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Amin Garbout: Soil Pore Network Visualisation and Quantification using ImageJ


Soil is one of the most complex materials on the earth, within which many biological, physical and chemical processes that support life and affect climate change take place. A much more detailed knowledge of the soil system is required to improve our ability to develop soil management strategies to preserve this limited resource. Many of those processes occur at micro scales. For long our ability to study soils non-destructively at microscopic scales has been limited, but recent developments in the use of X-ray Computed Tomography has offered great opportunities to quantify the 3-D geometry of soil pores.

In this study we look at how networks that summarize the geometry of pores in soil are affected by soil structure. One of the objectives is to develop a robust and reproducible image analysis technique to produce quantitative knowledge on soil architecture from high resolution 3D Computed Tomography data. We used ImageJ to analyze images of pore geometries in soils generated by X-ray micro Computed Tomography. Soil samples were scanned at 30 μm resolution, and we produced replicated samples with different pore geometries by packing different sized soil aggregates at pre-defined densities. First, scanned grayscale data of soil volumes were thresholded to separate solid and pore phases. Then, pore networks were extracted with the Skeletonize3D plug-in (Ignacio Arganda-Carreras), exploiting an ITK algorithm: binary thinning was used for finding the centerlines (”skeleton”) of pores in the input image. Several parameters (number of networks, junctions, branches…) were used to describe the networks in the sample, and we discuss how these can be used to describe soil structure.


Soil,networks,pore,X-ray micro Computed Tomography,Skeletonize3D

Administrative data

Presenting author: Amin Garbout
Organisation: Arhus University, Department of Agroecology and Environment, Research Centre Foulum Blichers Allé, Postbox 50, DK-8830 Tjele, Denmark. Tel: +45 50 366 472, Fax: +45 8999 1200

co-authors: Radoslaw Pajor and Wilfred Otten from The SIMBIOS Centre, University of Abertay Dundee, DD1 1HG, Dundee, Scotland

Type: Poster (portrait)

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