The files provide ImageJ scripts for the segmentation of roots and biopores in 3D X-ray CT images of soil. Files found under the Files branch.
Copy the files into your ImageJ plugin folder to use them. There will be new 'Biopores' and a 'Roots' comannds under 'Plugin'.
Find an example for a bath file in Root_batch.ijm
This workflows were developed for: Lucas et al. 2022: Cover crop influence on pore size distribution and biopore dynamics: Enumerating root and soil faunal effects (Please cite: doi: 10.3389/fpls.2022.928569)