All Classes

This plugin implements the Help/About ImageJ command by opening the about.jpg in ij.jar, scaling it 400% and adding some text.

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.

This plugin implements the Image/Transform/Bin command.

ImageJ bit blitting classes must implement this interface.

Implements the File/Save As/BMP command.

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.

This is an 8-bit image and methods that operate on that image.

Calibration objects contain an image's spatial and density calibration data.

Implements the Analyze/Calibrate command.

This plugin implements the Image/Colors/Arrange Channels command, which allows the user to change the order of channels.

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

Checks for duplicate class and JAR files in the plugins folders and deletes older duplicates.

This class does bit blitting of RGB images.

Implements the Image/Color/Color Picker command.

This plugin implements most of the Edit/Options/Colors command.

RGB image statistics, including histogram.

This class is used by the Plugins/Shortcuts/List Shortcuts command to display a list keyboard shortcuts.

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.

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.

Runs ImageJ as an applet and optionally opens up to nine images using URLs passed as a parameters.

Plugins that implement this interface are notified when an image is opened, closed or updated.

This class is used by GenericDialog to add images to dialogs.

This abstract class is the superclass for classes that process the four data types (byte, short, float and RGB) supported by ImageJ.

Reads raw 8-bit, 16-bit or 32-bit (float or RGB) images from a stream or URL.

This class represents an expandable array of images.

Implements the Image/Stacks/Images to Stack" command.

Writes a raw image described by a FileInfo object to an OutputStream.

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.

Saves an ROI to a file or stream.

This class interpolates between ROIs in the ROI Manager.

This plugin implements the Analyze/Tools/ROI Manager command.

Opens ImageJ, NIH Image and Scion Image for windows ROI outlines.

This plugin implements the Edit/Selection/Rotate command.

Saves the current ROI outline to a file.

This plugin implements the Image/Rotate/Arbitrarily command.

A modal dialog box with a one line message and "Don't Save", "Cancel" and "Save" buttons.

This plugin implements the Analyze/Tools/Draw Scale Bar command.

This plugin implements the Image/Scale command.

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.

Implements the commands in the Process/Shadows submenu.

This class does bit blitting of 16-bit images.

16-bit image statistics, including histogram.

Implements the Image/Stacks/Reslice command.

This class fits a spline function to a set of 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.

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, big-endian 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.