W. Brent Lindquist

Pore and throat size distributions measured from synchrotron X-ray tomographic images of Fontainebleau sandstones

The three-dimensional geometry and connectivity of pore space controls the hydraulic transport behavior of crustal rocks. We report on direct measurement of flow-relevant geometrical properties of the void space in a suite of four samples of Fontainebleau sandstone ranging from 7.5 to 22% porosity. The measurements are obtained from computer analysis of three-dimensional, synchrotron X-ray computed microtomographic images. We present measured distributions of coordination number, channel length, throat size, and pore volume and of correlations between throat size/pore volume and nearest-neighbor pore volume/pore volume determined for these samples. In order to deal with the ambiguity of where a nodal pore ends and a channel begins, we apportion the void space volume solely among nodal pores, with the channel throat surfaces providing the nodal pore delineations. Pore channels thus have length but no associated volume; channel length is defined by nodal pore center to nodal pore center distance. For a sample of given porosity our measurements show that the pore coordination number and throat area are exponentially distributed, whereas the channel length and nodal pore volume follow gamma and lognormal distributions, respectively. Our data indicate an overall increase in coordination number and shortening of pore channel length with increasing porosity. The average coordination number ranges from 3.4 to 3.8; the average channel length ranges from 200 to 130 μm. Average throat area increases from 1600 to 2200 μm 2 with increasing porosity, while average pore volume remains essentially unchanged at around 0.0004 mm 3 .

Image thresholding by indicator kriging

We consider the problem of segmenting a digitized image consisting of two univariate populations. Assume a priori knowledge allows incomplete assignment of voxels in the image, in the sense that a fraction of the voxels can be identified as belonging to population II/sub 0/, a second fraction to II/sub 1/, and the remaining fraction have no a priori identification. Based upon estimates of the short length scale spatial covariance of the image, we develop a method utilizing indicator kriging to complete the image segmentation.

Medial axis analysis of void structure in three-dimensional tomographic images of porous media

We introduce the medial axis as a tool in the analysis of geometric structure of void space in porous media. The medial axis traces the fundamental geometry of the void pathways. We describe an algorithm for generating the medial axis of the void structure from digitized three dimensional images of porous media obtained from X ray CAT scans. The medial axis is constructed during an iterative erosion procedure which, at each step, replaces the image of the void structure with a smaller version obtained by eroding its surface layer of voxels. The algorithm is applied to high (5 μm) resolution microtomographic images of two rock chips (Berea sandstone and Danish chalk) and a sample of uniform (100 μm) diameter, packed glass beads. We statistically investigate several geometrical properties of the structure of the medial axes obtained. The first is the distribution of relative volumes in each erosion layer of the void space. We find the distributions to be exponential for the two real rock samples and normal for the packed glass beads. The second property investigated is the distribution of volumes of disconnected segments of the medial axis which are in one-to-one correspondence with disconnected void segments of the sample. We find indications for a universal power law behavior governing the distribution of volumes of the smallest disconnected pieces. The final behavior studied is a geometric tortuosity as measured by shortest paths through the medial axis. This tortuosity distribution appears well described by a gamma distribution.

An image analysis algorithm for dendritic spines

The structure of neuronal dendrites and their spines underlie the connectivity of neural networks. Dendrites, spines, and their dynamics are shaped by genetic programs as well as sensory experience. Dendritic structures and dynamics may therefore be important predictors of the function of neural networks. Based on new imaging approaches and increases in the speed of computation, it has become possible to acquire large sets of high-resolution optical micrographs of neuron structure at length scales small enough to resolve spines. This advance in data acquisition has not been accompanied by comparable advances in data analysis techniques; the analysis of dendritic and spine morphology is still accomplished largely manually. In addition to being extremely time intensive, manual analysis also introduces systematic and hard-to-characterize biases. We present a geometric approach for automatically detecting and quantifying the three-dimensional structure of dendritic spines from stacks of image data acquired using laser scanning microscopy. We present results on the measurement of dendritic spine length, volume, density, and shape classification for both static and timelapse images of dendrites of hippocampal pyramidal neurons. For spine length and density, the automated measurements in static images are compared with manual measurements. Comparisons are also made between automated and manual spine length measurements for a time-series data set. The algorithm performs well compared to a human analyzer, especially on time-series data. Automated analysis of dendritic spine morphology will enable objective analysis of large morphological data sets. The approaches presented here are generalizable to other aspects of neuronal morphology.

Chronic alcohol drinking alters neuronal dendritic spines in the brain reward center nucleus accumbens.

Alcohol is known to affect glutamate transmission. However, how chronic alcohol affects the synaptic structure mediating glutamate transmission is unknown. Repeated alcohol exposure in a subject with familial alcoholic history often leads to alcohol addiction. The current study adopts alcohol-preferring rats, which are known to develop high drinking. Two-photon microscopy analysis indicates that chronic alcohol of 14 weeks either, under continuous alcohol (C-Alc) or with repeated deprivation (RD-Alc), causes dysmorphology--thickened, beaded, and disoriented dendrites that are reminiscent of reactive astrocytes--in a subpopulation of medium spiny neurons. The density of dendritic spines was found differentially lower in the nucleus accumbens of RD-Alc and C-Alc groups as compared with those of Water groups. Large-sized spines and multiple-headed spines were increased in the RD-Alc group. The NMDA receptor subunit NR1 proteins, as analyzed with Western blot, were upregulated in C-Alc, but not in RD-Alc. The upregulated NMDA receptor subunits of NR1 however, are predominantly a splice variant isoform with truncated exon 21, which is required for membrane-bound trafficking or anchoring into a spine synaptic site. These maladaptations may contribute to the transformation of spines. The changes, in density and head-size of spines and the corresponding NMDA receptors, demonstrated an alteration of microcircuitry for glutamate reception. The current study demonstrates for the first time that chronic alcohol exposure causes structural alteration of dendrites and their spines in the key reward brain region in animals that have a genetic background leading to alcohol addiction.

Automated algorithms for multiscale morphometry of neuronal dendrites

We describe the synthesis of automated neuron branching morphology and spine detection algorithms to provide multiscale three-dimensional morphological analysis of neurons. The resulting software is applied to the analysis of a high-resolution (0.098 m 0.098 m 0.081 m) image of an entire pyramidal neuron from layer III of the superior temporal cortex in rhesus macaque monkey. The approach provides a highly automated, complete morphological analysis of the entire neuron; each dendritic branch segment is characterized by several parameters, including branch order, length, and radius as a function of distance along the branch, as well as by the locations, lengths, shape classification (e.g., mushroom, stubby, thin), and density distribution of spines on the branch. Results for this automated analysis are compared to published results obtained by other computer-assisted manual means.

Direct observations of three dimensional growth of hydrates hosted in porous media

The visualization of time-resolved three-dimensional growth of tetrahydrofuran hydrates with glass spheres of uniform size as porous media using synchrotron x-ray computed microtomography is presented. The images of hydrate patches, formed from excess tetrahydrofuran in aqueous solution, show random nucleation and growth concomitant with grain movement but independent of container-wall effect. Away from grain surfaces, hydrate surface curvature was convex showing that liquid, not hydrate, was the wetting phase, similar to ice growth in porous media. The extension of the observed behavior to methane hydrates could have implications in understanding their role in seafloor stability and climate change.

Quantitative analysis of three-dimensional x-ray tomographic images

The leading X-ray computed microtomographic imaging facilities can now provide 10243 voxel images of rock and other porous media samples at a voxel resolution of under 5 microns. Such data sets are extremely rich in information, and overwhelming in size; a 10243 data set corresponds to a gigabyte of character data. Automated computer analysis is necessary in order to extract quantitative information from such images. In this paper we discuss automated extraction of geometrical features using computerized image analysis. Typical algorithms required include segmentation to identify the material type of each voxel in the image; medial axis reduction of objects in the image to provide a skeleton enabling efficient searching and geometrical characterization as well as a network for the application of graph theoretic tools; feature extraction; measurement of length, cross sectional area and volume; and stochastic characterization of measured properties. With current memory limitations in desktop workstations, data sets beyond 5123 voxels in size require parallelization of the algorithms.

An algorithm for neurite outgrowth reconstruction

We present a numerical method which provides the ability to analyze digitized microscope images of retinal explants and quantify neurite outgrowth. Few parameters are required as input and limited user interaction is necessary to process an entire experiment of images. This eliminates fatigue related errors and user-related bias common to manual analysis. The method does not rely on stained images and handles images of variable quality. The algorithm is used to determine time and dose dependent, in vitro, neurotoxic effects of 1 GeV per nucleon iron particles in retinal explants. No neurotoxic effects are detected until 72 h after exposure; at 72 h, significant reductions of neurite outgrowth occurred at doses higher than 10 cGy.

Use of X-ray computed microtomography to understand why gels reduce relative permeability to water more than that to oil

Abstract X-ray computed microtomography (XMT) was used to investigate why gels reduce relative permeability to water more than that to oil in strongly water-wet Berea sandstone. XMT allows saturation differences to be monitored for individual pores during various stages of oil, water, and gelant flooding. The method also characterizes distributions of pore size, aspect ratio, and coordination number for the porous media. We studied a Cr(III) acetate–HPAM gel that reduced permeability to water (at Sor) by a factor 80–90 times more than that to oil (at Swr). In Berea, the gel caused disproportionate permeability reduction by trapping substantial volumes of oil that remained immobile during water flooding (i.e., 43.5% Sor before gel placement versus 78.7% Sor after gel placement). With this high trapped oil saturation, water was forced to flow through narrow films, through the smallest pores, and through the gel itself. In contrast, during oil flooding, oil pathways remained relatively free from constriction by the gel.