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 window.

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 plugin implements the Image/Duplicate command.

This plugin implements the Euclidean Distance Map (EDM), Watershed, Ultimate Eroded Points and Voronoi commands in the Process/Binary submenu.

This class implements the ellipse selection tool.

Runs ImageJ menu commands in a separate thread.

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

The class implements the Process/FFT/Math command.

This class consists of public fields that describe an image file.

Opens or reverts an image specified by a FileInfo object.

This plugin implements ImageJ's Fill, Clear, Clear Outside and Draw commands.

This plugin saves a 16 or 32 bit image in FITS format.

This class implements an expandable float array similar to an ArrayList or Vector but more efficient.

Used by the Roi classes to return float coordinate arrays and to determine if a point is inside or outside of spline fitted selections.

32-bit (float) image statistics, including histogram.

Implements the File/Import/Image Sequence command, which opens a folder of images as a stack.

Calculate the so-called "capacity" fractal dimension.

This class implements the text editor's Macros/Find Functions command.

This plug-in filter uses convolution with a Gaussian function for smoothing.

This plugin generates gel profile plots that can be analyzed using the wand tool.

This plugin opens GIFs and Animated GIFs.

This class implements the Analyze/Tools/Grid command.

This class consists of static GUI utility methods.

Implements the Plugins/Hotkeys/Create Shortcut and Remove commands.

Implements the "Stack to HyperStack", "RGB to HyperStack" and "HyperStack to Stack" commands.

Implements the Image/HyperStacks/Reduce Dimensionality command.

This is a Canvas used to display images in a Window.

This plugin implements the Image/Show Info command.

This plugin implements the Help/Update ImageJ command.

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.

This plugin implements the Plugins/Utilities/Unlock, Image/Rename and Plugins/Utilities/Search commands.

This plugin implements the Edit/Selection/Specify command.

This plugin implements the Image/Stacks/Statistics command.

This class does stack type conversions.

This plugin, which implements the Image/Stacks/Tools/Insert command, inserts an image or stack into another image or stack.

The plugin implements the Image/Stacks/Tools/Montage to Stack command.

This class processes stacks.

This plugin implements the Image/Transform/Flip Z and Image/Stacks/Tools/Reverse commands.

This class is an extended ImageWindow that displays stacks and hyperstacks.

This plugin implements the Edit/Options/Startup command.

This plugin implements the Edit/Selection/Straighten command.

This plugin is used by the Image/Stacks/Tools/Make Substack command to create substacks of hyperstacks.

This class "synchronizes" mouse input in multiple windows.

This plugin implements the Edit/Options/Fonts command and the dialog displayed when you double click on the text tool.

This plugin displays the contents of a text file in a window.

This plugin opens a tab or comma delimeted text file as an image.

Uses a TextPanel to displays text in a window.

Displays thread information in a text window.

Adjusts the lower and upper threshold levels of the active image.

Saves an image described by a FileInfo object as an uncompressed TIFF file.

The ImageJ toolbar.

Implements the Flip and Rotate commands in the Image/Transform submenu.

This is an extended Button class used to reduce the width of the HUGE buttons on Mac OS X.

This class consists of static methods and fields that implement ImageJ's Undo command.

Opens TIFFs, ZIP compressed TIFFs, DICOMs, GIFs and JPEGs using a URL.

This is a non-modal dialog box used to ask the user to perform some task while a macro or plugin is running.

This plugin implements the Edit/Options/Wand Tool command.

This class consists of static methods used to manage ImageJ's windows.

Writes the XY coordinates and pixel values of all non-background pixels to a tab-delimited text file.

A modal dialog box with a one line message and "Yes", "No" and "Cancel" buttons.

This plugin implements the commands in the Image/Zoom submenu.