Characterizing Low-Permeable Granitic Rock from Micrometer to Centimeter Scale: X-ray Microcomputed Tomography, Confocal Laser Scanning Microscopy and 14C-PMMA Method

AbstractFirst results of combining X-ray microcomputer tomography (µCT), confocal laser-scanning microscopy (CLSM) and 14C-polymethylmethacrylate (14C-PMMA) impregnation techniques in the study of granitic rock samples are reported. Combining results of µCT and CLSM with those of the 14C-PMMA technique, the mineral-specific porosity and morphology of the open pore space, as well as its connectivity, could be analyzed from a micrometer up to a decimeter scale.Three different types of granite were studied. In two cases part of the micro-fissure and pore apertures were found to be in a micrometer scale, but in one case all grain-boundary openings were below the detection limit. Micrometer-scal…

The Effect of Tomography Imaging Artefacts on Structural Analysis and Numerical Permeability Simulations

Fluid flow phenomena in porous materials can be found in many important processes in nature and in society. In particular, fluid flow through a porous medium contribute to several technological problems, e.g. extraction of oil or gas from porous rocks, spreading of contaminants in fluid-saturated soils and certain separation processes, such as filtration (Torquato, 2001). In paper and wood industry single and multi phase fluid flow properties in porous media play important roles related to manufacturing process and product development. The general laws describing creeping fluid flows are well known. However, a detailed study of fluid flow in porous heterogeneous media is complicated. This i…

Statistical classification and proportion estimation - an application to a macroinvertebrate image database

We apply and compare a random Bayes forest classifier and three traditional classification methods to a dataset of complex benthic macroinvertebrate images of known taxonomical identity. Since in biomonitoring changes in benthic macroinvertebrate taxa proportions correspond to changes in water quality, their correct estimation is pivotal. As classification errors are passed on to the allocated proportions, we explore a correction method known as a confusion matrix correction. Classification methods were compared using the misclassification error and the χ2 distance measures of the true proportions to the allocated and to the corrected proportions. Using low misclassification error and small…

A prospect for computing in porous materials research: Very large fluid flow simulations

Abstract Properties of porous materials, abundant both in nature and industry, have broad influences on societies via, e.g. oil recovery, erosion, and propagation of pollutants. The internal structure of many porous materials involves multiple scales which hinders research on the relation between structure and transport properties: typically laboratory experiments cannot distinguish contributions from individual scales while computer simulations cannot capture multiple scales due to limited capabilities. Thus the question arises how large domain sizes can in fact be simulated with modern computers. This question is here addressed using a realistic test case; it is demonstrated that current …

Effects of diet-induced obesity and voluntary wheel running on the axial and peripheral skeleton microstructure in mice

Classification and retrieval on macroinvertebrate image databases

Aquatic ecosystems are continuously threatened by a growing number of human induced changes. Macroinvertebrate biomonitoring is particularly efficient in pinpointing the cause-effect structure between slow and subtle changes and their detrimental consequences in aquatic ecosystems. The greatest obstacle to implementing efficient biomonitoring is currently the cost-intensive human expert taxonomic identification of samples. While there is evidence that automated recognition techniques can match human taxa identification accuracy at greatly reduced costs, so far the development of automated identification techniques for aquatic organisms has been minimal. In this paper, we focus on advancing …

On-chip purification via liquid immersion of arc-discharge synthesized multiwalled carbon nanotubes

Arc-discharge synthesized multiwalled carbon nanotubes (AD-MWNT) have been proven to be of high quality, but their use is very limited due to difficulties in obtaining them in a clean and undamaged form. Here, we present a simple method that purifies raw AD-MWNT material in laboratory scale without damage, and that in principle can be scaled up. The method consists of depositing raw AD-MWNT material on a flat substrate and immersing the substrate slowly in water, whereby the surface tension force of the liquid–substrate contact line selectively sweeps away the larger amorphous carbon debris and leaves relatively clean MWNTs on the substrate. We demonstrate the utility of the method by prepa…

The number of contacts in random fibre networks

There is a wide range of materials that can be considered as nonwoven random networks of fibres. Such materials include glass-fibre mats, filters, various paper products and structural components of cells and tissues. The mechanical properties of these kinds of networks have been studied extensively for many decades. As many of such networks form more or less two-dimensional structures, they can, to a good approximation, be considered to consist of randomly distributed fibres or filaments connected at their crossings points. Recent development of the resolution of X-ray computed tomography have enabled imaging of the three dimensional structure of such materials with a resolution sufficient…

Microstructure, porosity and mineralogy around fractures in Olkiluoto bedrock

3D distributions of minerals and porosities were determined for rock-core samples that included water-conducting fractures. The analysis of these samples was performed using conventional petrography methods, C-14-PMMA porosity analysis and X-ray tomography. It seems that the properties of rock around a water-conducting fracture depend on so many uncorrelated factors that no clear pattern emerged even for rock samples with a given type of fracture. We can conclude, however, that the present combination of methods can be used to infer novel structural information about alteration zones adjacent to fracture surfaces.

Dynamics and interactions of parvoviral NS1 protein in the nucleus

Summary Nuclear positioning and dynamic interactions of viral proteins with nuclear substructures play essen- tial roles during infection with DNA viruses. Visual- ization of the intranuclear interactions and motility of the parvovirus replication protein (NS1) in living cells gives insight into specific parvovirus protein- cellular structure interactions. Confocal analysis of highly synchronized infected Norden Laboratory Feline Kidney cells showed accumulation of nuclear NS1 in discrete interchromosomal foci. NS1 fused with enhanced yellow fluorescence protein (NS1- EYFP) provided a marker in live cells for dynamics of NS1 traced by photobleaching techniques. Fluo- rescence Recovery after…

Interface Detection Using a Quenched-Noise Version of the Edwards-Wilkinson Equation

We report here a multipurpose dynamic-interface-based segmentation tool, suitable for segmenting planar, cylindrical, and spherical surfaces in 3D. The method is fast enough to be used conveniently even for large images. Its implementation is straightforward and can be easily realized in many environments. Its memory consumption is low, and the set of parameters is small and easy to understand. The method is based on the Edwards-Wilkinson equation, which is traditionally used to model the equilibrium fluctuations of a propagating interface under the influence of temporally and spatially varying noise. We report here an adaptation of this equation into multidimensional image segmentation, an…

Evaluating the performance of artificial neural networks for the classification of freshwater benthic macroinvertebrates

Abstract Macroinvertebrates form an important functional component of aquatic ecosystems. Their ability to indicate various types of anthropogenic stressors is widely recognized which has made them an integral component of freshwater biomonitoring. The use of macroinvertebrates in biomonitoring is dependent on manual taxa identification which is currently a time-consuming and cost-intensive process conducted by highly trained taxonomical experts. Automated taxa identification of macroinvertebrates is a relatively recent research development. Previous studies have displayed great potential for solutions to this demanding data mining application. In this research we have a collection of 1350 …

Dependence of thermal conductivity on structural parameters in porous samples

The in-plane thermal conductivity of porous sintered bronze plates was studied both experimentally and numerically. We developed and validated an experimental setup, where the sample was placed in vacuum and heated while its time-dependent temperature field was measured with an infrared camera. The porosity and detailed three-dimensional structure of the samples were determined by X-ray microtomography. Lattice-Boltzmann simulations of thermal conductivity in the tomographic reconstructions of the samples were used to correct the contact area between bronze particles as determined by image analysis from the tomographic reconstructions. Small openings in the apparent contacts could not be de…

A stochastic shape and orientation model for fibres with an application to carbon nanotubes

Methods are introduced for analysing the shape and orientation of planar fibres from greyscale images of fibrous systems. The sequence of image processing techniques needed for segmentation of fibres is described. The identified fibres were interpreted as deformed line segments for which two shape and two orientation parameters are estimated by the maximum likelihood method. The methods introduced are shown to perform quite well for simulated systems of deformed line segments with known properties. They were applied to TEM images of carbon nanotubes embedded in polycarbonate.

Effects of diet-induced obesity and voluntary wheel running on the microstructure of the murine distal femur

Abstract Background Obesity and osteoporosis, two possibly related conditions, are rapidly expanding health concerns in modern society. Both of them are associated with sedentary life style and nutrition. To investigate the effects of diet-induced obesity and voluntary physical activity we used high resolution micro-computed tomography (μCT) together with peripheral quantitative computed tomography (pQCT) to examine the microstructure of the distal femoral metaphysis in mice. Methods Forty 7-week-old male C57BL/6J mice were assigned to 4 groups: control (C), control + running (CR), high-fat diet (HF), and high-fat diet + running (HFR). After a 21-week intervention, all the mice were sacrifi…

TopoCell – An image analysis tool to study intracellular topography

Intrusion of nonwetting liquid in paper

The saturation curve of a sample of paper board was measured with mercury-intrusion porosimetry, and the three-dimensional structure of its pore space was determined by x-ray tomographic imaging. Ab initio numerical simulation of intrusion on the tomographic reconstruction, based on the lattice-Boltzmann method, was in excellent agreement with the measured saturation curve. A numerical invasion-percolation simulation in the same tomographic reconstruction showed good agreement with the lattice-Boltzmann simulation. The access function of the sample, determined from the saturation curve and the pore-throat distribution determined from the tomographic reconstruction, indicated that the ink-bo…

Cellulose nanofibrils prepared by gentle drying methods reveal the limits of helium ion microscopy imaging

TEMPO-oxidized cellulose nanofibrils (TCNFs) have unique properties, which can be utilised in many application fields from printed electronics to packaging. Visual characterisation of TCNFs has been commonly performed using Scanning Electron Microscopy (SEM). However, a novel imaging technique, Helium Ion Microscopy (HIM), offers benefits over SEM, including higher resolution and the possibility of imaging non-conductive samples uncoated. HIM has not been widely utilized so far, and in this study the capability of HIM for imaging of TCNFs was evaluated. Freeze drying and critical point drying (CPD) techniques were applied to preserve the open fibril structure of the gel-like TCNFs. Both dr…

Analysis of microtomographic images of porous heterogeneous materials

In this work, we study the phases of image processing chain of microtomographic imag- ing in order to obtain reliable results while optimizing the time spent on denoising and segmentation. We consider that the decisions made at the early phases of the processing chain are most important and the selection made there essentially determine the overall quality of imaging process. We also compare here various denoising method qualita- tively, however, we think that the pure noise removal ability is not the only requirement for noise removal in microtomographic images. By proper denoising we can affect selec- tion of segmentation methods and, thus, also the quality of the analysis. Additionally, …

Enlarged PLIN5-uncoated lipid droplets in inner regions of skeletal muscle type II fibers associate with type 2 diabetes

Skeletal muscle physiology remains of paramount importance in understanding insulin resistance. Due to its high lipid turnover rates, regulation of intramyocellular lipid droplets (LDs) is a key factor. Perilipin 5 (PLIN5) is one of the most critical agents in such regulation, being often referred as a protector against lipotoxicity and consequent skeletal muscle insulin resistance. We examined area fraction, size, subcellular localization and PLIN5 association of LDs in two fiber types of type 2 diabetic (T2D), obese (OB) and healthy (HC) individuals by means of fluorescence microscopy and image analysis. We found that T2D type II fibers have a significant sub-population of large and inter…

Effects of diet-induced obesity and voluntary wheel running on the microstructure of the murine distal femur

Background. Obesity and osteoporosis, two possibly related conditions, are rapidly expanding health concerns in modern society. Both of them are associated with sedentary life style and nutrition. To investigate the effects of diet-induced obesity and voluntary physical activity we used high resolution micro-computed tomography (μCT) together with peripheral quantitative computed tomography (pQCT) to examine the microstructure of the distal femoral metaphysis in mice. Methods. Forty 7-week-old male C57BL/6J mice were assigned to 4 groups: control (C), control + running (CR), high-fat diet (HF), and high-fat diet + running (HFR). After a 21-week intervention, all the mice were sacrificed and…