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, ITT 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, though downloading does require registering with ITT. Align3D requires a fully licensed version of IDL to use.

Blob3D

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).

Quant3D

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.

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).

Align3D

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

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.

References

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.
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).
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., 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., 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., 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.
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.
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.
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, Online First.
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.
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., 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.
Gopalakrishnan, K., Ceylan, H., and Inanc, F. (2007) Using X-ray computed tomography to study paving materials. Construction Materials, 160, 15-23.
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.
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.
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.
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, in press.
Ketcham, R.A. (2005) Computational methods for quantitative analysis of three-dimensional features in geological specimens. Geosphere, 1, 32-41.
Ketcham, R.A. (2005) Three-dimensional textural measurements using high-resolution X-ray computed tomography. Journal of Structural Geology, 27, 1217-1228.
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
Ketcham, R.A., and Ryan, T. (2004) Quantification and visualization of anisotropy in trabecular bone. Journal of Microscopy, 213, 158-171.
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., 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.
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.
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.
Mote, A.S., Kyle, J.R., Ketcham, R.A., Melker, M.D., Jahraus, M.J., Brown, T.R., and Wawrzyniec, T.F. (2005) High-resolution X-ray computed tomography investigations of high grade gold ore zones in the Cripple Creek District, Colorado, in Rhoden, H.N., Steininger, R.C., and Vikre, P.G., eds., Geological Society of Nevada Symposium 2005: Window to the World, Reno, Nevada, May 2005, 1169-1175.
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.
Polacci, M., Baker, D.R., Mancini, L., Tromba, G., and Zanini, F. (2006) Three-dimensioanl investigation of volcanic textures by X-ray microtomography and implications for conduit processes. Geophysical Research Letters, 33, L13312.
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.
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., 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. (2006) Characterizing pore-scale configuraion 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.
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.
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.
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.
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.
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.
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.