plugin

• 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.