Object feature extraction

• 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.

TrakEM2 is an ImageJ plugin for morphological data mining, three-dimensional modeling and image stitching, registration, editing and annotation (Fiji comes with TrakEM2). It supports arbitrary-sized datasets. 

The plugin analyses a point pattern (positions of objects of interest) distributed within a reference structure.

This analysis allows in particular to assess deviation from spatial randomness, and to reveal trends for clustering (attraction) or regularity (repulsion). No edge correction is performed, as it is assumed that no point is expected outside the reference structure.

This plugin comes together with 3D ImageJ suites plugin.