Difference between revisions of "Fiji/Menu"

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Revision as of 16:25, 19 May 2008

The hierarchy of the Plugins Menu is show here, with a few words of explanation for each plugin and links to more documentation where available. If you know about a plugin that is in this list, but which doesn't yet have a description, please add it. Also please update this page if you change the menu structure in any way.

FIXME: ideally we should generate this page automatically from the fiji source tree...


[Ungrouped Plugins]

  • 3D Viewer: This will launch the ImageJ 3D viewer so that you can visualize an image in 3D, either volume- or surface-rendered. Further documentation.
  • Get Class Versions:
  • Multiple Image Processor:
  • View5D:
  • Volume Viewer:


  • Grid:
  • Find differences:
  • Delaunay Voronoi:
  • Measure RGB:
  • Plot Dots:
  • VIB Protocol:
  • 2D Histogram: draw a 2D histogram showing the distribution of values in pairs of points in two images
  • Visual Grep:
  • Compute Curvatures: calculate the principal curvatures of an image at each point
  • Tubeness: calculate a score of how "tube-like" each point in an image is, based on the principal curvatures
  • Surfaceness: calculate a score of how "surface-like" each point in an image is, based on the principal curvatures


  • Average Color:
  • RGB to CIELAB:


  • Blobs Demo in Ruby: Implementation of the Blobs demo macro in the JRuby language. All relevant ImageJ macro functions are reimplemented in JRuby.
  • blend two images: Fetches the mandril (RGB) and bridge (8-bit) sample images, and blends the bridge image into each color channel of the mandril image. Written in Clojure (lisp).
  • celsius to fahrenheit: Shows a swing GUI with buttons and labels, with attached listeners to transform celsius degrees to fahrenheit. Written in Clojure (lisp).
  • Example Plot: Creates a plot with two colored lines in it. Written in Java.
  • list all threads: Lists all threads to stdout (the terminal, or Console.app in MacOSX). Written in Jython.
  • random noise example: Generates two 8-bit images with random pixel value in each. Written in Clojure (lisp).
  • T2 Select All: Selects all objects in an open TrakEM2 display. Writen in Jython.
  • T2 set all transforms to identity: Resets the transformation matrix (translation,rotation,scaling and shear) of all objects in a TrakEM2 display to identity (zero translation, scaling of 1.0, zero rotation and no shear). Written in Jython.

Image IO

This submenu should be removed and the image loaders and writers moved into Import> or Save as...>


  • New Image5D:
  • Open Image5D:
  • Save Image5D:
  • Open Series As Image5D:
  • Virtual Image5D Opener:
  • Hypervolume Opener:
  • Stack to Image5D:
  • RGB to Image5D:
  • Image5D to Stack:
  • Set Position:
  • Set Channel Display:
  • Set Channel Labels:
  • Make Montage:
  • Z Project:
  • Image5D Stack to RGB:
  • Transfer Channel Settings:


  • 4D Data Browser:
  • Bio-Formats Importer:
  • Bio-Formats Exporter:
  • Bio-Formats Remote Importer:
  • Download from OME:
  • Upload to OME:


This submenu should be removed, and the individual macros place in appropriate places in the menu hierarchy

  • About Plugin Macros:
  • Bulls Eye:
  • Macro Interpreter:
  • Polygon:
  • RGB Histogram:
  • batch convert any to tif:


  • Bilateral Filter:
  • IFT:
  • Implicit Interpolate Binary:
  • Replace value:
  • Distance Transform 3D:
  • Fill holes:
  • Moving Least Squares:
  • Reslice Z:
  • Shape-based averaging:
  • Seam remover:
  • Show label centers:
  • Triangle Algorithm:
  • Mask of Nearby Points: create a mask of all points within a given distance of any point above a given threshold Further documentation
  • Find Connected Regions: find connected regions in an image stack based on various criteria Further documentation
  • Quantile Based Normalization: a method of histogram equalization across several images Futher documentation
  • Resample: resample to reduce the size of an image
  • Convolve (3D):
  • Dilate (3D):
  • Erode (3D):
  • FFT (3D):
  • Flood Fill (3D):
  • Gradient (3D):
  • IFT (3D):
  • Laplace (3D):
  • Maximum (3D):
  • Max (3D): FIXME: don't need both this an the one above
  • Median (3D):
  • Minimum (3D):
  • Particle Analyzer (3D):
  • Plot Dots (3D):
  • Rebin (3D):
  • Smooth (3D):


  • Align Image by line ROI: Set a line ROI in two images and run this plugin to register the second to the first, with scale/rotate/translate according to the orientation and length of the lines. See Align image by line ROI.
  • Rigid Registration:
  • Moving Least Squares: Given two sets of points in two images, register one image to the other according to the point correspondences. You can define the points manually with Point Roi (just click and hold shift to add more than one point), and also from a script. See Moving Least Squares.
  • bUnwarpJ: see bUnwarpJ
  • Register Virtual Stack Slices: Given a folder of ordered images, where each image is a slice in a series, register each slice to the previous using SIFT (only translation or translation+rotation) or phase-correlation (no rotation). For more information see Register Virtual Stack Slices.
  • Stiching (3D): Given two stacks, stitch them together (translation only, but in X, Y and Z axes). Very useful for joining two confocal stacks. Accepts retangular ROIs in each stack to limit the area to search into. For more information see Stitching 3D.


  • BeanShell Interpreter: This plugin launches an interactive BeanShell interpeter. For more information on BeanShell support, see BeanShell Scripting
  • Clojure Interpreter: This plugin launches an interactive Clojure interpeter. For more information on Clojure support, see Clojure Scripting
  • JRuby Interpreter: This plugin launches an interactive JRuby interpeter. For more information on JRuby support, see JRuby Scripting
  • Jython Interpreter: This plugin launches an interactive Jython interpeter. For more information on Jython support, see some examples.
  • Javascript Interpreter: This plugin launches an interactive Javascript interpeter. For more information on Javascript support, see Javascript Scripting
  • Macro Interpreter: This plugin launches an interactive ImageJ Macro interpeter. For more information see Macro Interpreter and examples.

See also Scripting Help and the Scripting_comparisons.


  • Segmentation Editor: This plugin provides a user interface for manually segmenting images by painting over regions in an image stack. Futher documentation.
  • Simple Neurite Tracer: A plugin for semi-automated tracing of neurons in a 3D image stack Further documentation


If we keep this option, I think it should be restricted to plugins that operate a stack but which don't care about the content, e.g. those for cropping or reslicing. (At least there needs to be some distinction since practically every plugin operates on stacks.)

  • Crop (3D): Crop an image stack Further documentation
  • Stack Reverser: This plugin reverses the order of the slices in an image stack.


  • Close All Without Saving:


TransformJ is non-free, and in any case not have its own submenu - probably should rename this to Transform

  • TJ Affine:
  • TJ Crop:
  • TJ Embed:
  • TJ Mirror:
  • TJ Options:
  • TJ Panel:
  • TJ Rotate:
  • TJ Scale:
  • TJ Shift:
  • TJ Turn:


  • KD Cartoon:
  • Lasso:


  • Collect Garbage:
  • Install Java3D:
  • Adjust Menu Font:
  • Thread killer:


  • Test Marching Cubes:
  • Test Java3D: