plugin

Displays a scale bar overlay on the sequence.
Warning: this plugin needs correct sequence metadata to be effective. Otherwise it will display wrong values.

Fiji Archipelago is a tool designed to make it easy for programmers to export Fiji/ImageJ functionality over a network to several other computers.

Color space conversions between image modes.

ExpandOrShrinkObjects expands or shrinks objects by a defined distance.

H2 database packaged as an Icy plugin

See http://www.h2database.com

DisplayDensityPlot plots measurements as a two-dimensional density plot.

Identifies dead worms based on a couple of parameters. 

This tutorial explain how to create an intensity profile over an ROI.

A canvas plugin using JFreeChart to show intensity profile of a specific row or column. Initially used in a 1-row image of 1D signal representation. Can also used with Micro-Manager for Icy Plugin to show 1D signal from hardware like data acquisition device as waveform. Common 2D+ sequence is also supported. Using it by select the plugin icon in the canvas type combobox of the sequence window, a JFreeChart line chart will show up. As an alternative plugin to Intensity Profile, this plugin is modified from "Intensity Profile" by fab, special thanks to him for giving me the idea to make such a plugin.

MonogenicJ performs multiresolution monogenic analyses of 2D images. It extracts wavelet-domain features that characterize the local orientation, the phase and the dominant frequency of an image patch at various levels of resolution.

Wavelet-based method to merge a stack of micrographs taken at different focal positions (aligned along the optical axis) into a single, entirely focused composite image.

This plugin allows the creation of custom animations for 3D viewing. It will generate a new sequence that can be edited in Icy, and saved.

The animation is based on key framing, as in most of 3D rendering software projects.

This plugin has two components:

• Elastic Montage
  • montaging mosaics from overlapping tiles where the tiles have non-linear relative deformation
• Elastic Stack Alignment
  • alignment of deformed section series from serially sectioned volumes

Layer for the 3D Viewer, allowing the user to move the camera in a more intuitive way.

Manual angle measurements. 

No javadoc accessible, but can be downloaded from the webpage. 

Mice Profiler tracks multiple mice from a top view video.

Outline The incessant development of improved microscopy imaging techniques, as well as the advent of highly selective fluorescent dyes has made possible the precise identification of tagged molecules in almost any biological specimen. Of particular interest are the visualization and the study of living cells, which induce tight constraints on the imaging process. To avoid the alteration of the sample and to achieve a high temporal resolution, low fluorophore concentrations, low-power illumination and short exposure time need to be used in practice. Such restrictions have a tremendous impact on the image quality. This is why we have recently introduced a new method, coined PURE-LET [1,2,3], for efficient, fast, and automatic denoising of multidimensional fluorescence microscopy images.

This plugin calculates the optic flow for each pair of images made with the given stack.

This plugin provides an extended depth of field algorithm to obtain in focus microscopic images of 3D objects and organisms using different algorithms: Sobel, variance, real and complex wavelets.

Manually selecting line ROIs and align two images. 

Automatically segment the boundary of a nucleus or cell starting from an approximate ROI. Supports 2D and 3D images and tracking of slowly moving cells. Ideal to study cell morphodynamics.

Six 2D differential operations are implemented in this ImageJ plugin. - Gradient Magnitude - Gradient Direction - Laplacian - Largest Hessian - Smallest Hessian - Hessian Orientation

Plugin to perform Delaunay Triangulation, or draw the Voronoi Diagram for a given point ROI.

This plugin comes with Fiji.

 Fast edge and ridge detection, irrespective of their orientation.

Exports connected components data in XLS. Exports All, by T or by ROI

A Mathematica package available for the symbolic computation of exponential spline related quantities: B-splines, Gram sequence, Green function, and localization filter.

Fill holes in objects 

Included into EBImage Image processing and analysis toolbox for R

Automatically crops an image by finding the smallest bounding box which still contains all pixels of the specified value.

Options include Pixel values, Margin, and more...

This KNIME node is included in the KNIME Image Processing Extension

Library used by Micro-Manager for fast acquisition.

Anisotropic filters are a class of filter that reduces noise in an image while trying to preserve sharp edges

There are two implementations of Tschumperle/ R. Deriche filter ("anisotropic diffusion") for ImageJ Plugin

1. in the "imaging book" codes: see the javadoc here.

2. in Xlib

Automatic finding of image features are very convenient for registering two images to align them in proper orientation. Two image plugins are implemented for extracting image features and are placed as menu items at: [Plugins > Feature Extraction > Extract SIFT Correspondences] and [Plugins > Feature Extraction > Extract MOPS Correspondences].

For more details, see the linked page in Fiji wiki. For details about SIFT algorithm, see 2569. For more details about MOPS algorithm, see 2570.

The Sholl technique is used to describe neuronal arbors. This plugin can perform Sholl directly on 2D and 3D grayscale images of isolated neurons. Its internal algorithm to collect data is based upon how Sholl analysis is done by hand — it creates a series of concentric shells (circles or spheres) around the focus of a neuronal arbor, and counts how many times connected voxels defining the arbor intersect the sampling shells. The major advantages of this plugin over other implementations are:

• When analyzing images directly, it does not require previous tracing of the arbor (although it can also analyze traced arbors)
• It combines curve fitting with several methods to automatically retrieve quantitative descriptors from sampled data, which allows direct statistical comparisons between arbors
• It allows continuous and repeated sampling around user-defined foci
• It allows batch processing

Some functions for PDE filtering.

"This ImageJ plugin (CGE) is a semi-automatic tool to detect and track moving cell, and to measure the fluorescent protein expression level. CGE extracts the trajectory of the cells by tracking their displacements, makes the delineation of cell nucleus or whole cell, and finally yields measurements of various features, like reporter protein expression level, cell displacement."

GUI tool, to view intensity profile dynamically as the position of ROI is changed by mouse-dragging a ROI. In more recent ImageJ, the native plot-profile window is equipped with "Live" mode, so this plugin function became a part of ImageJ.

This plugin is a good scripting example using Clojure (see source code).

This plugin stabilizes jittery image stacks using the Lucas-Kanade algorithm. It supports both grayscale and color images.

See also this tweet