I would like to bundle the SoilJ plugin with Fiji.
It is a wrapper that is designed to semi-automatize 3-D image analyses of soil samples.
The plugin is presented in the following publication.
SoilJ comes as a mavenized ImageJ 1 plugin that relies on
ImageJ, Fiji, Java-8, 3D ImageJ Suite, IJPB-plugins.
It is stored under https://github.com/johnkoestel/soilj.
I am presently reading through the howto on imagej.net. But I would be glad about some more personalized guidance.
Cheers from the North,