Visualizing three-dimensional root networks using computed tomography

• Published in: Geoderma Vol. 136; no. 1; pp. 459 - 469
• Main Authors: Kaestner, Anders, Schneebeli, Martin, Graf, Frank
• Format: Journal Article
• Language: English
• Published: Amsterdam Elsevier B.V 01.12.2006; Elsevier
• Subjects: Agronomy. Soil science and plant productions; Biological and medical sciences; Computed tomography; Earth sciences; Earth, ocean, space; Exact sciences and technology; Fundamental and applied biological sciences. Psychology; Image analysis; Roots; Soil; Soils; Surficial geology; Soil; 3D; Image analysis; Computed tomography; Roots; experimental studies; algorithms; diffusion; Photographic image; data; X-rays; networks; Soil air; image analysis; noise; Three dimensional system; Extraction; quartz sand; soils; moraines; interfaces; morphology; Plexiglas; Method; roots; Filter; Nonlinearity; Computerized axial tomography; Performance; X ray absorption
• ISSN: 0016-7061; 1872-6259
• DOI: 10.1016/j.geoderma.2006.04.009

We describe a method to reconstruct the root network from a three-dimensional image generated with computed tomography. The X-ray absorption of roots and the interface of the air–soil material is very similar and the contrast extremely low. The method consists of three steps: contrast enhancement using a non-linear diffusion filter, thresholding based on Rosin's method and extraction of the main features using a morphological connectivity algorithm. With this approach, we are also capable of reconstructing fine roots with high fidelity, which is shown with a performance experiment using artificial images with increasing noise. The method is applied to an X-ray microtomography data set of two alder roots, grown for 4 months in a natural moraine soil. To simplify the soil material, the bare roots were transferred into a Plexiglas receptacle filled with quartz sand. The reconstructed image is compared with a photograph of the real roots.