plots of vector fields (arrows) can be drawn on and displayed.

This class implements the Plot Window's Data>"Add from Plot", "Add form Table", "Add Fit" and "More>Contents Style" dialogs

Plugins that generate "Live" profile plots (Profiler and ZAxisProfiler) displayed in PlotWindows implement this interface.

This class implements the Analyze/Plot Profile command.

ImageJ uses this class loader to load plugins and resources from the plugins directory and immediate subdirectories.

ImageJ plugins that process an image should implement this interface.

This is a closeable window that plugins can extend.

Plugins that run scripts (e.g., BeanShell, Jython) extend this class.

Saves in PNG format using the ImageIO classes.

This class represents a collection of points that can be associated with counters.

This class fills polygons using the scan-line filling algorithm described at "http://www.cs.rit.edu/~icss571/filling/".

This class contains the ImageJ preferences, which are loaded from the "IJ_Props.txt" and "IJ_Prefs.txt" files.

Creates a density profile plot of a rectangular selection or line selection.

An object of this type is a tokenized macro file and the associated symbol table.

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).

This class uses a memory cache to allow seeking within an InputStream.

This plugin implements the File/Import/Raw command.

This is ImageJ's macro recorder.

This plugin implements the Edit/Crop and Image/Adjust/Size commands.

This class implements the Apply Macro command in tables.

This plugin implements the Image/Color/Merge Channels command.

A rectangular region of interest and superclass for the other ROI classes.

This plugin implements the Edit/Options/Roi Defaults command.

This plugin, which enlarges or shrinks selections, implements the Edit/Selection/Enlarge command.

Plugins that implement this interface are notified when an ROI is created, modified or deleted.

Displays a dialog that allows the user to specify ROI properties such as color and line width.

This plugin implements the Edit/Selection/Scale command.

This class implements the rotated rectangle selection tool.

Implements ImageJ's Process/Noise/Salt and Pepper command.

This class displays a dialog window from which the user can save a file.

Implements the Analyze/Set Scale command.

This plugin implements the Plugins/Utilities/Capture Screen and Plugins/Utilities/Capture Image commands.

This plugin implements the commands in the Edit/Selection submenu.

A subclass of ij.gui.Roi (2D Regions Of Interest) implemented in terms of java.awt.Shape.

ShortProcessors contain a 16-bit unsigned image and methods that operate on that image.

An extended ShortProcessor that supports signed 16-bit images (experimental).

Implements the Image/Stacks/Reslice command.

This class interpolates a set of points using natural cubic splines (assuming zero second derivatives at end points).

This plugin implements the Image/Stacks/Combine command.

Implements the AddSlice, DeleteSlice and "Stack to Images" commands.

This plugin implements the Image/Stacks/Label command.

This plugin implements the Image/Stacks/Tools/Reduce command.

Statistics, including the histogram, of a stack.

This plugin, which saves the images in a stack as separate files, implements the File/Save As/Image Sequence command.

Runs the RunAtStartup (created by Edit/Options/Startup) and AutoRun (in StartupMacros) macros.

A simple QuickSort for String arrays.

This plugin implements the Image/Stacks/Tools/Make Substack command.

Objects of this class are used as entries in the macro language symbol table.

Plugins that implement this interface are notified when a table is opened, closed or updated.

Saves an image described by an ImageProcessor object as a tab-delimited text file.

This is an unlimited size text panel with tab-delimited, labeled and resizable columns.

This class is a rectangular ROI containing text.

This plugin implements the File/Save As/Text command, which saves the contents of Editor windows and TextWindows (e.g., "Log" and "Results").

This plugin implements the Process/Binary/Make Binary and Convert to Mask commands.

Decodes single and multi-image TIFF files.

This class converts an imageJ macro file file into a token stream.

This class contains static utility methods.

This plugin implements the Image/Translate command.

This class converts an ImageProcessor to another data type.

This plugin-filter implements ImageJ's Unsharp Mask command.

A plugin should implement this interface for minimizing a single-valued function or fitting a curve with a custom fit function.

This class represents an array of disk-resident images.

This class implements ImageJ's wand (tracing) tool.

This class allows for simple wildcard pattern matching.

This class implements the Window menu's "Show All", "Main Window", "Cascade" and "Tile" commands.

This plugin implements the File/Import/XY Coordinates command.

Saves the XY coordinates of the current ROI boundary.

Implements the Image/Stacks/Plot Z-axis Profile command, which plots the selection mean gray value versus slice number.

This plugin performs a z-projection of the input stack.