HRXCT Quantitation Software

UTCT has developed a number of specialized software packages for quantitative analysis of HRXCT datasets. Blob3D measures three-dimensional geometric information on up to thousands of discrete objects within a data volume. Quant3D quantifies three-dimensional fabrics using a variety of metrics. Align3D performs a three-dimensional alignment and subtraction of two data sets, allowing differences between them to be determined and analyzed precisely. All of these programs are freely available for academic use in academic research.

All of the programs described here are written in IDL (Interactive Data Language, Exelis Visual Information Solutions). Blob3D and Quant3D can be run using either a fully licensed version of IDL, or the IDL "Virtual Machine" which can be downloaded free of charge by following the instructions here, though downloading does require registering with Exelis. Align3D requires a fully licensed version of IDL.


The following overview is excerpted from: Ketcham, R.A. (2005a) Computational methods for quantitative analysis of three-dimensional features in geological specimens. Geosphere, 1, 32-41.

Blob3D is designed for efficient measurement of up to thousands of discrete features (e.g. clasts, mineral grains, porphyroblasts, voids) within a single sample. Blob3D is unique because it gives the program operator primary control over data interpretation and measurement, and all computations are carried out in 3D, rather than individually on a series of 2D slices.

A "blob" is a contiguous set of voxels (3D pixels) that meets some user-defined criteria. Three steps are involved in Blob3D data processing. In the first step, Segment, a set of criteria are defined by the user that defines which voxels belong to the material of interest. The second step, Separate, distinguishes contiguous sets of segmented voxels (i.e. blobs) and allows the operator to divide interconnected or touching objects into individual objects. The third step, Extract, performs measurements on separated objects, such as size, shape, orientation, and contact relationships. Another feature in the Extract module allows the user to input sample coordinates (e.g. strike and dip) and the program calculates geographic coordinates for mineral grains or other features of interest in a sample.

Blob3D is a powerful quantitative tool for CT data and has been applied to the study of a wide variety of problems. Geological examples include textural analysis of porphyroblasts in metamorphic rocks (Ketcham et al., 2005), measurement of vesicles in meteoritic basalts (Benedix et al., 2003; McCoy et al., 2002) and troilite particles in chondritic meteorites (Nettles and McSween, 2006), and grading and orientation analysis of gold grains in ores (Kyle and Ketcham, 2003; Mote et al., 2005). It can also be used for engineering applications, such as quantifying aggregate clasts in asphalt concretes (Ketcham and Shashidhar, 2001) and the pore structure of tissue scaffolds (Dunkers et al., 2005). It can also be used for segmenting and quantifying complex three-dimensional structures such as nasal passageways (Rowe et al., 2005).

Click here to download Blob3D via ftp.

Example of BLOB3D processing for cluster of garnet porphyroblasts. Because garnet is the only porphyroblast, it can be segmented using a simple grayscale threshold (A, B). When inspected in two dimensions (B) and three dimensions (C) it is apparent that the cluster consists of four individual crystals. Separation was accomplished (D) using erosion-dilation operations. To estimate the extended volume and center of nucleation for lower-right crystal (E), a sphere primitive was fit to outer surface (F) by excluding from consideration points in contact with other garnet (from Ketcham, 2005a).

Example of typical processing operations in Separate module. Part A shows a sample of computed tomography (CT) data of a cluster of spheres; field of view is 70 mm. A three-dimensional volume searching algorighm finds all voxels in contact, up to limits imposed by computer memory (B); faces truncated by the algorithm are marked in red. "Stair steps" on upper and lower portions of spheres are caused by 3:1 voxel aspect ratio (inter-slice vs. inter-pixel spacing). An erosion/dilation operator successfully separates most of the spheres (C). Those contacting truncated faces have their processing postponed (D), allowing interior spheres to be processed (from Ketcham, 2005a).


The following overview is excerpted from: Ketcham, R.A. (2005b) Three-dimensional textural measurements using high-resolution X-ray computed tomography. Journal of Structural Geology, 27, 1217-1228 and Ketcham, R.A., and Ryan, T. (2004) Quantification and visualization of anisotropy in trabecular bone. Journal of Microscopy, 213, 158-171.

Quant3D is a versatile program that can be used to analyze fabrics in any three-dimensional data set; examples include quantification of anisotropy in trabecular bone (Ketcham and Ryan, 2004; Ryan and Ketcham, 2005) and textural analysis of metamorphic rocks (Ketcham, 2005b). Fabric tensors are produced based on the star volume distribution (SVD), star length distribution (SLD), and mean intercept length (MIL) methods. Principal component directions and magnitudes are provided by the tensors, providing the degree of anisotropy and shape indices of the phase of interest. Three-dimensional rose diagrams are a unique feature implemented in Quant3D for analyzing non-orthogonal directional fabric components; they are VRML-format graphics files that can be rotated and viewed interactively.

Click here to download Quant3D via ftp.

Example of fabric analysis of quartzofeldspathic layers using Quant3D. In (a) the scan data are first segmented to isolate the material of interest, in this case garnet (white), biotite + kyanite (gray), and quartz + feldspar (black). ‘Star’ analyses proceed by placing a series of points within the material of interest, and measuring the distance from each point to the material boundary in many directions (red lines). Only two dimensions shown here, but measurements are actually made in 3D. The analysis directions are uniformly distributed in three dimensions on a grid defined by the line intersections on the sphere shown in (b). To create a 3D rose diagram, each intersection in (b) is projected from the origin by its relative star volume component value (c). Colors are assigned based on SVD/Max(SVD), and color coding from 0 (violet) to 1 (red) (from Ketcham, 2005b).

3D rose diagrams showing relative SVD component magnitudes for quartz + plagioclase (upper row) and garnet (lower row) in sample MD generated in Quant3D. First diagram in each row (a,d) is viewed down the 'Up' axis; second diagram (b,c) is viewed along the second eigenvector, and third (c,f) is an arbitrary orientation. The diagrams are stored in VRML 97 format, and can be viewed interactively with a number of software applications and browser plug-ins (from Ketcham, 2005b).


The following overview is excerpted from: Ketcham, R.A., and Iturrino, G.J. (2005) Nondestructive high-resolution visualization and measurement of anisotropic effective porosity in complex lithologies using high-resolution X-ray computed tomography. Journal of Hydrology, 302, 92-106.

Align3D is a collection of IDL routines that implement a three-dimensional alignment and subtraction of two HRXCT data sets, also known as "subtraction analysis." If a sample is scanned twice in different states, once dry and once saturated with a fluid, the difference between the two data sets corresponds to the location of fluid in the second scan. This in turn reveals the interconnected, or "effective" porosity of the sample. A uniquely powerful aspect of this analysis is that it provides the porosity in each data voxel as a fractional value (i.e. from 0 to 100%), and provides essentially limitless resolution: even micro-pores far smaller than the resolution of the CT data are reflected in the fractional porosity data. The three-dimensional effective porosity map provided by this analysis can be used to gain insight into the rock and mineral structures behind permeability and flow characteristics. It also opens the possibility of determining the three-dimensional anisotropy of permeability. The HRXCT analysis is essentially non-destructive, as any fluid, including distilled water or groundwater in equilibrium with the sample material, can be employed.

Click here to download Align3D via ftp.

Example of Align3D data-alignment procedure. Top left shows slice from the “dry” scan of ODP deep-sea sample 1189A-8R, a rock that was probably originally a diorite but has been extensively altered by hydrothermal fluids associated with ocean-floor spreading. Image field of view is 24 mm. Top right shows the same slice with the corresponding slice from the “wet” scan subtracted and renormalized; light and dark areas show misfit. Bottom left shows subtraction after an intermediate stage of fitting, and bottom right shows the final fit after best-fit three-dimensional transformation has been found; subtle gray-level variations now reveal location of porosity-filling water (from Ketcham and Iturrino, 2005).

Example scan images (left) and porosity maps (right) for various deep-sea samples. Field of view for each image is 24 mm, and each CT slice represents a 57.8 mm thickness of material. Top left sample has many vesicles (gas bubbles), but porosity scan shows that few of them are interconnected, even by microporosity, explaining the low permeability of this rock. Top right sample is cross-cut by a sulfide-anhydrite vein, which was once a fluid conduit but now is a fluid barrier; the microporosity fabric to either side is actually perpendicular to the vein. Anhydrite-filled vesicles are also non-porous. Extensive alteration in the bottom right sample has produced a complex network of microporosity defined by alteration rims and occasional conduits (from Ketcham and Iturrino, 2005).

Additional Software


MuCalcTool is a Microsoft Excel workbook that can be used to compare the x-ray attenuation of various minerals. The key to distinguishing between different minerals in a rock using HRXCT is to scan the rock at an energy where each mineral has a different x-ray attenuation (if possible). This workbook allows a user to determine if the various minerals in their rock will be distinguishable in the scan data, and if there is an optimal energy at which to scan in order to maximize their differences in attenuation. The x-ray attenuations of over 200 minerals and elements are already included in the workbook. It is also possible to create a solid solution mineral out of the existing minerals in the workbook and to add additional minerals. The mass x-ray attenuation coefficients for the minerals in this workbook were retrieved using the NIST XCOM Database.

Click here to download MuCalcTool via ftp.

Example x-ray attenuation graph of quartz, kspar, biotite, and zircon.

Papers Utilizing Blob3D

Altman, S.J., Aminzadeh, B., Balhoff, M.T., Bennett, P.C., Bryant, S.L., Cardenas, M.B., Chaudhary, K., Cygan, R.T., Deng, W., Dewers, T., DiCarlo, D.A., Eichhubl, P., Hesse, M. A., Huh, C., Matteo, E.N., Mehmani, Y., Tenney, C.M., and Yoon, H. (2014) Chemical and Hydrodynamic Mechanisms for Long-Term Geological Carbon Storage. Journal of Physical Chemistry C, 118, 15103-15113.
Alvarez-Barreto, J.F., Shreve, M.C., Deangelis, P.L., and Sikavitsas, V.I. (2007) Preparation of a functionally flexible, three-dimensional, biomimetic poly(L-lactic acid) scaffold with improved cell adhesion. Tissue Engineering, 13, 1205-1217.
Andronico, D., Corsaro, R.A., Cristaldi, A., and Polacci, M. (2008) Characterizing high energy explosive eruptions at Stromboli volcano using multidisciplinary data: an example from the 9 January 2005 explosion. Journal of Volcanology and Geothermal Research, 176, 541-550.
Astolfo, A., Arfelli, F., Schültke, E., James, S., Mancini, L., and Menk, R.-H. (2013) A detailed study of gold-nanoparticle loaded cells using X-ray based techniques for cell-tracking applications with single-cell sensitivity. Nanoscale, 5, 3337-3345.
Bai, L., Baker, D.R., and Hill, R.J. (2010) Permeability of vesicular Stromboli basaltic glass: Lattice Boltzmann simultations and laboratory measurements. Journal of Geophysical Research, 115, 16.
Bai, L., Baker, D.R., Polacci, M., and Hill, R.J. (2011) In-situ degassing study on crystal-bearing Stromboli basaltic magmas: Implications for Stromboli explosions. Geophysical Research Letters, 38, 5.
Baker, D.R., Polacci, M., and LaRue, A. (2011) A study on the reproducibility of counting vesicles in volcanic rocks. Geosphere, 7, 70-78.
Balen, D., and Petrinec, Z. (2011) Contrasting tourmaline types from peraluminous granites: a case study from Moslavaca Gora (Croatia). Mineralogy and Petrology, 102, 117-134.
Benedix, G.K., Ketcham, R.A., McCoy, T.J., and Wilson, L. (2003) Vesiculation in ordinary chondrites due to impact melting: the “PAT” 91501 answers. LPSC XXXIV (Abstract #1947; CD-ROM).
Berger, A., Herwegh, M., Schwarz, J.-O., and Putlitz, B. (2011) Quantitative analysis of crystal/grain sizes and their distributions in 2D and 3D. Journal of Structural Geology, 33, 1751-1763.
Bernasconi, A., Diella, V., Marinoni, N., Pavese, A., and Francescon, F. (2012) Influence of composition on some industrially relevant properties of traditional sanitary-ware glaze. Ceramics International, 38, 5859-5870.
Brusseau, M.L., Peng, S., Schnaar, G., and Costanza-Robinson, M.S. (2006) Relationships among air-water interfacial area, capillary pressure, and water saturation for a sandy porous medium. Water Resources Research, 42, W03501.
Buran, B.N., Strenzke, N., Neef, A., Gundelfinger, E.D., Moser, T., and Liberman, M.C. (2010) Onset coding is degraded in auditory nerve fibers from mutant mice lacking synaptic ribbons. The Journal of Neuroscience, 30, 7587-7597.
Caricchi, L, Pommier, A., Pistone, M., Castro, J., Burgisser, A., and Perugini, D. (2011) Strain-induced magma degassing: insights from simple-shear experiments on bubble bearing melts. Bulletin of Volcanology, 73, 1245-1257.
Carlson, W.D., and Gordon, C.L. (2004) Effects of matrix grain size on the kinetics of intergranular diffusion. Journal of Metamorphic Geology, 22, 733-742.
Castro, J.M., Burgisser, A., Schipper, I., and Mancini, S. (2012) Mechanisms of bubble coalescence in silicic magmas. Bulletin of Volcanology, 74, 2339-2352.
Costanza-Robinson, M.S., Estabrook, B.D., and Fouhey, D.F. (2011) Representative elementary volume estimation for porosity, moisture saturation, and air-water interfacial areas in unsaturated porous media: data quality implications. Water Resources Research, 47, W07513.
Degruyter, W., Bachmann, O., and Burgisser, A. (2009) Controls on magma permeability in the volcanic conduit during the climactic phase of the Kos Plateau Tuff eruption (Aegean Arc). Bulletin of Volcanology, 72, 63-74.
Degruyter, Burgisser, A., Bachmann, O., and Malaspinas, O. (2010) Synchrotron X-ray microtomography and lattice Boltzmann simulations of gas flow through volcanic pumices. Geosphere, 6, 470-481.
Dunkers, J.P., Tesk, J.A., Dean, D., Cooke, M.N., Ketcham, R.A., and Cicerone, M.T. (2005) Quantitative analysis of a candidate porosity reference scaffold: Type 1. 2005 Summer ASME Bioengineering Conference, June 22-26, Vail, CO.
Dunkers, J.P., Leigh, S.D., Dean, D., Cooke, M.N., Ketcham, R.A., and Cicerone, M.T. (2007) Methodology for evaluating candidate geometric reference scaffolds. Journal of Testing and Evaluation, 35, 1-8.
Dyess, J. E., Hansen, V. L., Goscinak, C. (2014) Constrains on vorticity and non-coaxial shear direction in Neoarchean L-S tectonites, an example from northern Minnesota, USA. Precambrian Research, 256, 189-200.
Friedrich, J.M. (2013) A Classroom-Based Distributed Workflow Initiative for the Early Involvement of Undergraduate Students in Scientific Research. Journal of Science Education and Technology, 35, 1-8.
Friedrich, J.M., and Rivers, M.L. (2013) Three-dimensional imaging of ordinary chondrite microporosity at 2.6 micrometer resolution. Geochimica et Cosmochimica Acta, 116, 63-70.
Friedrich, J.M., Macke, R.J., Wignarajah, D.P., Rivers, M.L., Britt, D.T., and Ebel, D.S. (2008) Pore size distribution in an uncompacted equilibrated ordinary chondrite. Planetary and Space Science, 56, 895-900.
Friedrich, J.M., Wignarajah, D.P., Chaudhary, S., Rivers, M.L., Nehru, C.E., and Ebel, D.S. (2008) Three-dimensional petrography of metal phases in equilibrated L chondrites—: effects of shock loading and dynamic compaction. Earth and Planetary Science Letters, 275, 172-180.
Friedrich, J.M., Wignarajah, D.P., Chaudhary, S., Rivers, M.L., Nehru, C.E., and Ebel, D.S. (2008) Dynamic compaction of asteroids: impact-induced preferred 3D orientation of metal grains in L chondrites. Asteroids, Comets, Meteors 2008, Baltimore, Maryland.
Friedrich, J.M., Troiano, J., Rumble III, D., and Rivers, M.L. (2011) Compositional studies of four low-FeO ordinary chondrites: is a new chondritic meteorite parent body necessary? 42nd Lunar and Planetary Science Conference, Abstract 1885, Houston, Texas.
Friedrich, J.M., Rivers, M.L., Perlowitz, M.A., Meinhart, Z., and Ramirez, V.V. (2012) Characterization of particle size standard NIST 1019b with synchrotron X-ray microtomography and digital data extraction. Particle & Particle Systems Characterization, 29, 35-42.
Friedrich, J.M., Ruzicka, A., Rivers, M.L., Ebel, D.S., Thostenson, J.O., and Rudolph, R.A. (2013) Metal veins in the Kernouvé (H6 S1) chondrite: evidence for pre- or syn-metamorphic shear deformation. Geochimica et Cosmochimica Acta, 116, 71-83.
Fu, Y., Xie, H., Deng, B., Du, G., Chen, R., Xiao, T. (2014) Three-dimensional structure of polystyrene colloidal crystal by synchrotron radiation X-ray phase-contrast computed tomography. Materials Science & Processing, 115, 781-790.
Gaidies, F., Petley-Ragan, A., Chakraborty, S., Dasgupta, S., Jones, P. (2014) Constraining the conditions of Barrovian metamorphism in Sikkim, India: P-T-t paths of garnet crystallization in the Lesser Himalayan Belt. Journal of Metamorphic Geology, 33, 23-44.
Gardner, J.E., and Ketcham, R.A. (2011) Bubble nucleation in rhyolite and dacite melts: temperature dependence of surface tension. Contributions to Mineralogy and Petrology, 162, 929-943.
Giachetti, T., Burgisser, A., Arbaret, L., Druitt, T.H., and Kelfoun, K. (2011) Quantitative textural analysis of Vulcanian pyroclasts (Montserrat) using multi-scale X-ray computed microtomography: comparison with results from 2D image analysis. Bulletin of Volcanology, 73, 1295-1309.
Gopalakrishnan, K., Ceylan, H., and Inanc, F. (2007) Using X-ray computed tomography to study paving materials. Construction Materials, 160, 15-23.
Gostic, R.C. (2010) Characterization of plutonium particles originating from the BOMARC accident - 1960. PhD dissertation, Chemistry, The University of Nevada, Las Vegas.
Gualda, G.A.R. (2006) Crystal size distributions derived from 3D datasets: Sample size versus uncertainties. Journal of Petrology, 47, 1245-1254.
Gualda, G.A.R., and Rivers, M. (2006) Quantitative 3D petrography using X-ray tomography: Application to Bishop Tuff pumice clasts. Journal of Volcanology and Geothermal Research, 154, 48-62.
Gualda, G.A.R., Pamukcu, A.S., Claiborne, L.L., and Rivers, M.L. (2010) Quantitative 3D petrography using X-ray tomography 3: Documenting accessory phases with differential absorption tomography. Geosphere, 6, 782-792.
Hirsch, D.M. (2011) Reduce3D: a tool for three-dimensional spatial statistical analysis of crystals. Geosphere, 7, 724-732.
Huddlestone-Holmes, C.R., and Ketcham, R.A. (2010) An X-ray computed tomography study of inclusion trail orientations in multiple porphyroblasts from a single sample. Tectonophysics, 480, 305-320.
Jerram, D.A., and Higgins, M.D. (2007) 3D analysis of rock textures: quantifying igneous microstructures. Elements, 3, 239-245.
Jerram, D.A., Mock, A., Davis, G.R., Field, M., and Brown, R.J. (2009) 3D crystal size distributions: a case study on quantifying olivine populations in kimberlites. Lithos, 112, 223-235.
Ketcham, R.A. (2005a) Computational methods for quantitative analysis of three-dimensional features in geological specimens. Geosphere, 1, 32-41.
Ketcham, R.A. (2005b) Three-dimensional textural measurements using high-resolution X-ray computed tomography. Journal of Structural Geology, 27, 1217-1228.
Ketcham, R., A., Hildebrandt, J. (2014) Characterizing, measuring, and utilizing the resolution of CT imagery for improved quantification of fine-scale features. Nuclear Instruments and Methods in Physics Research Section B: Beam Interaction with Materials and Atoms, 324, 80-87.
Ketcham, R.A., and Shashidhar, N. (2001) Quantitative analysis of 3-D images of asphalt concrete, Paper No. 01-0321. Transportation Research Board 80th Annual Meeting. Transportation Research Board, Washington, D.C.
Ketcham, R.A., Meth, C., Hirsch, D.M., and Carlson, W.D. (2005) Improved methods for quantitative analysis of three-dimensional porphyroblastic textures. Geosphere, 1, 42-59. Supplemental material: http://www.ctlab.geo.utexas.edu/pubs/ketcham_et_al/ketcham_et_al.htm
Kyle, J.R., and Ketcham, R.A. (2003) In-situ distribution of gold ores using high-resolution X-ray computed tomography. Economic Geology, 98, 1697-1701. Supplemental material: http://www.ctlab.geo.utexas.edu/pubs/kyle&ketcham/k&k.htm
Kyle, J. R., Ketcham, R. A. (2015) Application of high resolution X-ray computed tomography to mineral deposit origin, evaluation, and processing. Ore Geology Reviews, 65, 821-839.
Kyle, J.R., Mote, A.S., and Ketcham, R.A. (2008) High resolution X-ray computed tomography studies of Grasberg porphyry Cu-Au ores, Papua, Indonesia. Mineralium Deposita, 43, 519-532.
Lindgren, P., Hanna, R.D., Dobson, K.J., Tomkinson, T., and Lee, M.R. (2015) The paradox between low shock-stage and evidence for compaction in CM carbonaceous chondrites explained by multiple low-intensity impacts. Geochimica et Cosmochimica Acta, 148, 159-178.
Marinoni, N., Voltolini, M., Mancini, L., and Cella, F. (2012) Influence of aggregate mineralogy on alkali-silica reaction studied by X-ray powder diffraction and imaging techniques. Journal of Materials Science, 47, 2845-2855.
McCoy, T.J., Ketcham, R.A., and Benedix, G.K. (2002) Vesicular basalts from asteroids: Clues to physical processes in their parent magmas. Lunar and Planetary Science Conference XXXIII, Abstract 1213. Lunar and Planetary Science Institute, Houston.
Mote, A.S., Ketcham, R.A., and Watson, W.P. (2006) Extracting particle orientations from three-dimensional datasets using BLOB3D, in Desrues, J., Viggiani, G., and Besuelle, P., eds., Advances in X-ray tomography for Geomaterials, ISTE, London, 407-413.
Nachlas, W.O., Whitney, D.L., Teyssier, C., Bagley, B., Mulch, A. (2014) Titanium concentration in quartz as a record of multiple deformation mechanism in an extensional shear zone. Journal of Geochemistry, Geophysics, Geosystems, 15, 1374-1397.
Narter, M.E. (2012) Characterizing non-wetting fluid in natural porous media using synchrotron X-ray microtomography. PhD dissertation, Soil, Water, and Environmental Science, University of Arizona, 172 p.
Nettles, J.W., and McSween, H.Y. Jr. (2006) A comparison of metal-troilite grain size distributions for type 3 and type 4 ordinary chondrites using X-ray CT data. 37th Lunar and Planetary Science Conference, League City, Texas.
Packman, A.I., Marion, A., Zaramella, M., Chen, C., Gaillard, J.-F., and Keane, D.T. (2006) Development of layered sediment structure and its effects on pore water transport and hyporheic exchange, in Kronvang, B., Faganeli, J., and Ogrinc, N., eds., The Interactions Between Sediments and Water, Springer, New York, 69-78.
Pamukcu, A.S. (2010) The evolution of the peach spring tuff magmatic system as revealed by accessory mineral textures and compositions. MS Thesis, Earth and Environmental Science, Vanderbilt University, 304 p.
Pamukcu, A.S., and Gualda, G.A.R. (2010) Quantitative 3D petrography using X-ray tomography 2: Combining information at various resolutions. Geosphere, 6, 775-781.
Pamukcu, A.S., Gualda, G.A.R., and Anderson, A.T. Jr. (2012) Crystallization stages of the Bishop Tuff magma body recorded in crystal textures in pumice clasts. Journal of Petrology, 53, 589-609.
Peng, D., Huang, T., and Meng, C. (2012) Study on imaging arsenic aggregates in porous media by X-ray difference micro-tomography. Advances in Materials Research, 356-360, 2362-2366.
Polacci, M., Baker, D.R., Mancini, L., Tromba, G., and Zanini, F. (2006) Three-dimensional investigation of volcanic textures by X-ray microtomography and implications for conduit processes. Geophysical Research Letters, 33, L13312.
Polacci, M., Baker, D.R., La Rue, A., Mancini, L., and Allard, P. (2012) Degassing behaviour of vesiculated basaltic magmas: an example from Ambrym volcano, Vanuatu Arc. Journal of Volcanology and Geothermal Research, 233-24, 55-64.
Porter, M.L. (2008) Investigating capillary pressure and interfacial area for multiphase flow in porous media using pore-scale imaging and Lattice-Boltzmann modeling. PhD dissertation, Water Resources Engineering, Oregon State University, 127 p.
Porter, M.L., and Wildenschild, D. (2009) Image analysis algorithms for estimating porous media multiphase flow variables from computed microtomography data: a validation study. Computational Geosciences, 14, 15-30.
Robert, G., Baker, D.R., Rivers, M.L., Allard, E., and Larocque, J. (2004) Comparison of the bubble size distribution in silicate foams using 2-dimensional images and 3-dimensional x-ray microtomography, in Bonse, U., ed., Developments in X-Ray Tomography IV, Proceedings of SPIE, 5535, Bellingham, WA, 505-513.
Rowe, T.B., Eiting, T.P., Macrini, T.E., and Ketcham, R.A. (2005) Organization of the olfactory and respiratory skeleton in the nose of the gray short-tailed opossum Monodelphis domestica. Journal of Mammalian Evolution, 12, 303-336.
Sasso, M.R., Macke, R.J., Boesenberg, J.S., Britt, D.T., Rivers, M.L., Ebel, D.S., and Friedrich, J.M. (2009) Incompletely compacted equilibrated ordinary chondrites. Meteoritics and Planetary Science, 44, 1743-1753.
Sasso, M.R., Macke, R.J., Britt, D.T., Rivers, M.L., Ebel, D.S., and Friedrich, J.M. (2009) Physical properties of incompletely compacted equilibrated ordinary chondrites: implications for asteroidal structure and impact processing. 40th Lunar and Planetary Science Conference, The Woodlands, Texas.
Schnaar, G., and Brusseau, M.L. (2005) Pore-scale characterization of organic immiscible-liquid morphology in natural porous media using synchrotron X-ray microtomography. Environmental Science Technology, 39, 8403-8410.
Schnaar, G., and Brusseau, M.L. (2006) Characterizing pore-scale configuration of organic immiscible liquid in multiphase systems with synchrotron X-ray microtomography. Vadose Zone Journal, 5, 641-648.
Schnaar, G., and Brusseau, M.L. (2006) Characterizing pore-scale dissolution of organic immiscible liquid in natural porous media using synchrotron X-ray microtomography. Environmental Science Technology, 40, 6622-6629.
Schopa, A., Floess, D., de Saint Blanquat, M., Annen, C., Launeau, P. (In Press) The Relation between Magnetite and Silicate Fabric in Granitoids of the Adamello Batholith. Tectonophysics.
Shield, J. K., Mader, H. M., Pistone, M., Caricchi, L., Floess, D., Putlitz, B. (2014) Strain-induced outgassing of three-phase magmas during simple shear. Journal of Geophysical Research, 119, 6936-6957.
Som, S.M., Hagadorn, J.W., Thelen, W.A., Gillespie, A.R., Catling, D.C., and Buick, R. (2013) Quantitative discrimination between geological materials with variable density contrast by high resolution X-ray computed tomography: an example using amygdule size-distribution in ancient lava flows. Computers & Geosciences, 54, 231-238.
Subroy, V., Gimenez, D., Qin, M., Krogmann, U., Strum, P.F., Miskewitz, R.J. (2013) Hydraulic properties of coarsely and finely ground woodchips. Journal of Hydrology, 517, 201-212.
Troiano, J., Rumble, D., III, Rivers, M.L., and Friedrich, J.M. (2011) Compositions of three low-FeO ordinary chondrites: Indications of a common origin with the H chondrites. Geochimica et Cosmochimica Acta, 75, 6511-6519.
Turk, J. K., Graham, R. C. (2014) Analysis of Vesicular Porosity in Soils using High Resolution X-Ray Computed Tomography. Soil Science Society of America Journal, 78, 868-880.
Uchida, T., Wang, Y., Westferro, F., Rivers, M.L., Gebhardt, J., and Sutton, S.R. (2007) X-ray microtomography under high pressure, in Ohtani, E., ed., Advances in High-pressure Mineralogy, Geological Society of America, Washington, DC, 227-238.
Voltolini, M., Marinoni, N., and Mancini, L. (2011) Synchrotron X-ray computed microtomography investigation of a mortar affected by alkali-silica reaction: a quantitative characterization of its microstructural features. Journal of Materials Science, 46, 6633-6641.
Voltolini, M., Zandomeneghi, D., Mancini, L., and Polacci, M. (2011) Texture analysis of volcanic rock samples: Quantitative study of crystals and vesicles shape preferred orientation from X-ray microtomography data. Journal of Volcanology and Geothermal Research, 202, 83-95.
Wang, Y., Lesher, C., Fiquet, G., Rivers, M.L., Nishiyama, N., Siebert, J., Roberts, J., Morard, G, Gaudio, S., Clark, A., Watson, H., Menguy, N., and Guyot, F. (2011) In situ high-pressure and high-temperature X-ray microtomographic imaging during large deformation: a new technique for studying mechanical behavior of multiphase composites. Geosphere, 7, 40-53.
Whitney, D.L., Goergen, E.T., Ketcham, R.A., and Kunze, K. (2008) Formation of garnet polycrystals during metamorphic crystallization. Journal of Metamorphic Geology, 26, 365-383.
Wittmann, A., Friedrich, J.M., Troiano, J., Macke, R.J., Britt, D.T., Swindle, T.D., Weirich, J.R., Rumble, D. III, Lasue, J., and Kring, D.A. (2011) H /L chondrite LaPaz Icefield 031047 - A feather of Icarus? Geochimica et Cosmochimica Acta, 75, 6140-6159.
Yang, P., Ehajjar, R. (2014) Porosity Content Evaluation in Carbon-Fiber/Epoxy Composites Using X-ray Computed Tomography. Polymer-Plastics Technology and Engineering, 53, 217-222.
Yuan, Q. (2007) Experimental and modeling studies of contaminant transport in capped sediments during gas bubble ebullition. PhD dissertation, Chemical Engineering, Louisiana State University, 207 p.
Zolensky, M., Herrin, J., Mikouchi, T., Ohsumi, K., Friedrich, J., Steele, A., Rumble, D., Fries, M., Sandford, S., Milam, S., Hagiya, K., Takeda, H., Satake, W., Kurihara, T., Colbert, M., Hanna, R., Maisano, J., Ketcham, Goodrich, C., Le, L., Robinson, G., Martinez, J., Ross, K., Jenniskens, P., Shaddad, M.H. (2010) Mineralogy and petrography of the Almahata Sitta ureilite. Meteoritics & Planetary Science, 45, 1618-1637.
Wang, Y., Uchida, T., Westferro, F., Rivers, M.L., Nishiyama, N., Gebhardt, J., Lesher, C.E., and Sutton, S.R. (2005) High-pressure x-ray tomography microscope: synchrotron computed microtomography at high pressure and temperature. Review of Scientific Instruments, 76, 073709.

Zucali, M., Voltolini, M., Ouladdiaf, B., Mancini, L., Chateigner, D. (2014) The 3D quantitative lattice and shape preferred orientation of a mylonitised metagranite from Monte Rosa (Western Alps): Combining neutron diffraction texture analysis and synchrotron X-ray microtomography. Journal of Structural Geology, 63, 91-105.

Papers Utilizing Quant3D

Bernasconi, A., and Cosmi, F. (2008) Analisi sperimentale dell'anisotropia in prossimità di intagli in materie plastiche rinforzate con fibre corte. XXXVII Convegno Nazionale, Università di Roma, Italy, 10 p.

Bernasconi, A., and Cosmi, F. (2011) Analysis of the dependence of the tensile behavior of a short fibre reinforced polyamide upon fibre volume fraction, length and orientation. Procedia Engineering, 10, 2129-2134.
Bernasconi, A., Cosmi, F., and Dreossi, D. (2008) Local anisotropy analysis of injection moulded fibre reinforced polymer composites. Composites Science and Technology, 68, 2574-2581.
Bernasconi, A., Cosmi, F., and Dreossi, D. (2008) Analisi dell’anisotropia microstrutturale in materiali compositi rinforzati con fibre corte. Frattura ed Integrità Strutturale, 3, 18-29.
Bernasconi, A., Broznic, M., Cosmi, F., Dreossi, D., and Tromba, G. (2007) Resistenza e anisotropia in compositi rinforzati con fibre corte: analisi mediante tomografia con luce di sincrotrone. Atti del Congresso IGF 19, Milan, Italy, 8 p.
Bernasconi, A., Cosmi, F., and Zappa, E. (2010) Combined effect of notches and fibre orientation on fatigue behavior of short fiber reinforced polyamide. Strain, 46, 435-445.
Bhasin, A., Izadi, A., and Bedgaker, S. (2010) Three dimensional distribution of the mastic in asphalt composites. Construction and Building Materials, 25, 4079-4087.
Cosmi, F., and Bernasconi, A. (2010) Elasticity of short fibre reinforced polyamide: morphological and numerical analysis of fibre orientation effects. Materials Engineering, 17, 6-10.
Cosmi, F., Scozzese, S., and Bernasconi, A. (2010) Studio del danneggiamento mediante tomografia in luce del sincrotrone: impatto di un cono d'ombra sulla qualitá finale delle ricostruzioni. Frattura ed Integritá Strutturale, 13, 17-23.
Cosmi, F., Bernasconi, A., and Sodini, N. (2011) Phase contrast micro-tomography and morphological analysis of a chort carbon fibre reinforced polyamide. Composites Science and Technology, 71, 23-30.
Cotter, M.M., Loomis, D.A., Simpson, S.W., Latimer, B., and Hernandez, C.J. (2011) Human evolution and osteoporosis-related spinal fractures. PLoS ONE, 6(10), e26658.
Dal Ferro, N., Delmas, P., Duwig, C., Simonetti, G., and Morari, F. (2012) Coupling X-ray microtomography and mercury intrusion porosimetry to quantify aggregate structures of a cambisol under different fertilisation treatments. Soil and Tillage Research, 119, 13-21.
Dyess, J. E., Hansen, V. L., Goscinak, C. (2014) Constrains on vorticity and non-coaxial shear direction in Neoarchean L-S tectonites, an example from northern Minnesota, USA. Precambrian Research, 256, 189-200.
Fu, Y., Xie, H., Deng, B., Du, G., Chen, R., Xiao, T. (2014) Three-dimensional structure of polystyrene colloidal crystal by synchrotron radiation X-ray phase-contrast computed tomography. Materials Science & Processing, 115, 781-790.
Gosman, J.H., and Ketcham, R.A. (2009) Patterns in ontogeny of human trabecular bone from SunWatch Village in the prehistoric Ohio Valley: general features of microarchitectural change. American Journal of Physical Anthropology, 138, 318-332.
Griffin, N.L. (2008) Bone architecture of the hominin second proximal pedal phalanx: a preliminary investigation. Journal of Human Evolution, 54, 162-168.
Griffin, N.L., D'Août, K., Ryan, T.M., Richmond, B.G., Ketcham, R.A., Postnov, A. (2010) Comparative forefoot trabecular bone architecture in extant hominids. Journal of Human Evolution, 59, 202-213.
Hill, C.A. (2011) Ontogenetic change in temporal bone pneumatization in humans. The Anatomical Record, 294, 1103-1115.
Hill, C.A., and Richtsmeier, J.T. (2008) A quantitative method for the evaluation of three-dimensional structure of temporal bone pneumatization. Journal of Human Evolution, 55, 682-690.
Ketcham, R.A. (2005b) Three-dimensional textural measurements using high-resolution X-ray computed tomography. Journal of Structural Geology, 27, 1217-1228.
Ketcham, R.A., and Ryan, T. (2004) Quantification and visualization of anisotropy in trabecular bone. Journal of Microscopy, 213, 158-171.
Maga, M., Kappelman, J., Ryan, T.M., and Ketcham, R.A. (2006) Preliminary observations on the calcaneal trabecular microarchitecture of extant large-bodied hominoids. American Journal of Physical Anthropology, 129, 410-417.
Ryan, T.M., Colbert, M., Ketcham, R.A., and Vinyard, C.J. (2009) Trabecular bone structure in the mandibular condyles of gouging and nongouging platyrrhine primates. American Journal of Physical Anthropology, 141, 583-593.
Ryan, T.M., and Ketcham, R.A. (2005) Angular orientation of trabecular bone in the femoral head and its relationship to hip joint loads in leaping primates. Journal of Morphology, 265, 249-263.
Ryan, T.M., and Walker, A. (2010) Trabecular bone structure in the humeral and femoral heads of anthropoid primates. The Anatomical Record, 293, 719-729.
Schopa, A., Floess, D., de Saint Blanquat, M., Annen, C., Launeau, P. (In Press) The Relation between Magnetite and Silicate Fabric in Granitoids of the Adamello Batholith. Tectonophysics.
Skedros, J.G., Knight, A.N., Farnsworth, R.W., and Bloebaum, R.D. (2012) Do regional modifications in tissue mineral content and microscopic mineralization heterogeneity adapt trabecular bone tracts for habitual bending? Analysis in the context of trabecular architecture of deer calcanei. Journal of Anatomy, 220, 242-255.
Wang, Q., Smith, A.L., Strait, D.S., Wright, B.W., Richmond, B.G., Grosse, I.R., Byron, C.D., and Zapata, U. (2010) The global impact of sutures assessed in a finite element model of a macaque cranium. The Anatomical Record, 293, 1477-1491.

Papers Utilizing Align3D

Ketcham, R.A., and Iturrino, G.J. (2005) Nondestructive high-resolution visualization and measurement of anisotropic effective porosity in complex lithologies using high-resolution X-ray computed tomography. Journal of Hydrology, 302, 92-106. Supplemental material: http://www.ctlab.geo.utexas.edu/pubs/ketcham&iturrino/k&i.htm

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