plugin

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 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.

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)

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

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".

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.

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

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.

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

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.

This plugin allows to open images embedded in PDFs.

This plugin parses arbitrary mathematical expressions and compute results using images as variables.

This plugin combines the idea of using fiduciary markers, local descriptors and geometric hashing and applies global optimization. It can register an arbitrary number of partially overlapping point clouds. It is robust with respect to the amount of incorporated beads, bead distribution, amount of overlap, and can reliably detect non-affine disturbances (e.g. abrupt agarose movement) that might occur during imaging.

For details about the SPIM registration, fusion & deconvolution please have a look at the Multiview Reconstruction Plugin. It is much more powerful, flexible and completely integrated with the BigDataViewer.

• Counts the number of 3D objects in a stack.
• quantifies for each found object the following parameters:
  • 3D intensity related measurement (with possible redirection to an image with the actual intensity value to be measured, for example for two channels measurements)
  • Volume and shape factors measurements, surface etc...
• generates results representations such as:
  • Objects' map;
  • Surface voxels' map;
  • Centroids' map;
  • Centres of masses' map.

As ImageJ's “Analyze Particles” function, 3D-OC also has a “redirect to” option, allowing one image to be taken as a mask to quantify intensity related parameters on a second image. But unlike the Analyze particle, it include a thresholding option, meaning that you can start from a gray level  stack, not necessarily a binary mask.

To use it, first set the list of measurements by editing 3D OC Options. Both (3D Object counter and 3D OC Options are now in the default Fiji "Analyze" menu.

Short Description

Execute complex math operations on sequences, such as '3*sequence1 + log(sequence2)/sequence3', in a single step. All the operations are executed pointwise.

Documentation

This plugin is similar to the Math operations plugin: it provides usual pointwise math operations on sequences, such as addition, product, absolute value extraction, rounding to the closest integer, etc. However, it also allows the user to perform complex combinations of theses operations, using a mathematical expression interpretor.

A set of classes and functions which can be used by plugins performing spot detection and spot tracking.

Add some noise with customizable characteristics (Gaussian noise, Poisson noise, salt & pepper, etc.) to a sequence. ICY plugin.

Plots an intensity profile of a given ROI.

Can plot mean over T or/and Z too.

A fun simulator. It's not very useful for biology but it's a good demo!

This module has been deprecated; in Cell Profiler 3.0, it is a function in module "Measurement"

CellProfiler FlagImage module allows to assign a flag if an image meets certain measurement criteria that you specify (for example, if the image fails a quality control measurement). The value of the flag is 1 if the image meets the selected criteria (for example, if it fails QC), and 0 if it does not meet the criteria (if it passes QC).

Displays 3D data as 2D montages of all slices.

The SSIM is an index measuring the structural similarity between two images. It is valued between -1 and 1. When two images are nearly identical, their SSIM is close to 1.

Displays a live tool tip on the current focused ROI in an image.

The tooltip displays the following informations about the ROI:
– position and size.
– number of interior points and contour points.
– perimeter, area, surface area, volume.
– min, max, mean intensity.

This plugin is a daemon plugin, that means plugin is automatically loaded when Icy starts.

Dedicated to score tracking dataset from the ISBI tracking challenge

An ImageJ plugin for evaluate intra-nuclear 3D cross-distances between fluorescent spots in multi-channel images 

An ImageJ plugin for iterative deblurring.