Free and open source

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.