plugin

This plugin generates theoretical PSFs, assuming they arise only from diffraction.

This plugin permit to measure the signal spread of a molecule with respect to the cell area.

This plugin comes with Fiji

This plugin can be used to estimate nonlinear distortions induced by the image acquisition process[1] . It does not require special calibration samples, but needs sufficient overlapping image areas with preferably high contrast. For further information on how to best arrange calibration images please see the documentation.

a dynamic version of the Reslice command.

Bundled with Fiji.

2D Image registration method based on elastic deformations represented by B-splines.

An ImageJ plugin for manually tracking objects by mouse clicking. 

This plugin is bundled with Fiji. 

This plugins allows debleaching of time sequences of fluorescence images.

Bundled with Fiji. "Do all" is the great feature...

This software implements an active contour (a.k.a. snake) segmentation method using exponential splines as basis functions to represent the outline of the shape. While the snake is versatile enough to provide a good approximation of any closed curve in the plane, its most important feature is that it perfectly reproduces circular and elliptical shapes. These features are very appropriate to delineate cross sections of cylindrical-like conduits and to outline blob-like objects.

This plugin shows the color distribution within a 3D-color-space. Extensive documentation is available atwww.f4.fhtw-berlin.de/~barthel/ImageJ/ColorInspector/help.htm.

Color Inspector 3D is also available as a stand-alone program that uses ImageJ as a library. To run it, download ColorInspector3D.jar and double click on it. On Windows, Java 5.0 or later must be installed

Choose the best auto thresholding technique for your data. 

Diagnose bugs in Icy

This tutorial explain how to create a simple Area ROI.

View a single channel of a 2D image as a 3D elevation map (X,Y,Intensity).

This plugin takes a sequence of image slices stored in a folder, and delivers a list of registered image slices (with enlarged canvas). One of the images in the sequence can be selected by the user as reference and it will remain intact.

The plugin can perform 6 types of image registration techniques:

• Translation
• Rigid (translation + rotation)
• Similarity (translation + rotation + isotropic scaling)
• Affine
• Elastic (via bUnwarpJ with cubic B-splines)
• Moving least squares

All models are aided by automatically extracted SIFT features.

Source code

Installation

This plugin is bundled with the Fijij package.

The purpose of the ImageJ Updater is to keep you up-to-date with all components of ImageJ (or Fiji), i.e. the macros, scripts, plugins and the core components (libraries) needed by the plugins.

As of 2011, the ImageJ Updater can handle 3rd-party update sites, i.e. anybody can set up their own update site which users can follow.

Allows the identification of objects by subtracting secondary objects from primary objects. For example allows to segment the cytoplasm by subtracting nuclei from cells. 

This plugin provides import and export Icy sequences into Matlab native .mat files from the protocol framework.

Fill holes in a binary image.

Edge detection by Deriche's method.

FilterObjects eliminates objects based on their measurements (e.g., area, shape, texture, intensity).

This module lets you outline the objects in an image using the mouse.

Tutorial explaining how to display a JFreeChart graph in Icy.

Extract image features based on one or more intensity thresholds, and output the result as a labeled image or as a region of interest.

An example of a very simple overlay.

PSF Generator is a software package that allows one to generate and visualize various 3D models of a microscope PSF. The current version has more than fifteen different models.

3D diffractive models: scalar-based diffraction model Born & Wolf, scalar-based diffraction model with 3 layers Gibson & Lanni, and vectorial-based model Richards & Wolf, and Variable Refractive Index Gibson & Lanni model.

Defocussing a 2D lateral function with 1D axial function: the available lateral functions are: "Gaussian", "Lorentz", "Cardinale-Sine", "Cosine", "Circular-Pupil", "Astigmatism", "Oriented-Gaussian", "Double-Helix".

Optical Transfer Function generated in the Fourier domain: Koehler simulation, defocus simulation.

This tool compute measures on the ROIs of the chosen sequence, updates the measures live when ROIs are changed and allows to copy/paste the measures to 3rd-party sheet edition softwares. Measures include geometric (bounding box) and intensity information.

It can complement the default ICY built inROI table, where measurements such as volume meausirements, intensity measurements, ... are built in and can be exported as excel as well.

This plugin can display a 2D flow as a color-coded sequence, following the Middlebury color code.