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This segmentation method performs a N-class thresholding based on a K-Means classification of the image histogram, then extracts objects in a bottom-up manner using user-defined minimum and maximum object sizes. Very useful to detect clustered objects in fluorescence microscopy.

Plugins for 3D Image processing and Analyisis in ImageJ. Previously (?) known as 3D ImageJ Suite.

Display your data in real time 3D (depending on your hardware).

This plugin creates a non-destructive grid of lines, crosses or points on the current image or stack. You can specify the grid type (lines, crosses or points), the area per point (in pixels or physical units), and the color.

A Jython scripting example (but is included as a menu item in Fiji) for screen capturing with certain time delay.

The tool implements a series of optimized contour and ridge detectors. The filters are steerable and are based on the optimization of a Canny-like criterion. They have a better orientation selectivity than the classical gradient or Hessian-based detectors.

Enhances the global contrast by equalizing the histogram. This plugin transforms pixel intensities so that they are uniformly distributed over the gray-scale range. It operates on the selected channel of each image of a sequence. This operation is also called "histogram flattening".

Import ROI from a zip file produced with ImageJ's ROI manager. Works as a standalone plugin and as a block for Protocols

This plugin provides low-level tools needed to execute some functions on Icy from a Matlab application. The Matlab X server plugin, which turns Icy into an image/video/sequence viewer for Matlab, is a typical example of what can be done with Matlab communicator.

(last activity Feb 2013)

This module can perform addition, subtraction, multiplication, division, or averaging of two or more image intensities, as well as inversion, log transform, or scaling by a constant for individual image intensities.

Plugin designed to allow easy semi-automatic tracing of neurons or other filament-like structures (e.g., microtubules, blood vessels) through either 2D images or 3D image stacks. Data can be imported and exported in SWC files for interaction with other software, or details of the traces can be exported as CSV files for analysis in spreadsheets or statistical software.

This plugin is included in Fiji by default.

This plugin explores the algorithms for reconstructing scientific images as a combination of other scientific images drawing from a large database of scientific imagery.