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).
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.
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