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 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.

This plugin implements the Image/Stacks/Tools/Grouped Z Project command.

This plugin implements the Analyze/Histogram command.

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.

Displays the Java system properties in a text window.

The File/Save As/Jpeg command (FileSaver.saveAsJpeg() method) uses this plugin to save images in JPEG format.

Dedicated point iterator for thin lines.

Adjusts the width of line selections.

This class provides the functionality to divert output sent to the System.out and System.err streams to ImageJ's log console.

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.

Displays the active image's look-up table.

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 class runs macros in a separate thread.

This ImageJ plug-in filter finds the maxima (or minima) of an image.

Writes measurements to a csv or tab-delimited text file.

This plugin implements the Edit/Options/Memory command.

This class installs and updates ImageJ's menus.

Minimizer based on Nelder-Mead simplex method (also known as polytope method), including the 'outside contraction' as described in: J.C.

Custom component for displaying multiple lines.

This class creates a new macro or the Java source for a new plugin.

This is an extension of GenericDialog that is non-model.

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 projects dynamically orthogonal XZ and YZ views of a stack.

Oval region of interest

This plugin implements the Image/Overlay/Labels command.

Implements ImageJ's Paste Control window.

This plugin continuously displays the pixel values of the cursor and its surroundings.

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 is a virtual stack of frozen plots.

Plugins that acquire images or display windows should implement this interface.

This is a non-modal dialog that plugins can extend.

Installs plugins dragged and dropped on the "ImageJ" window, or plugins, macros or scripts opened using the Plugins/Install command.

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

This class represents a polygon region of interest or polyline of interest.

This plugin implements the File/Page Setup and File/Print commands.

Implements the Analyze/Plot Profile and Edit/Options/Profile Plot Options commands.

This is the progress bar that is displayed in the lower right hand corner of the ImageJ window.

This plugin implements the Plugins/Utilities/Proxy Settings command.

This plugin implements the Mean, Minimum, Maximum, Variance, Median, Open Maxima, Close Maxima, Remove Outliers, Remove NaNs and Despeckle commands.

Opens, in a separate thread, files selected from the File/Open Recent submenu.

This plugin implements the rounded rectangle tool dialog box.

This plugin implements the Results Table's Sort command.

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.