Anderson, S. H. (2014). Tomography-measured macropore parameters to estimate hydraulic properties of porous media. Procedia Comput. Sci. 36, 649-654. doi: 10.1016/j.procs.2014.09.069
Ball, B. C., and Schjønning, P. (2002). "Air permeability, "in Methods of Soil Analysis, Part 1, ed. J. H. Dane and G. C Topp (Madison, WI: Soil Science Society of America), 1141-1158
Baveye, P. C., and Laba, M. (2015). Moving away from the geostatistical lamppost: why, where, and how does the spatial heterogeneity of soils matter? Ecol. Model. 298, 24-38. doi: 10.1016/j.ecolmodel.2014.03.018
Baveye, P. C., Pot, V., and Garnier, P. (2017). Accounting for sub-resolution pores in models of water and solute transport in soils based on computed tomography images: are we there yet? J. Hydrol. 555, 253-256. doi: 10.1016/j.jhydrol.2017.10.021
Beckers, E., Plougonven, E., Gigot, N., Léonard, A., Roisin, C., Brostaux, Y., et al. (2014a). Coupling X-ray microtomography and macroscopic soil measurements: a method to enhance near saturation functions? Hydrol. Earth Syst. Sci. 18, 1805-1817. doi: 10.5194/hess-18-1805-2014
Beckers, E., Plougonven, E., Roisin, C., Hapca, S., Léonard, A., and Degr, é, A. (2014b). X-ray microtomography: a porosity-based thresholding method to improve soil pore network characteristization? Geoderma 219-220, 145-154. doi: 10.1016/j.geoderma.2014.01.004
Blagodatsky, S., and Smith, P. (2012). Soil physics meets soil biology: towards better mechanistic prediction of greenhouse gas emissions from soil. Soil Biol. Biochem. 47, 78-92. doi: 10.1016/j.soilbio.2011.12.015
Corey, A. T. (1986). "Air permeability, "in Methods of Soil Analysis. Part I. 2nd Edn, ed A. Klute (Madison, WI: Agronomy Monograph 9, American Society of Agronomy, Inc.; Soil Science Society of America, Inc.,), 1121-1136
Cousin, I., Levitz, P., and Bruand, A. (1996). Three-dimensional analysis of a loamy-clay soil using pore and solid chord distributions. Eur. J. Soil Sci. 47, 439-452. doi: 10.1111/j.1365-2389.1996.tb01844.x
Crestana, S., Mascarenhas, S., and Pozzi-Mucelli, R. S. (1985). Static and dynamic three-dimensional studies of water in soil using computed tomographic scanning. Soil Sci. 140, 326-332. doi: 10.1097/00010694-198511000-00002
Dal Ferro, N., Charrier, P., and Morari, F. (2013). Dual-scale micro-CT assessment of soil structure in a long-term fertilization experiment. Geoderma 204-205, 84-93. doi: 10.1016/j.geoderma.2013.04.012
Dal Ferro, N., Sartori, L., Simonetti, G., Berti, A., and Morari, F. (2014). Soil macro-and microstructure as affected by different tillage systems and their effects on maize root growth. Soil Til. Res. 140, 55-65. doi: 10.1016/j.still.2014.02.003
Dal Ferro, N., Strozzi, A. G., Duwig, C., Delmas, P., Charrier, P., and Morari, F. (2015). Application of smoothed particle hydrodynamics (SPH) and pore morphologic model to predict saturated water conductivity from X-ray CT imaging in a silty loam Cambisol. Geoderma 255-256, 27-34. doi: 10.1016/j.geoderma.2015.04.019
DIN ISO 11274 (2012). Soil Quality-Determination of the Water Retention Characteristics-Laboratory Methods (ISO 11274:1998 + Cor. 1:2009) English Translation of DIN ISO 11274, 2012-04. Deutsches Institut für Normung, Berlin
Doube, M., Klosowski, M. M., Arganda-Carreras, I., et al. (2010). Bone-J: free and extensible bone image analysis in ImageJ. Bone 47, 1076-1079. doi: 10.1016/j.bone.2010.08.023
Durner, W. (1994). Hydraulic conductivity estimation for soils with heterogeneous pore structure. Water Resour. Res. 30, 211-223. doi: 10.1029/93WR02676
Elliot, T. R., Reynolds, W. D., and Heck, R. J. (2010). Use of existing pore models and X-ray computed tomography to predict saturated soil hydraulic conductivity. Geoderma 156, 133-142. doi: 10.1016/j.geoderma.2010.02.010
Falconer, E. R., Houston, A. N., Otten, W., and Baveye, P. C. (2012). Emergent behavior of soil fungal dynamics: influence of soil architecture and water distribution. Soil Sci. 177, 111-119. doi: 10.1097/SS.0b013e318241133a
Garbout, A., Munkholm, L. J., and Hansen, S. B. (2013). Tillage effects on topsoil structural quality assessed using X-ray CT, soil cores and visual soil evaluation. Soil Til. Res. 128, 104-109. doi: 10.1016/j.still.2012.11.003
Grevers, M. C. J., De Jong, E., and St Arnaud, R. J. (1989). The characterization of soil macroporosity with CT scanning. Can. J. Soil Sci. 69, 629-637. doi: 10.4141/cjss89-062
Gutiérrez Castorena, E. V., Gutiérrez Castorena, M. D. C., Vargas, T. G., Bontemps, L. C., Martinez, J. D., Mendez, E. S., et al. (2016). Micromapping of microbial hotspots and biofilms from different crops using image mosaics of soil thin sections. Geoderma 279, 11-21. doi: 10.1016/j.geoderma.2016.05.017
Harrigan, T. P., and Mann, R. W. (1984). Characterization of microstructural anisotropy in orthotropic materials using a 2nd rank tensor. J. Mater. Sci. 19, 761-767. doi: 10.1007/BF00540446
Houston, A. N., Otten, W., Falconer, R., Monga, O., Baveye, P. C., and Hapca, S. M. (2017). Quantification of the pore size distribution of soils: assessment of existing software using tomographic and synthetic 3D images. Geoderma 299, 73-82. doi: 10.1016/j.geoderma.2017.03.025
Houston, A. N., Schmidt, S., Tarquis, A. M., Otten, W., Baveye, P. C., and Hapca, S. (2013). Effect of scanning and image reconstruction settings in X-ray computed microtomography on quality and segmentation of 3D soil images. Geoderma 207-208, 154-165. doi: 10.1016/j.geoderma.2013.05.017
Hunt, A. G., Ewing, R. P., and Horton, R. (2013). What's wrong with soil physics? Soil Sci. Soc. Am. J. 77, 1877-1887. doi: 10.2136/sssaj2013.01.0020
Jarvis, N., Larsbo, M., and Koestel, J. (2017). Connectivity and percolation of structural pore networks in a cultivated silt loam soil quantified by X-ray tomography. Geoderma 287, 71-79. doi: 10.1016/j.geoderma.2016.06.026
Jeffreys, H. (1961). Theory of Probability. Oxford, UK: Oxford University Press
Katuwal, S., Moldrup, P., Lamandé, M., Tuller, M., and de Jonge, L. W. (2015a). Effect of CT number derived matrix density on preferential flow and transport in a macroporous agricultural soil. Vadose Zone J. 14, 1-13. doi: 10.2136/v15.01.0002
Katuwal, S., Norgaard, T., Moldrup, P., Lamandé, M., Wildenschild, D., and de Jonge, L. W. (2015b). Linking air and water transport in intact soils to macropore characteristics inferred from X-ray computed tomography. Geoderma 237-238, 9-20. doi: 10.1016/j.geoderma.2014.08.006
Kim, H., Anderson, S. H., Motavalli, P. P., and Gantzer, C. J. (2010). Compaction effects on soil macropore geometry and related parameters for an arable field. Geoderma 160, 244-251. doi: 10.1016/j.geoderma.2010.09.030
Koestel, J., and Larsbo, M. (2014). Imaging and quantification of preferential solute transport in soil macropores. Water Resour. Res. 50, 4357-4378. doi: 10.1002/2014WR015351
Köhne, J. M., Schlüter, S., and Vogel, H.-J. (2011). Predicting solute transport in structured soil using pore network models. Vadose Zone J. 10, 1082-1096. doi: 10.2136/vzj2010.0158
Kravchenko, A. N., and Guber, A. K. (2017). Soil pores and their contributions to soil carbon processes. Geoderma 287, 31-39. doi: 10.1016/j.geoderma.2016.06.027
Kravchenko, A. N., Wang, A. N. W., Smucker, A. J. M., and Rivers, M. L. (2011). Long-term differences in tillage and land use affect intra-aggregate pore heterogeneity. Soil Sci. Soc. Am. J. 75, 1658-1666. doi: 10.2136/sssaj2011.0096
Lamandé, M., Wildenschild, D., Berisso, F. E., Garbout, A., Marsh, M., Moldrup, P., et al. (2013). X-ray CT and laboratory measurements on glacial till subsoil cores: assessment of inherent and compaction-affected soil structure characteristics. Soil Sci. 178, 359-368. doi: 10.1097/SS.0b013e3182a79e1a
Larsbo, M., Koestel, J., and Jarvis, N. (2014). Relations between macropore network characteristics and the degree of preferential solute transport. Hydrol. Earth Syst. Sci. 18, 5255-5269. doi: 10.5194/hess-18-5255-2014
Legland, D., Arganda-Carreras, I., and Andrey, P. (2016). MorphoLibJ: integrated library and plugins for mathematical morpholofy with ImageJ. Bioinformatics 32, 3532-3534. doi: 10.1093/bioinformatics/btw413
Liang, F., Paulo, R., Molina, G., Clyde, M. A., and Berger, J. O. (2008). Mixtures of g-priors for Bayesian variable selection. J. Am. Stat. Assoc. 103, 410-423. doi: 10.1198/016214507000001337
Loll, P., Moldrup, P., Schjønning, P., and Riley, H. (1999). Predicting saturated hydraulic conductivity from air permeability: application in stochastic water infiltration modeling. Water Resour. Res. 35, 2387-2400. doi: 10.1029/1999WR900137
Luo, L., Lin, H., and Halleck, P. (2008). Quantifying soil structure and preferential flow in intact soil using X-ray computed tomography. Soil Sci. Soc. Am. J. 72, 1058-1069. doi: 10.2136/sssaj2007.0179
Luo, L., Lin, H., and Schmidt, J. (2010). Quantitative relationships between soil macropore characteristics and preferential flow and transport. Soil Sci. Soc. Am. J. 74, 1929-1937. doi: 10.2136/sssaj2010.0062
Marin, J.-M., and Robert, C. P. (2007). Bayesian Core. A Pratical Approach to Computational Bayesian Statistics. New York, NY: Springer
McKenzie, N., Coughlan, K., and Cresswell, H. (2002). Soil Physical Measurement and Interpretation for Land Evaluation. Collingwood: CSIRO Publishing
Moldrup, P., Yoshikawa, S., Olesen, T., Komatsu, T., and Rolston, D. E. (2003). Air permeability in undisturbed volcanic ash soils: predictive model test and soil structure finderprint. Soil Sci. Soc. Am. J. 67, 32-40. doi: 10.2136/sssaj2003.3200
Monga, O., Garnier, P., Pot, V., Coucheney, E., Nunan, N., Otten, W., et al. (2014). Simulating microbial degradation of organic matter in a simple porous system using the 3-D diffusion-based model MOSAIC. Biogeosciences 11, 2201-2209. doi: 10.5194/bg-11-2201-2014
Morey, R. D., and Rouder, J. N. (2015). BayesFactor: Computation of Bayes Factors for Common Designs. R package version 0.9.12-2. Available online at: https://CRAN.R-project.org/package=BayesFactor
Mossadeghi-Björklund, M., Arvidsson, J., Keller, T., Koestel, J., Lamandé, M., Larsbo, M., et al. (2016). Effects of subsoil compaction on hydraulic properties and preferential flow in a Swedish clay soil. Soil Til. Res. 156, 91-98. doi: 10.1016/j.still.2015.09.013
Naveed, M., Moldrup, P., Arthur, E., Wildenschild, D., Eden, M., Lamandé, M., et al. (2012). Revealing soil structure and functional macroporosity along a clay gradient using X-ray computed tomography. Soil Sci. Soc. Am. J. 77, 403-411. doi: 10.2136/sssaj2012.0134
Naveed, M., Moldrup, P., Schaap, M. G., Tuller, M., Kulkarni, R., Vogel, H.-J., et al. (2016). Prediction of biopore-and matrix-dominated flow from X-ray CT-derived macropore networkds characteristics. Hydrol. Earth. Syst. Sci. 20, 4017-4030. doi: 10.5194/hess-20-4017-2016
Nuijten, M. B., Wetzels, R., Matzke, D., Dolan, C. V., and Wagenmakers, E.-J. (2015). BayesMed: Default Bayesian Hypothesis Tests for Correlation, Partial Correlation, and Mediation. R package version 1.0.1. Available online at: http://CRAN.R-project.org/package=BayesMed
Olson, M. S., Tillman, F. D. Jr., Choi, J.-W., and Smith, J. A. (2001). Comparison of three techniques to measure unsaturated-zone air permeability at Picatinny Arsenal, N. J. J. Contam. Hydrol. 53, 1-19. doi: 10.1016/S0169-7722(01)00135-8
Or, D., Smets, B. F., Wraith, J. M., Deschene, A., and Friedman, S. P. (2007). Physical constraint affecting bacterial habittats and activity in unsaturated porous media-a review. Adv. Wat. Res. 30, 1505-1527. doi: 10.1016/j.advwatres.2006.05.025
Otsu, N. (1979). A threshold selection method from gray-level histograms. IEEE Trans. Syst. Man Cybern. 9, 62-66. doi: 10.1109/TSMC.1979.4310076
Pachepsky, Y. A., Giménez, D., Crawford, J. W., and Rawls, W. J. (2000). "Conventional and fractal geometry in soil science, "in Developments in Soil Science, eds Y. A. Pachepsky, J. W. Crawford and W. J. Rawls (Elsevier), 7-18
Paradelo, M., Katuwal, S., Moldrup, P., Norgaard, T., Herath, L., and de Jonge, L. W. (2016). X-ray CT-derived characteristics explain varying air, water, and solute transport properties across a loamy field. Vadose Zone J. 192, 194-202. doi: 10.2136/vzj2015.07.0104
Parvin, N., Beckers, E., Plougonven, E., Léonard, A., and Degré, A. (2017). Dynamic of soil drying close to saturation: what can we learn from a comparison between X-ray computed microtomography and the evaporation method? Geoderma 302, 66-75. doi: 10.1016/j.geoderma.2017.04.027
Peng, S., Marone, F., and Dultz, S. (2014). Resolution effect in X-ray microcomputed tomography imaging and small pore's contribution to permeability for a Berea sandstone. J. Hydrol. 510, 403-411. doi: 10.1016/j.jhydrol.2013.12.028
Perret, J. S., Prasher, S. O., and Kacimov, A. R. (2003). Mass fractal dimension of soil macropores using computed tomography: from the box-counting to the cube-counting algorithm. Eur. J. Soil Sci. 54, 569-579. doi: 10.1046/j.1365-2389.2003.00546.x
Perret, J. S., Prasher, S. O., Kantzas, A., and Langford, C. (1999). Three-dimensional quantification of macropore networks in undisturbed soil cores. Soil Sci. Soc. Am. J. 63, 1530-1543. doi: 10.2136/sssaj1999.6361530x
Plougonven, E. (2009). Link between the Microstructure of Porous Materials and their Permeability. Ph. D. thesis, Université Sciences et Technologies, Bordeaux
Pöhlitz, J., Rücknagel, J., Koblenz, B., Schlüter, S., Vogel, H.-J., and Christen, O. (2018). Computed tomography and soil physical measurements of compaction behavior under strip tillage, mulch tillage and no tillage. Soil Til. Res. 175, 205-2016. doi: 10.1016/j.still.2017.09.007
Pot, V., Peth, S., Monga, O., Vogel, L. E., Genty, A., Garnier, P., et al. (2015). Three-dimensional distribution of water and air in soil pores: comparison of two-phase two-relaxation-times lattice-Boltzmann and morphological model outputs with synchrotron X-ray computed tomography data. Adv. Water Res. 87, 87-102. doi: 10.1016/j.advwatres.2015.08.006
Raats, P. A. C., Zhang, Z. F., Ward, A. L., and Gee, G. W. (2004). The relative connectivity-tortuosity tensor for conduction of water in anisotropic unsaturated soils. Vadose Zone J. 3, 1471-1478. doi: 10.2136/vzj2004.1471
Rab, M. A., Haling, R. E., Aarons, S. R., Hannah, M., Young, I. M., and Gibson, D. (2014). Evaluation of X-ray computed tomography for quantifying macroporosity of loamy pasture soils. Geoderma 213, 460-470 doi: 10.1016/j.geoderma.2013.08.037
Rabot, E., Wiesmeier, M., Schlüter, S., and Vogel, H.-J. (2018). Soil structure as an indicator of soil functions: a review. Geoderma 314, 122-137. doi: 10.1016/j.geoderma.2017.11.009
Rachman, A., Anderson, S. H., and Gantzer, C. J. (2005). Computed-Tomographic measurement of soil macroporosity parameters as affected by stiff-stemmed grass hedges. Soil Sci. Soc. Am. J. 69, 1609-1616. doi: 10.2136/sssaj2004.0312
R Core Team (2015). R: A Language and Environment for Statistical Computing. Vienna: R Foundation for Statistical Computing
Renard, P., and Allard, D. (2013). Connectivity metrics for subsurface flow and transport. Adv. Wat. Res. 51, 168-196. doi: 10.1016/j.advwatres.2011.12.001
Richards, L. A. (1948). Porous plate apparatus for measuring moisture retention and transmission by soils. Soil Sci. 66, 105-110. doi: 10.1097/00010694-194808000-00003
Roose, T., Keyes, S. D., Daly, K. R., Carminati, A., Otten, W., Vetterlein, D., et al. (2016). Challenges in imaging and predictive modeling of rhizosphere processes. Plant Soil. 407, 9-38. doi: 10.1007/s11104-016-2872-7
Rowell, D. L. (1994). Soil Science: Methods and Application. Harlow, UK: Longman Group Limited, Longman Scientific & Technical
Sammartino, S., Lissy, A.-S., Bogner, C., Van Den Bogeart, R., Capowiez, Y., et al. (2015). Identifying the functional macropore network related to preferential flow in structured soils. Vadose Zone J. 14, 1-16. doi: 10.2136/vzj2015.05.0070
Sandin, M., Koestel, J., Jarvis, N., and Larsbo, M. (2017). Post-tillage evolution of structural pore space and saturated and near-saturated hydraulic conductivity in a clay loam soil. Soil Til. Res. 165, 161-168. doi: 10.1016/j.still.2016.08.004
Schaap, M. G., Porter, M. L., Christensen, B. S. B., and Wildenschild, D. (2007). Comparison of pressure-saturation characteristics derived from computed tomography and lattice Boltzmann simulations. Water Resour. Res. 43:W12S06. doi: 10.1029/2006WR005730
Schmid, B., Schindelin, J., Cardona, A., Longhair, M., and Heisenberg, M. (2010). A high-level 3D visualization API for Java and ImageJ. BMC Bioinformatics 11:274. doi: 10.1186/1471-2105-11-274
Schneider, C. A., Rasband, W. S., and Eliceiri, K. W. (2012). NIH Image to ImageJ: 25 years of image analysis. Nat. Methods 9, 671-675. doi: 10.1038/nmeth.2089
Shah, S. M., Gray, F., Crawshaw, J. P., and Boek, E. S. (2016). Micro-computed tomography pore-scale study of flow in porous media: effect of voxel resolution. Adv. Wat. Res. 95, 276-287. doi: 10.1016/j.advwatres.2015.07.012
Smet, S., Plougonven, E., Léonard, A., Degré, A., and Beckers, E. (2017). X-ray Micro-CT: how soil pore space description can be altered by image processing. Vadose Zone J. 17:160049. doi: 10.2136/vzj2016.06.0049
Smith, K. A., Ball, T., Conen, F., Dobbie, K. E., Massheder, J., and Rey, A. (2003). Exchange of greenhouse gases between soil and atmosphere: interactions of soil physical factors and biological processes. Eur. J. Soil Sci. 54, 779-791. doi: 10.1046/j.1351-0754.2003.0567.x
Taina, I. A., Heck, R. J., and Elliot, T. R. (2008). Application of X-ray computed tomography to soil science: a literature review. Can. J. Soil Sci. 88, 1-20. doi: 10.4141/CJSS06027
Tarplee, M., and Corps, N. (2008). Skyscan 1072 desktop X-ray microtomograph. sample scanning reconstruction, analysis and visualisation (2D and 3D) Protocols. Guidelines, notes, selected references and F.A. Qs
Tracy, S. R., Daly, K. R., Sturrock, C. J., Crout, N. M. J., Mooney, S. J., and Roose, T. (2015). Three-dimensional quantification of soil hydraulic properties using X-ray computed tomography and image-based modeling. Water Resour. Res. 51, 1006-1022. doi: 10.1002/2014WR016020
Udawatta, R. P., and Anderson, S. H. (2008). CT-measured pore characteristics of surface and subsurface soils influenced by agroforestry and grass buffers. Geoderma 145, 381-389. doi: 10.1016/j.geoderma.2008.04.004
Ursino, N., Roth, K., Gimmi, T., and Flühler, H. (2000). Upscaling of anisotropy in unsaturated Miller-similar porous media. Water Resour. Res. 36, 421-430. doi: 10.1029/1999WR900320
van Genuchten, M. T. (1980). A closed-form equation for prediction the hydraulic conductivity of unsaturated soils. Soil Sci. Soc. Am. J. 44, 892-898. doi: 10.2136/sssaj1980.03615995004400050002x
Vogel, H.-J. (2000). A numerical experiment on pore size, pore connectivity, water retention, permeability, and solute transport using network models. Eur. J. Soil Sci. 51, 99-105. doi: 10.1046/j.1365-2389.2000.00275.x
Vogel, H.-J., and Roth, K. (1998). A new approach for determining effective soil hydraulic functions. Eur. J. Soil Sci. 49, 547-556. doi: 10.1046/j.1365-2389.1998.4940547.x
Vogel, H.-J., Tölke, J., Schulz, V. P., Krafczyk, M., and Roth, K. (2005). Comparison of a lattice-boltzmann model, a full-morphology model, and a pore network model for determining capillary pressure-saturation relationships. Vadose Zone J. 4, 380-388. doi: 10.2136/vzj2004.0114
Vogel, L. E., Makowski, D., Garnier, P., Vieublé-Gonod, L., Coquet, Y., Raynaud, X., et al. (2015). Modeling the effect of soil meso-and macropores topology on the biodegradation of a soluble carbon substrate. Adv. Water Res. 83, 123-136. doi: 10.1016/j.advwatres.2015.05.020
Vogel, H.-J., Weller, U., and Schlüter, S. (2010). Quantification of soil structure based on Minkowski functions. Comput. Geosci. 36, 1236-1245. doi: 10.1016/j.cageo.2010.03.007
Wagenmakers, E.-J., Verhagen, J., and Ly, A. (2016). How to quantify the evidence for the absence of correlation. Behav. Res. 48, 412-426. doi: 10.3758/s13428-015-0593-0
Wetzels, R., and Wagenmakers, E.-J. (2012). A default Bayesian hypothesis test for correlations and partial correlations. Psychon. Bull. Rev. 19, 1057-1064. doi: 10.3758/s13423-012-0295-x
Wildenschild, D., and Sheppard, A. P. (2013). X-ray imaging and analysis techniques for quantifying pore-scale structure and processes in subsurface porous medium systems. Adv. Water Res. 51, 217-246. doi: 10.1016/j.advwatres.2012.07.018
Young, I. M., Blanchart, E., Chenu, C., Dangerfield, M., Fragoso, C., Grimaldi, M., et al. (1998). The interaction of soil biota and soil structure under global change. Global Change Biol. 4, 703-712. doi: 10.1046/j.1365-2486.1998.00194.x
Zhang, Z. F. (2014). Relationship between anisotropy in soil hydraulic conductivity and saturation. Vadose Zone J. 13:vzj2013.09.0172. doi: 10.2136/vzj2013.09.0172
