Computational Geosciences

, Volume 20, Issue 1, pp 231–244 | Cite as

Quantifying fracture geometry with X-ray tomography: Technique of Iterative Local Thresholding (TILT) for 3D image segmentation

  • Hang Deng
  • Jeffrey P. Fitts
  • Catherine A. Peters
Open Access


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.


Fracture 3D image xCT Image segmentation Permeability Indiana limestone 

Supplementary material

10596_2016_9560_MOESM1_ESM.docx (1.7 mb)
(DOCX 1.72 MB)


  1. 1.
    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)CrossRefGoogle Scholar
  2. 2.
    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)CrossRefGoogle Scholar
  3. 3.
    Remeysen, K., Swennen, R.: Application of microfocus computed tomography in carbonate reservoir characterization: possibilities and limitations. Mar. Pet. Geol. 25, 486–99 (2008)CrossRefGoogle Scholar
  4. 4.
    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)CrossRefGoogle Scholar
  5. 5.
    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)CrossRefGoogle Scholar
  6. 6.
    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)CrossRefGoogle Scholar
  7. 7.
    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)CrossRefGoogle Scholar
  8. 8.
    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)CrossRefGoogle Scholar
  9. 9.
    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)CrossRefGoogle Scholar
  10. 10.
    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)Google Scholar
  11. 11.
    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)CrossRefGoogle Scholar
  12. 12.
    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)Google Scholar
  13. 13.
    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)CrossRefGoogle Scholar
  14. 14.
    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)CrossRefGoogle Scholar
  15. 15.
    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)CrossRefGoogle Scholar
  16. 16.
    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)CrossRefGoogle Scholar
  17. 17.
    Petchsingto, T., Karpyn, Z.T.: Simulation of fluid percolation in a rough-walled rock fracture. Hydrogeol J., 18 (2010)Google Scholar
  18. 18.
    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)CrossRefGoogle Scholar
  19. 19.
    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)CrossRefGoogle Scholar
  20. 20.
    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 CrossRefGoogle Scholar
  21. 21.
    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)CrossRefGoogle Scholar
  22. 22.
    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)CrossRefGoogle Scholar
  23. 23.
    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)CrossRefGoogle Scholar
  24. 24.
    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)CrossRefGoogle Scholar
  25. 25.
    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)CrossRefGoogle Scholar
  26. 26.
    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 CrossRefGoogle Scholar
  27. 27.
    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)CrossRefGoogle Scholar
  28. 28.
    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)CrossRefGoogle Scholar
  29. 29.
    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)CrossRefGoogle Scholar
  30. 30.
    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)CrossRefGoogle Scholar
  31. 31.
    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)CrossRefGoogle Scholar
  32. 32.
    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)CrossRefGoogle Scholar
  33. 33.
    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)CrossRefGoogle Scholar
  34. 34.
    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)CrossRefGoogle Scholar
  35. 35.
    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)CrossRefGoogle Scholar
  36. 36.
    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)Google Scholar
  37. 37.
    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)CrossRefGoogle Scholar
  38. 38.
    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
  39. 39.
    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
  40. 40.
    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)CrossRefGoogle Scholar
  41. 41.
    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)CrossRefGoogle Scholar
  42. 42.
    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)Google Scholar
  43. 43.
    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)CrossRefGoogle Scholar
  44. 44.
    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)CrossRefGoogle Scholar
  45. 45.
    Detwiler, R.: Permeability alteration due to mineral dissolution in partially saturated fractures. J. Geophys. Res., 115 (2010)Google Scholar
  46. 46.
    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)Google Scholar
  47. 47.
    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 CrossRefGoogle Scholar
  48. 48.
    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)CrossRefGoogle Scholar
  49. 49.
    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)CrossRefGoogle Scholar
  50. 50.
    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)CrossRefGoogle Scholar
  51. 51.
    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)CrossRefGoogle Scholar
  52. 52.
    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)CrossRefGoogle Scholar
  53. 53.
    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)CrossRefGoogle Scholar
  54. 54.
    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)CrossRefGoogle Scholar
  55. 55.
    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)CrossRefGoogle Scholar
  56. 56.
    Nikolaidis, N., Pitas, I.: Image Processing Algorithms, 3D, 1St. Wiley, New York (2000)Google Scholar
  57. 57.
    Ketcham, R.A.: Computational methods for quantitative analysis of three-dimensional features in geological specimens. Geosphere 1, 32–41 (2005)CrossRefGoogle Scholar
  58. 58.
    Kaestner, A., Lehmann, E., Stampanoni, M.: Imaging and image processing in porous media research. Adv. Water Resour. 31, 1174–87 (2008)CrossRefGoogle Scholar
  59. 59.
    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 Google Scholar
  60. 60.
    Otsu, N.: Threshold selection method from gray-level histograms. IEEE Trans. Syst. Man Cybern. 9, 62–66 (1979)CrossRefGoogle Scholar
  61. 61.
    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)CrossRefGoogle Scholar
  62. 62.
    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)CrossRefGoogle Scholar
  63. 63.
    Oh, W., Lindquist, W.B.: Image thresholding by indicator kriging. IEEE Trans. Pattern Anal. Mach. Intell. 21, 590–602 (1999)CrossRefGoogle Scholar
  64. 64.
    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)CrossRefGoogle Scholar
  65. 65.
    Ketcham, R.A.: Three-dimensional grain fabric measurements using high-resolution X-ray computed tomography. J. Struct. Geol. 27, 1217–28 (2005)CrossRefGoogle Scholar
  66. 66.
    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)CrossRefGoogle Scholar
  67. 67.
    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)CrossRefGoogle Scholar
  68. 68.
    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)CrossRefGoogle Scholar
  69. 69.
    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)CrossRefGoogle Scholar
  70. 70.
    Zuiderveld, K. In: Heckbert, P.S. (ed.) : Graphics gems, vol. IV. Academic Press Professional, Inc, San Diego (1994)Google Scholar
  71. 71.
    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)CrossRefGoogle Scholar
  72. 72.
    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)CrossRefGoogle Scholar
  73. 73.
    Münch, B., Trtik, P., Marone, F., Stampanoni, M.: Stripe and ring artifact removal with combined wavelet-Fourier filtering. Opt. Express 17, 8567–91 (2009)CrossRefGoogle Scholar
  74. 74.
    Fang, Q., Boas, D.A.: Tetrahedral mesh generation from volumetric binary and grayscale images (2009)Google Scholar
  75. 75.
    Belem, T., Homand-Etienne, F., Souley, M.: Quantitative parameters for rock joint surface roughness. Rock Mech. Rock Eng. 33, 217–42 (2000)CrossRefGoogle Scholar
  76. 76.
    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)CrossRefGoogle Scholar
  77. 77.
    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)CrossRefGoogle Scholar
  78. 78.
    Rangel-German, E., Akin, S., Castanier, L.: Multiphase-flow properties of fractured porous media. J. Pet. Sci. Eng. 51, 197–213 (2006)CrossRefGoogle Scholar
  79. 79.
    Peters, C.A.: Accessibilities of reactive minerals in consolidated sedimentary rock: an imaging study of three sandstones. Chem. Geol. 265, 198–208 (2009)CrossRefGoogle Scholar
  80. 80.
    Xu, X., Xu, S., Jin, L., Song, E.: Characteristic analysis of Otsu threshold and its applications. Pattern Recog. Lett. 32, 956–61 (2011)CrossRefGoogle Scholar

Copyright information

© The Author(s) 2016

Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (, which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.

Authors and Affiliations

  • Hang Deng
    • 1
  • Jeffrey P. Fitts
    • 1
  • Catherine A. Peters
    • 1
  1. 1.Department of Civil and Environmental EngineeringPrinceton UniversityPrincetonUSA

Personalised recommendations