All Classes Interface Summary Class Summary Enum Summary
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 implements ImageJ's Analyze/Measure and Analyze/Set Measurements commands.
This plugin animates stacks.
This plugin implements the Edit/Options/Appearance command.
This is an Roi subclass for creating and displaying arrows.
This plugin implements the Edit/Options/Arrow Tool command.
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.
This plugin implements the File/Save As/AVI command.
Implements ImageJ's Subtract Background command.
This plugin implements the File/ /Convert command,
which converts the images in a folder to a specified format.
This plugin implements the File/Batch/Measure command,
which measures all the images in a user-specified folder.
This plugin implements the File/Batch/Macro and File/Batch/Virtual Stack commands.
Implements the Plugins/Utilities/Run Benchmark command.
Implements the Plugins/Utilities/Run Benchmark command when
the current image is 512x512 and RGB.
Implements the Erode, Dilate, Open, Close, Outline, Skeletonize
and Fill Holes commands in the Process/Binary submenu.
This class processes binary images.
This plugin implements the Image/Transform/Bin command.
A class for reading arbitrary numbers of bits from a byte array.
ImageJ bit blitting classes must implement this interface.
This plugin reads BMP files.
Implements the File/Save As/BMP command.
This plugin implements the File/Import/URL command and the commands in the Help menu that
open web pages.
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 class does bit blitting of byte images.
This is an 8-bit image and methods that operate on that image.
8-bit image statistics, including histogram.
Calibration objects contain an image's spatial and density calibration data.
This plugin implements the Analyze/Tools/Calibration Bar command.
Implements the Analyze/Calibrate command.
This plugin implements the Image/Adjust/Canvas Size command.
This plugin implements the Image/Colors/Arrange Channels command,
which allows the user to change the order of channels.
Displays the ImageJ "Channels" dialog.
This plugin implements the Image/Color/Split Channels command.
This class implements the Process/FFT/Make Circular Selection command.
Checks for duplicate class and JAR files in the plugins folders.
Copies/pastes images to/from the system clipboard.
This class does bit blitting of RGB images.
Displays a dialog that allows the user to select a color using three sliders.
Implements the Image/Color/Color Picker command.
This is an 32-bit RGB image and methods that operate on that image..
This plugin implements most of the Edit/Options/Colors command.
RGB image statistics, including histogram.
Selects pixels according to hsb or rgb components.
Plugins that implement this interface are notified when ImageJ
is about to run a menu command.
This class is used by the Plugins/Shortcuts/List Shortcuts
command to display a list keyboard shortcuts.
Runs miscellaneous File and Window menu commands.
This plugin implements the Plugins>Utiltiees>Recent Commands command.
Compiles and runs plugins using the javac compiler.
This plugin implements the Image/Color/Make Composite command.
This plugin, which concatenates two or more images or stacks,
implements the Image/Stacks/Tools/Concatenate command.
This plugin implements the Brightness/Contrast, Window/level and
Color Balance commands, all in the Image/Adjust sub-menu.
Implements ImageJ's Process/Enhance Contrast command.
Implements the conversion commands in the Image/Type submenu.
This plugin convolves images using user user defined kernels.
The plugin implements the Image/Adjust/Coordinates command.
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.
This plugin decodes DICOM files.
This class displays a dialog box that allows the user can select a directory.
This plugin implements the Analyze/Distribution command.
A table for easier downsizing by convolution with a kernel.
This class opens images, roi's, luts and text files dragged and dropped on the "ImageJ" window.
This class handles drag&drop onto JFileChoosers.
This plugin implements the Image/Duplicate command.
This is a simple TextArea based editor for editing and compiling plugins.
This plugin implements the Euclidean Distance Map (EDM), Watershed,
Ultimate Eroded Points and Voronoi commands in the Process/Binary submenu.
This class fits an ellipse to an ROI.
This class implements the ellipse selection tool.
This plugin implements the Plugins/Utilities/Monitor Events command.
Runs ImageJ menu commands in a separate thread.
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/Custom Filter command.
This class implements the Process/FFT/Bandpass Filter command.
The class implements the Process/FFT/Math command.
This class contains a Java implementation of the Fast Hartley
This class consists of public fields that describe an image file.
This plugin opens a multi-page TIFF file, or a set of raw images, as a
Opens or reverts an image specified by a FileInfo object.
Saves images in tiff, gif, jpeg, raw, zip and text format.
This plugin implements ImageJ's Fill, Clear, Clear Outside and Draw commands.
This plugin implements the Invert, Smooth, Sharpen, Find Edges,
and Add Noise commands.
Opens and displays FITS images.
This plugin saves a 16 or 32 bit image in FITS format.
ImageJ plugin that does curve fitting using the modified CurveFitter class.
This class implements an expandable float array similar
to an ArrayList or Vector but more efficient.
This class does bit blitting of 32-bit floating-point images.
Used by the Roi classes to return float coordinate arrays and to
determine if a point is inside or outside of spline fitted selections.
This is an 32-bit floating-point image and methods that operate on that image.
32-bit (float) image statistics, including histogram.
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.
Implements the File/Import/Image Sequence command, which
opens a folder of images as a stack.
This class contains static utility methods for replacing fonts that are not available on the
Calculate the so-called "capacity" fractal dimension.
Freehand region of interest or freehand line of interest
This class implements the text editor's Macros/Find Functions command.
This class implements the built-in macro functions.
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 class is a customizable modal dialog box.
This plugin opens GIFs and Animated GIFs.
Saves the active image in GIF format, or as an animated GIF if the image is a stack.
This class implements the Analyze/Tools/Grid command.
Implements the Image/Stacks/Tools/Grouped Z Project command.
This class consists of static GUI utility methods.
This plugin implements the Analyze/Histogram command.
This class is an extended ImageWindow that displays histograms.
Implements the Plugins/Hotkeys/Create Shortcut and Remove commands.
This is modal or non-modal dialog box that displays HTML formated text.
Implements the "Stack to HyperStack", "RGB to HyperStack"
and "HyperStack to Stack" commands.
This plugin implements the File/New/Hyperstack command.
Implements the Image/HyperStacks/Reduce Dimensionality 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
This plugin implements the Process/Image Calculator command.
This is a Canvas used to display images in a Window.
This class converts an ImagePlus object to a different type.
This plugin implements the Image/Show Info command.
This frame is the main ImageJ class.
This plugin implements the Help/Update ImageJ command.
Handles exceptions on the EDT.
Runs ImageJ as an applet and optionally opens up to
nine images using URLs passed as a parameters.
This is a custom layout manager that supports resizing of zoomed
Plugins that implement this interface are notified when
an image is opened, closed or updated.
This plugin implements ImageJ's Process/Math submenu.
This class is used by GenericDialog to add images to dialogs.
An ImagePlus contain an ImageProcessor (2D image) or an ImageStack (3D, 4D or 5D image).
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.
An ImageRoi is an Roi that overlays an image.
This class represents an expandable array of images.
Statistics, including the histogram, of an image or selection.
Implements the Image/Stacks/Images to Stack" command.
A frame for displaying images.
Writes a raw image described by a FileInfo object to an OutputStream.
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 is an extended ColorProcessor that supports signed 32-bit int images.
This class contains static methods that use the Java 2 API.
Displays the Java system properties in a text window.
Implements the text editor's Macros/Run command, and the
IJ.runMacroFile() method, when the file name ends with ".js".
The File/Save As/Jpeg command (FileSaver.saveAsJpeg() method)
uses this plugin to save images in JPEG format.
This class represents a straight line selection.
Dedicated point iterator for thin lines.
Implements ImageJ's Analyze/Tools/Analyze Line Graph command.
Adjusts the width of line selections.
This plugin opens images specified by list of file paths as a virtual stack.
This class provides the functionality to divert output sent to the System.out
and System.err streams to ImageJ's log console.
This class represents a color look-up table.
This is an indexed color model that allows an
lower and upper bound to be specified.
This plugin implements the Image/Lookup Tables/Apply LUT command.
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.
Displays the active image's look-up table.
The class contains static methods that perform macro operations.
This class runs macros and scripts installed in the Plugins menu as well as
macros and scripts opened using the Plugins/Macros/Run command.
This plugin implements the Plugins/Macros/Install Macros command.
This class runs macros in a separate thread.
This ImageJ plug-in filter finds the maxima (or minima) of an image.
Saves a table as a csv or tab-delimited text file.
Converts an RGB image to 8-bit index color using Heckbert's median-cut
color quantization algorithm.
This plugin implements the Edit/Options/Memory command.
This plugin continuously plots ImageJ's memory utilization.
This class installs and updates ImageJ's menus.
A modal dialog box that displays information.
Minimizer based on Nelder-Mead simplex method (also known as polytope method),
including the 'outside contraction' as described in:
Implements the Image/Stacks/Make Montage command.
Custom component for displaying multiple lines.
New image dialog box plus several static utility methods for creating images.
This class creates a new macro or the Java source for a new plugin.
This is an extension of GenericDialog that is non-modal.
This class displays a dialog window from
which the user can select an input file.
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.
This plugin implements most of the commands
in the Edit/Options sub-menu.
This plugin projects dynamically orthogonal XZ and YZ views of a stack.
Oval region of interest
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.
This plugin implements the Image/Overlay/Labels command.
Implements ImageJ's Analyze Particles command.
Implements ImageJ's Paste Control window.
This plugin opens PxM format images.
This plugin continuously displays the pixel values of the cursor and
This class creates an image that line graphs, scatter plots and plots of vector fields
(arrows) can be drawn on and displayed.
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 frozen
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 is a virtual stack of frozen plots.
This class implements the Analyze/Plot Profile command.
Plugins that acquire images or display windows should
implement this interface.
ImageJ uses this class loader to load plugins and resources from the
plugins directory and immediate subdirectories.
This is a non-modal dialog that plugins can extend.
ImageJ plugins that process an image should implement this interface.
This is a closeable window that plugins can extend.
Installs plugins dragged and dropped on the "ImageJ" window, or plugins,
macros or scripts opened using the Plugins/Install command.
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
This plugin implements the Edit/Options/Point Tool command.
This class fills polygons using the scan-line filling algorithm
described at "http://www.cs.rit.edu/~icss571/filling/".
This class represents a polygon region of interest or polyline of interest.
This class contains the ImageJ preferences, which are
loaded from the "IJ_Props.txt" and "IJ_Prefs.txt" files.
This plugin implements the File/Page Setup and File/Print commands.
Creates a density profile plot of a rectangular selection or line selection.
Implements the Analyze/Plot Profile and Edit/Options/Profile Plot Options commands.
An object of this type is a tokenized macro file and the associated symbol table.
This is the progress bar that is displayed in the lower right hand corner of
the ImageJ window.
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 plugin implements the Plugins/Utilities/Proxy Settings command.
This class uses a memory cache to allow seeking within
This plugin implements the Mean, Minimum, Maximum, Variance, Median,
Remove Outliers, Remove NaNs and Despeckle commands.
This plugin implements the File/Import/Raw command.
Opens, in a separate thread, files selected from the File/Open Recent submenu.
This is ImageJ's macro recorder.
This plugin implements the rounded rectangle tool dialog box.
This plugin implements the Edit/Crop and Image/Adjust/Size commands.
This is a table for storing measurement results and strings as columns of values.
This class implements the Apply Macro command in tables.
Converts a 2 or 3 slice stack, or a hyperstack, to RGB.
This plugin implements the Image/Color/Merge Channels command.
Deprecated; replaced by ij.plugin.ChannelSplitter.
A rectangular region of interest and superclass for the other ROI classes.
This class decodes an ImageJ .roi file.
This plugin implements the Edit/Options/Roi Defaults command.
Saves an ROI to a file or stream.
This plugin, which enlarges or shrinks selections, implements the Edit/Selection/Enlarge command.
This class interpolates between ROIs in the ROI Manager.
Plugins that implement this interface are notified when
an ROI is created, modified or deleted.
This plugin implements the Analyze/Tools/ROI Manager command.
Displays a dialog that allows the user to specify ROI properties such as color and line width.
Opens ImageJ, NIH Image and Scion Image for windows ROI outlines.
This plugin implements the Edit/Selection/Rotate command.
This plugin implements the Edit/Selection/Scale command.
Saves the current ROI outline to a file.
This class implements the rotated rectangle selection tool.
This plugin implements the Image/Rotate/Arbitrarily command.
Implements ImageJ's Process/Noise/Salt and Pepper command.
A modal dialog box with a one line message and
"Don't Save", "Cancel" and "Save" buttons.
This class displays a dialog window from
which the user can save a file.
This plugin implements the Analyze/Tools/Scale Bar command.
Implements the Analyze/Set Scale command.
This plugin implements the Image/Scale command.
This plugin implements the Plugins/Utilities/Capture Screen
and Plugins/Utilities/Capture Image commands.
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.
This plugin implements the commands in the Edit/Selection submenu.
Implements the commands in the Process/Shadows submenu.
A subclass of
ij.gui.Roi (2D Regions Of Interest) implemented in terms of java.awt.Shape.
This class does bit blitting of 16-bit images.
ShortProcessors contain a 16-bit unsigned image
and methods that operate on that image.
16-bit image statistics, including histogram.
This plugin implements the Plugins/Utilities/Unlock, Image/Rename
and Plugins/Utilities/Search commands.
Implements the Image/Stacks/Reslice command.
This plugin implements the Edit/Selection/Specify command.
This class fits a spline function to a set of points.
This plugin implements the Image/Stacks/Statistics command.
This plugin implements the Image/Stacks/Combine command.
This class does stack type conversions.
Implements the AddSlice, DeleteSlice and "Stack to Images" commands.
This plugin, which implements the Image/Stacks/Tools/Insert
command, inserts an image or stack into another image or stack.
This plugin implements the Image/Stacks/Label command.
The plugin implements the Image/Stacks/Tools/Montage to Stack command.
This class processes stacks.
This plugin implements the Image/Stacks/Tools/Reduce command.
This plugin implements the Image/Transform/Flip Z and
Statistics, including the histogram, of a stack.
This class is an extended ImageWindow that displays stacks and hyperstacks.
This plugin, which saves the images in a stack as separate files,
implements the File/Save As/Image Sequence command.
This plugin implements the Edit/Options/Startup command.
Runs the RunAtStartup (created by Edit/Options/Startup) and AutoRun (in StartupMacros) macros.
This plugin implements the Edit/Selection/Straighten command.
A simple QuickSort for String arrays.
This plugin is used by the Image/Stacks/Tools/Make Substack
command to create substacks of hyperstacks.
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 class "synchronizes" mouse input in multiple windows.
Plugins that implement this interface are notified when
a table is opened, closed or updated.
This plugin implements the Edit/Options/Fonts command and
the dialog displayed when you double click on the text tool.
Saves an image described by an ImageProcessor object as a tab-delimited text file.
This plugin displays the contents of a text file in a window.
This is an unlimited size text panel with tab-delimited,
labeled and resizable columns.
This plugin opens a tab or comma delimeted text file as an image.
This class is a rectangular ROI containing text.
Uses a TextPanel to displays text in a window.
This plugin implements the File/Save As/Text command, which saves the
contents of Editor windows and TextWindows (e.g., "Log" and "Results").
Displays thread information in a text window.
Adjusts the lower and upper threshold levels of the active image.
This plugin implements the Process/Binary/Make Binary
and Convert to Mask commands.
Decodes single and multi-image TIFF files.
Saves an image described by a FileInfo object as an uncompressed TIFF file.
This class converts an imageJ macro file file into a token stream.
The ImageJ toolbar.
This class contains static utility methods.
Implements the Flip and Rotate commands in the Image/Transform submenu.
This plugin implements the Image/Translate command.
This is an extended Button class used to reduce the width of the HUGE buttons on Mac OS X.
This class converts an ImageProcessor to another data type.
This class consists of static methods and
fields that implement ImageJ's Undo command.
This plugin-filter implements ImageJ's Unsharp Mask command.
Opens TIFFs, ZIP compressed TIFFs, DICOMs, GIFs and JPEGs using a URL.
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 is a non-modal dialog box used to ask the user to perform some task
while a macro or plugin is running.
This class implements ImageJ's wand (tracing) tool.
This plugin implements the Edit/Options/Wand Tool command.
This class allows for simple wildcard pattern matching.
This class consists of static methods used to manage ImageJ's windows.
This class implements the Window menu's "Show All", "Main Window", "Cascade" and "Tile" commands.
This plugin implements the File/Import/XY Coordinates command.
Writes the XY coordinates and pixel values of all non-background
pixels to a tab-delimited text file.
Saves the XY coordinates of the current ROI boundary.
A modal dialog box with a one line message and
"Yes", "No" and "Cancel" buttons.
Implements the Image/Stacks/Plot Z-axis Profile command,
which plots the selection mean gray value versus slice number.
This plugin implements the commands in the Image/Zoom submenu.
This plugin performs a z-projection of the input stack.