Abstract
This paper presents a new method—the Technique of Iterative Local Thresholding (TILT)—for processing 3D X-ray computed tomography (xCT) images for visualization and quantification of rock fractures. The TILT method includes the following advancements. First, custom masks are generated by a fracture-dilation procedure, which significantly amplifies the fracture signal on the intensity histogram used for local thresholding. Second, TILT is particularly well suited for fracture characterization in granular rocks because the multi-scale Hessian fracture (MHF) filter has been incorporated to distinguish fractures from pores in the rock matrix. Third, TILT wraps the thresholding and fracture isolation steps in an optimized iterative routine for binary segmentation, minimizing human intervention and enabling automated processing of large 3D datasets. As an illustrative example, we applied TILT to 3D xCT images of reacted and unreacted fractured limestone cores. Other segmentation methods were also applied to provide insights regarding variability in image processing. The results show that TILT significantly enhanced separability of grayscale intensities, outperformed the other methods in automation, and was successful in isolating fractures from the porous rock matrix. Because the other methods are more likely to misclassify fracture edges as void and/or have limited capacity in distinguishing fractures from pores, those methods estimated larger fracture volumes (up to 80 %), surface areas (up to 60 %), and roughness (up to a factor of 2). These differences in fracture geometry would lead to significant disparities in hydraulic permeability predictions, as determined by 2D flow simulations.
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Ketcham, R.A., Carlson, W.D.: Acquisition, optimization and interpretation of X-ray computed tomographic imagery: applications to the geosciences. Comput. Geosci. 27, 381– 400 (2001)
Wildenschild, D., Hopmans, J.W., Vaz, C.M.P., Rivers, M.L., Rikard, D., Christensen, B.S.B.: Using X-ray computed tomography in hydrology: systems, resolutions, and limitations. J. Hydrol. 267, 285–97 (2002)
Remeysen, K., Swennen, R.: Application of microfocus computed tomography in carbonate reservoir characterization: possibilities and limitations. Mar. Pet. Geol. 25, 486–99 (2008)
Werth, C.J., Zhang, C., Brusseau, M.L., Oostrom, M., Baumann, T.: A review of non-invasive imaging methods and applications in contaminant hydrogeology research. J. Contam. Hydrol. 113, 1–24 (2010)
Christe, P., Turberg, P., Labiouse, V., Meuli, R., Parriaux, A.: An X-ray computed tomography-based index to characterize the quality of cataclastic carbonate rock samples. Eng. Geol. 117, 180–8 (2011)
Baker, D.R., Mancini, L., Polacci, M., Higgins, M.D., Gualda, G.A.R., Hill, R.J., Rivers, M.L.: An introduction to the application of X-ray microtomography to the three-dimensional study of igneous rocks. Lithos 148, 262–76 (2012)
Chae, S., Moon, J., Yoon, S., Bae, S., Levitz, P., Winarski, R., Monteiro, P.J.M.: Advanced nanoscale characterization of cement based materials using x-ray synchrotron radiation: a review. International Journal of Concrete Structures and Materials 7, 95–110 (2013)
Cnudde, V., Boone, M.N.: High-resolution X-ray computed tomography in geosciences: a review of the current technology and applications. Earth-Sci. Rev. 123, 1–17 (2013)
Wildenschild, D., Sheppard, A.P.: X-ray imaging and analysis techniques for quantifying pore-scale structure and processes in subsurface porous medium systems. Adv. Water Resour. 51, 217–46 (2013)
Montemagno, C.D., Pyrak-Nolte, L.: Fracture network versus single fractures: measurement of fracture geometry with X-ray tomography. Physics and Chemistry of the Earth. Part A: Solid Earth and Geodesy 24, 575–9 (1999)
Gouze, P., Noiriel, C., Bruderer, C., Loggia, D., Leprovost, R.: X-ray tomography characterization of fracture surfaces during dissolution. Geophys. Res. Lett. 30, 1267 (2003)
Noiriel, C., Made, B., Gouze, P.: Impact of coating development on the hydraulic and transport properties in argillaceous limestone fracture. Water. Resour. Res. 43, W09406 (2007)
Karpyn, Z.T., Piri M.: Prediction of fluid occupancy in fractures using network modeling and x-ray microtomography. I: Data conditioning and model description. Phys. Rev. E. 76, 016315 (2007)
Karpyn, Z.T., Grader, A.S., Halleck, P.M.: Visualization of fluid occupancy in a rough fracture using micro-tomography. J. Colloid Interface Sci. 307, 181–7 (2007)
Petchsingto, T., Karpyn, Z.T.: Deterministic modeling of fluid flow through a CT-scanned fracture using computational fluid dynamics. Energy Sources, Part A 31, 897–905 (2009)
Renard, F., Bernard, D., Desrues, J., Ougier-Simonin, A.: 3D imaging of fracture propagation using synchrotron X-ray microtomography. Earth Planet Sci. Lett. 286, 285–91 (2009)
Petchsingto, T., Karpyn, Z.T.: Simulation of fluid percolation in a rough-walled rock fracture. Hydrogeol J., 18 (2010)
Ketcham, R.A., Slottke, D.T., Sharp, J.M.: Three-dimensional measurement of fractures in heterogeneous materials using high-resolution X-ray computed tomography. Geosphere 6, 499–514 (2010)
Nasseri, M.H.B., Rezanezhad, F., Young, R.P.: Analysis of fracture damage zone in anisotropic granitic rock using 3D X-ray CT scanning techniques. Int. J. Fract. 168, 1–13 (2011)
Ellis, B.R., Peters, C.A., Fitts, J.P., Bromhal, G.S., McIntyre, D.L., Warzinski, R.P., Rosenbaum, E.J.: Deterioration of a fractured carbonate caprock exposed to CO 2-acidified brine flow. Greenhouse Gases Sci. Technol. 1, 248–60 (2011). doi:10.1002/ghg.25
Deng, H., Ellis, B.R., Peters, C.A., Fitts, J.P., Crandall, D., Bromhal, G.S.: Modifications of carbonate fracture hydrodynamic properties by CO 2-acidified brine flow. Energy Fuels 27, 4221–31 (2013)
Lindquist, W.B., Venkatarangan, A., Dunsmuir, J., Wong, T.: Pore and throat size distributions measured from synchrotron X-ray tomographic images of Fontainebleau sandstones. J. Geophys. Res. Solid Earth 105, 21509–27 (2000)
Porter, M.L., Wildenschild, D.: Image analysis algorithms for estimating porous media multiphase flow variables from computed microtomography data: a validation study. Comput. Geosci. 14, 15–30 (2010)
Luquot, L., Gouze, P.: Experimental determination of porosity and permeability changes induced by injection of CO 2 into carbonate rocks. Chem Geol 265, 148–59 (2009)
Gouze, P., Luquot, L.: X-ray microtomography characterization of porosity, permeability and reactive surface changes during dissolution. J. Contam. Hydrol 120-121, 44–55 (2011)
Sun, W., Andrade, J.E., Rudnicki, J.W., Eichhubl, P.: Connecting microstructural attributes and permeability from 3D tomographic images of in situ shear-enhanced compaction bands using multiscale computations. Geophys. Res. Lett. 38, L10302 (2011). doi:10.1029/2011GL047683
Peng, S., Hu, Q., Dultz, S., Zhang, M.: Using X-ray computed tomography in pore structure characterization for a Berea sandstone: resolution effect. J. Hydrol. 472, 254–61 (2012)
Smith, M.M., Sholokhova, Y., Hao, Y., Carroll, S.A.: Evaporite caprock integrity: an experimental study of reactive mineralogy and pore-scale heterogeneity during brine-CO 2 exposure. Environ Sci. Technol. 47, 262–8 (2013)
Herring, A.L., Harper, E.J., Andersson, L., Sheppard, A., Bay, B.K., Wildenschild, D.: Effect of fluid topology on residual nonwetting phase trapping: implications for geologic CO 2 sequestration. Adv. Water Resour. 62, 47–58 (2013)
Kneafsey, T.J., Silin, D., Ajo-Franklin, J.: Supercritical CO 2 flow through a layered silica sand/calcite sand system: experiment and modified maximal inscribed spheres analysis. Int. J. Greenhouse Gas Control 14, 141–50 (2013)
Vega, B., Dutta, A., Kovscek, A.R.: CT Imaging Of low-permeability, dual-porosity systems using high x-ray contrast gas. Transp. Porous Media 101, 81–97 (2014)
Gualda, G.A.R., Rivers, M.: Quantitative 3D petrography using X-ray tomography: application to Bishop Tuff pumice clasts. J. Volcanol Geotherm. Res. 154, 48–62 (2006)
Pamukcu, A.S., Gualda, G.A.R.: Quantitative 3D petrography using X-ray tomography 2: combining information at various resolutions. Geosphere 6, 775–81 (2010)
Long, H., Swennen, R., Foubert, A., Dierick, M., Jacobs, P.: 3D quantification of mineral components and porosity distribution in Westphalian C sandstone by microfocus X-ray computed tomography. Sediment Geol 220, 116–25 (2009)
Kim, D., Lindquist, W.B.: Dependence of pore-to-core up-scaled reaction rate on flow rate in porous media. Transp. Porous Media 89, 459–73 (2011)
Kim, D., Peters, C.A., Lindquist, W.B.: Upscaling geochemical reaction rates accompanying acidic CO 2-saturated brine flow in sandstone aquifers. Water Resour. Res. 47, W01505 (2011)
Madonna, C., Almqvist, B.S.G., Saenger, E.H.: Digital rock physics: numerical prediction of pressure-dependent ultrasonic velocities using micro-CT imaging. Geophys. J. Int. 189, 1475–82 (2012)
Carroll, S., Hao, Y., Smith, M., Sholokhova, Y.: Development of scaling parameters to describe CO 2-rock interactions within Weyburn-Midale carbonate flow units. Int. J. Greenhouse Gas Control 16(Supplement 1:S185-S193) (2013). doi:10.1016/j.ijggc.2012.12.026
Ellis, B.R., Peters C.A.: 3D Mapping of calcite and a demonstration of its relevance to permeability evolution in reactive fractures. Adv. Water Resour. doi:10.1016/j.advwatres.2015.07.023
Ellis, B.R., Fitts, J.P., Bromhal, G.S., McIntyre, D.L., Tappero, R., Peters, C.A.: Dissolution-driven permeability reduction of a fractured carbonate caprock. Environ Eng. Sci. 30, 187–93 (2013)
Yasuhara, H., Polak, A., Mitani, Y., Grader, A.S., Halleck, P.M., Elsworth, D.: Evolution of fracture permeability through fluid-rock reaction under hydrothermal conditions. Earth Planet. Sci. Lett. 244, 186–200 (2006)
McGuire, T.P., Elsworth, D., Karcz, Z.K.: The effects of coupled chemical-mechanical processes on the evolution of permeability in a carbonate fracture (2010)
McGuire, T.P., Elsworth, D., Karcz, Z.: Experimental measurements of stress and chemical controls on the evolution of fracture permeability. Transp. Porous Media 98, 15–34 (2013)
Ishibashi, T., McGuire, T.P., Watanabe, N., Tsuchiya, N., Elsworth, D.: Permeability evolution in carbonate fractures: competing roles of confining stress and fluid pH. Water Resour. Res. 49, 2828–42 (2013)
Detwiler, R.: Permeability alteration due to mineral dissolution in partially saturated fractures. J. Geophys. Res., 115 (2010)
Elkhoury, J.E., Ameli, P., Detwiler, R.L.: Dissolution and deformation in fractured carbonates caused by flow of CO 2-rich brine under reservoir conditions. Int. J. Greenhouse Gas Control 16(Supplement 1:S203-S215) (2013)
Noiriel, C., Gouze, P., Bernard, D.: Investigation of porosity and permeability effects from microstructure changes during limestone dissolution. Geophys. Res. Lett. 31, L24603 (2004). doi:10.1029/2004GL021572
Sun, W.C., Andrade, J.E., Rudnicki, J.W.: Multiscale method for characterization of porous microstructures and their impact on macroscopic effective permeability. Int. J. Numer. Methods Eng. 88, 1260–79 (2011)
Beckingham, L.E., Peters, C.A., Um, W., Jones, K.W., Lindquist, W.B.: 2D And 3D imaging resolution trade-offs in quantifying pore throats for prediction of permeability. Adv. Water Resour. 62, 1–12 (2013)
Noiriel, C., Luquot, L., Made, B., Raimbault, L., Gouze, P., van der Lee, J.: Changes in reactive surface area during limestone dissolution: an experimental and modelling study. Chem. Geol. 265, 160–70 (2009)
Nogues, J.P., Fitts, J.P., Celia, M.A., Peters, C.A.: Permeability evolution due to dissolution and precipitation of carbonates using reactive transport modeling in pore networks. Water Resour. Res. 49, 6006–21 (2013)
Noiriel, C., Gouze, P., Made, B.: 3D analysis of geometry and flow changes in a limestone fracture during dissolution. J. Hydrol. 486, 211–23 (2013)
Smith, M.M., Sholokhova, Y., Hao, Y., Carroll, S.A.: CO 2-induced dissolution of low permeability carbonates. Part I: characterization and experiments. Adv. Water Resour. 62, 370–87 (2013)
Andrew, M., Menke, H., Blunt, M., Bijeljic, B.: The imaging of dynamic multiphase fluid flow using synchrotron-based x-ray microtomography at reservoir conditions. Transp. Porous Media 110, 1–24 (2015)
Deng, H., Fitts, J.P., Crandall, D., McIntyre, D., Peters, C.A.: Alterations of fractures in carbonate rocks by CO 2-acidified brines. Environ. Sci. Technol. 49, 10226–34 (2015)
Nikolaidis, N., Pitas, I.: Image Processing Algorithms, 3D, 1St. Wiley, New York (2000)
Ketcham, R.A.: Computational methods for quantitative analysis of three-dimensional features in geological specimens. Geosphere 1, 32–41 (2005)
Kaestner, A., Lehmann, E., Stampanoni, M.: Imaging and image processing in porous media research. Adv. Water Resour. 31, 1174–87 (2008)
Iassonov, P., Gebrenegus, T., Tuller, M.: Segmentation of X-ray computed tomography images of porous materials: a crucial step for characterization and quantitative analysis of pore structures. Water Resour. Res. 45, W09415 (2009). doi:10.1029/2009WR008087
Otsu, N.: Threshold selection method from gray-level histograms. IEEE Trans. Syst. Man Cybern. 9, 62–66 (1979)
Elliot, T.R., Heck, R.J.: A comparison of 2D vs. 3D thresholding of X-ray CT imagery. Can J. Soil Sci. 87, 405–12 (2007)
Yushkevich, P., Piven, J., Cody, H., Ho, S., Gee, J., Gerig, G.: User-guided level set segmentation of anatomical structures with ITK-SNAP. Neuroimage 31, 1116–28 (2005)
Oh, W., Lindquist, W.B.: Image thresholding by indicator kriging. IEEE Trans. Pattern Anal. Mach. Intell. 21, 590–602 (1999)
Landry, C.J., Karpyn, Z.T.: Single-phase lattice Boltzmann simulations of pore-scale flow in fractured permeable media. International Journal of Oil Gas and Coal Technology 5, 182–206 (2012)
Ketcham, R.A.: Three-dimensional grain fabric measurements using high-resolution X-ray computed tomography. J. Struct. Geol. 27, 1217–28 (2005)
Voorn, M., Exner, U., Rath, A.: Multiscale Hessian fracture filtering for the enhancement and segmentation of narrow fractures in 3D image data. Comput. Geosci. 57, 44–53 (2013)
Frangi, A.F., Niessen, W.J., Vincken, K.L., Viergever, M.A.: Multiscale vessel enhancement filtering. Medical Image Computing and Computer-Assisted Intervention - Miccai’98 1496, 130–137 (1998)
Iassonov, P., Tuller, M.: Application of segmentation for correction of intensity bias in x-ray computed tomography images. Vadose Zone J. 9, 187–91 (2010)
Wang, W., Kravchenko, A.N., Smucker, A.J.M., Rivers, M.L.: Comparison of image segmentation methods in simulated 2D and 3D microtomographic images of soil aggregates. Geoderma 162, 231–41 (2011)
Zuiderveld, K. In: Heckbert, P.S. (ed.) : Graphics gems, vol. IV. Academic Press Professional, Inc, San Diego (1994)
Sheppard, A.P., Sok, R.M., Averdunk, H.: Techniques for image enhancement and segmentation of tomographic images of porous materials. Physica A 339, 145–151 (2004)
Yushkevich, P.A., Piven, J., Hazlett, H.C., Smith, R.G., Ho, S., Gee, J.C., Gerig, G.: User-guided 3D active contour segmentation of anatomical structures: significantly improved efficiency and reliability. Neuroimage 31, 1116–28 (2006)
Münch, B., Trtik, P., Marone, F., Stampanoni, M.: Stripe and ring artifact removal with combined wavelet-Fourier filtering. Opt. Express 17, 8567–91 (2009)
Fang, Q., Boas, D.A.: Tetrahedral mesh generation from volumetric binary and grayscale images (2009)
Belem, T., Homand-Etienne, F., Souley, M.: Quantitative parameters for rock joint surface roughness. Rock Mech. Rock Eng. 33, 217–42 (2000)
James, S.C., Chrysikopoulos, C.V.: Transport of polydisperse colloids in a saturated fracture with spatially variable aperture. Water Resour. Res. 36, 1457–65 (2000)
Pyrak-Nolte, L., Morris, J.P.: Single fractures under normal stress: the relation between fracture specific stiffness and fluid flow. Int. J. Rock Mech. Min. Sci. 37, 245–62 (2000)
Rangel-German, E., Akin, S., Castanier, L.: Multiphase-flow properties of fractured porous media. J. Pet. Sci. Eng. 51, 197–213 (2006)
Peters, C.A.: Accessibilities of reactive minerals in consolidated sedimentary rock: an imaging study of three sandstones. Chem. Geol. 265, 198–208 (2009)
Xu, X., Xu, S., Jin, L., Song, E.: Characteristic analysis of Otsu threshold and its applications. Pattern Recog. Lett. 32, 956–61 (2011)
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Deng, H., Fitts, J.P. & Peters, C.A. Quantifying fracture geometry with X-ray tomography: Technique of Iterative Local Thresholding (TILT) for 3D image segmentation. Comput Geosci 20, 231–244 (2016). https://doi.org/10.1007/s10596-016-9560-9
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DOI: https://doi.org/10.1007/s10596-016-9560-9