Imaging and modeling of pore scale processes in porous media using X-ray computed tomography and lattice Boltzmann solver

In der Erdöl– und Gasindustrie sind bildgebende Verfahren und Simulationen auf der Porenskala im Begriff Routineanwendungen zu werden. Ihr weiteres Potential lässt sich im Umweltbereich anwenden, wie z.B. für den Transport und Verbleib von Schadstoffen im Untergrund, die Speicherung von Kohlendioxid und dem natürlichen Abbau von Schadstoffen in Böden. Mit der Röntgen-Computertomografie (XCT) steht ein zerstörungsfreies 3D bildgebendes Verfahren zur Verfügung, das auch häufig für die Untersuchung der internen Struktur geologischer Proben herangezogen wird. Das erste Ziel dieser Dissertation war die Implementierung einer Bildverarbeitungstechnik, die die Strahlenaufhärtung der Röntgen-Computertomografie beseitigt und den Segmentierungsprozess dessen Daten vereinfacht. Das zweite Ziel dieser Arbeit untersuchte die kombinierten Effekte von Porenraumcharakteristika, Porentortuosität, sowie die Strömungssimulation und Transportmodellierung in Porenräumen mit der Gitter-Boltzmann-Methode. In einer zylindrischen geologischen Probe war die Position jeder Phase auf Grundlage der Beobachtung durch das Vorhandensein der Strahlenaufhärtung in den rekonstruierten Bildern, das eine radiale Funktion vom Probenrand zum Zentrum darstellt, extrahierbar und die unterschiedlichen Phasen ließen sich automatisch segmentieren. Weiterhin wurden Strahlungsaufhärtungeffekte von beliebig geformten Objekten durch einen Oberflächenanpassungsalgorithmus korrigiert. Die Methode der „least square support vector machine” (LSSVM) ist durch einen modularen Aufbau charakterisiert und ist sehr gut für die Erkennung und Klassifizierung von Mustern geeignet. Aus diesem Grund wurde die Methode der LSSVM als pixelbasierte Klassifikationsmethode implementiert. Dieser Algorithmus ist in der Lage komplexe geologische Proben korrekt zu klassifizieren, benötigt für den Fall aber längere Rechenzeiten, so dass mehrdimensionale Trainingsdatensätze verwendet werden müssen. Die Dynamik von den unmischbaren Phasen Luft und Wasser wird durch eine Kombination von Porenmorphologie und Gitter Boltzmann Methode für Drainage und Imbibition Prozessen in 3D Datensätzen von Böden, die durch synchrotron-basierte XCT gewonnen wurden, untersucht. Obwohl die Porenmorphologie eine einfache Methode ist Kugeln in den verfügbaren Porenraum einzupassen, kann sie dennoch die komplexe kapillare Hysterese als eine Funktion der Wassersättigung erklären. Eine Hysterese ist für den Kapillardruck und die hydraulische Leitfähigkeit beobachtet worden, welche durch die hauptsächlich verbundenen Porennetzwerke und der verfügbaren Porenraumgrößenverteilung verursacht sind. Die hydraulische Konduktivität ist eine Funktion des Wassersättigungslevels und wird mit einer makroskopischen Berechnung empirischer Modelle verglichen. Die Daten stimmen vor allem für hohe Wassersättigungen gut überein. Um die Gegenwart von Krankheitserregern im Grundwasser und Abwässern vorhersagen zu können, wurde in einem Bodenaggregat der Einfluss von Korngröße, Porengeometrie und Fluidflussgeschwindigkeit z.B. mit dem Mikroorganismus Escherichia coli studiert. Die asymmetrischen und langschweifigen Durchbruchskurven, besonders bei höheren Wassersättigungen, wurden durch dispersiven Transport aufgrund des verbundenen Porennetzwerks und durch die Heterogenität des Strömungsfeldes verursacht. Es wurde beobachtet, dass die biokolloidale Verweilzeit eine Funktion des Druckgradienten als auch der Kolloidgröße ist. Unsere Modellierungsergebnisse stimmen sehr gut mit den bereits veröffentlichten Daten überein.

3D bloodstain pattern analysis: ballistic reconstruction of the trajectories of blood drops and determination of the centres of origin of the bloodstains

For crime scene investigation in cases of homicide, the pattern of bloodstains at the incident site is of critical importance. The morphology of the bloodstain pattern serves to determine the approximate blood source locations, the minimum number of blows and the positioning of the victim. In the present work, the benefits of the three-dimensional bloodstain pattern analysis, including the ballistic approximation of the trajectories of the blood drops, will be demonstrated using two illustrative cases. The crime scenes were documented in 3D, using the non-contact methods digital photogrammetry, tachymetry and laser scanning. Accurate, true-to-scale 3D models of the crime scenes, including the bloodstain pattern and the traces, were created. For the determination of the areas of origin of the bloodstain pattern, the trajectories of up to 200 well-defined bloodstains were analysed in CAD and photogrammetry software. The ballistic determination of the trajectories was performed using ballistics software. The advantages of this method are the short preparation time on site, the non-contact measurement of the bloodstains and the high accuracy of the bloodstain analysis. It should be expected that this method delivers accurate results regarding the number and position of the areas of origin of bloodstains, in particular the vertical component is determined more precisely than using conventional methods. In both cases relevant forensic conclusions regarding the course of events were enabled by the ballistic bloodstain pattern analysis.

Immediate Search in the IDE as an Example of Socio-Technical Congruence in Search-Driven Development

Search-driven development is mainly concerned with code reuse but also with code navigation and debugging. In this essay we look at search-driven navigation in the IDE. We consider Smalltalk-80 as an example of a programming system with search-driven navigation capabilities and explore its human factors. We present how immediate search results lead to a user experience of code browsing rather than one of waiting for and clicking through search results. We explore the socio-technical congruence of immediate search, ie unification of tasks and breakpoints with method calls, which leads to simpler and more extensible development tools. Eventually we conclude with remarks on the socio-technical congruence of search-driven development.

Seeing and identifying with a virtual body decreases pain perception

Pain and the conscious mind (or the self) are experienced in our body. Both are intimately linked to the subjective quality of conscious experience. Here, we used virtual reality technology and visuo-tactile conflicts in healthy subjects to test whether experimentally induced changes of bodily self-consciousness (self-location; self-identification) lead to changes in pain perception. We found that visuo-tactile stroking of a virtual body but not of a control object led to increased pressure pain thresholds and self-location. This increase was not modulated by the synchrony of stroking as predicted based on earlier work. This differed for self-identification where we found as predicted that synchrony of stroking increased self-identification with the virtual body (but not a control object), and positively correlated with an increase in pain thresholds. We discuss the functional mechanisms of self-identification, self-location, and the visual perception of human bodies with respect to pain perception.

Evaluation of a portable image overlay projector for the visualisation of surgical navigation data: phantom studies

Presenting visual feedback for image-guided surgery on a monitor requires the surgeon to perform time-consuming comparisons and diversion of sight and attention away from the patient. Deficiencies in previously developed augmented reality systems for image-guided surgery have, however, prevented the general acceptance of any one technique as a viable alternative to monitor displays. This work presents an evaluation of the feasibility and versatility of a novel augmented reality approach for the visualisation of surgical planning and navigation data. The approach, which utilises a portable image overlay device, was evaluated during integration into existing surgical navigation systems and during application within simulated navigated surgery scenarios.

More accurate component alignment in navigated total knee arthroplasty has no clinical benefit at 5-year follow-up

Computer navigation in total knee arthroplasty is somewhat controversial. We have previously shown that femoral component positioning is more accurate with computed navigation than with conventional implantation techniques, but the clinical impact of this is unknown. We now report the 5-year outcome of our previously reported 2-year outcome study.

Teaching the Millennial Generation in the Religious and Theological Studies Classroom

This essay provides an overview of the distinctive challenges presented to teaching and learning in religious and theological studies by the conditions and characteristics of “millennial” students. While the emerging literature on this generation is far from consistent, it is still instructive and important to engage, as students that are immersed in technology and social networking have different facilities and difficulties that educators would do well to carefully address and critically employ. Teachers in theological and religious studies are distinctly positioned to grapple with such conditions, particularly around the practices of identity formation, media literacy, and embodiment. Attention to the development of such practices engages key issues for both the millennial students and the religious and theological studies teacher: virtual reality, spiritual identity, globalization and violence, critical consumption and ethical creativity, focused and contemplative thinking, and intercultural and interpersonal respect.

Intraoperative three-dimensional fluoroscopic cholangiography

Precise intraoperative assessment of the architecture of the biliary tree could reduce lesions to intra- or extrahepatic bile ducts. The aim of this study was to test feasibility of intraoperative three-dimensional imaging during liver resections. Isocentric C-arm fluoroscopy acquires three-dimensional images during a 190 degrees orbital rotation. The bile ducts were displayed three-dimensionally by realtime rotational projections or multiplanar reconstructions. The technique was established ex vivo in a preserved cadaveric human liver. Intraoperative three-dimensional cholangiography was performed in five patients with centrally located liver malignancies. Complete data acquisition in 3 patients depicted precise anatomical details of the architecture of the biliary tree up to third order divisions. Biliary imaging can be improved by the application of real-time intraoperative three-dimensional cholangiography. For the development of computer-aided navigation in hepatobiliary procedures, this technique could be an important prerequisite for defining landmarks of the liver in a three-dimensional space.

Correspondence establishment in statistical modeling of shapes with arbitrary topology

Correspondence establishment is a key step in statistical shape model building. There are several automated methods for solving this problem in 3D, but they usually can only handle objects with simple topology, like that of a sphere or a disc. We propose an extension to correspondence establishment over a population based on the optimization of the minimal description length function, allowing considering objects with arbitrary topology. Instead of using a fixed structure of kernel placement on a sphere for the systematic manipulation of point landmark positions, we rely on an adaptive, hierarchical organization of surface patches. This hierarchy can be built on surfaces of arbitrary topology and the resulting patches are used as a basis for a consistent, multi-scale modification of the surfaces' parameterization, based on point distribution models. The feasibility of the approach is demonstrated on synthetic models with different topologies.

Magnetic resonance (MR) cholangiography: quantitative and qualitative comparison of 3.0 Tesla with 1.5 Tesla

OBJECTIVES: To determine quantitative and qualitative image quality in patients undergoing magnetic resonance (MR) cholangiography at 3.0 Tesla (T) compared with 1.5 T. MATERIALS AND METHODS: Fifty patients (30 women; mean age, 51 years) underwent MR cholangiography at 1.5 T; another 50 patients (25 women; mean age 51 years) were scanned at 3.0 T. MR sequence protocol consisted of breath-hold single-slice rapid acquisition with relaxation enhancement (RARE) and a respiratory-triggered 3D turbo spin echo (3D TSE) sequence. Maximum intensity projections were generated from the 3D TSE datasets. Contrast-to-noise ratio (CNR) measurements between the common bile duct (CBD), left and right intrahepatic duct (LHD, RHD), and periductal tissue were performed. Three radiologists assessed qualitatively the visibility of the CBD, LHD, and RHD and the overall diagnostic quality. RESULTS: Mean gain in CNR at 3.0 T versus 1.5 T in all 3 locations ranged for the RARE sequence from 7.7% to 38.1% and for the 3D TSE from 0.5% to 26.1% (P > 0.05 for all differences). Qualitative analysis did not reveal any significant difference between the 2 field strengths (P > 0.05). CONCLUSIONS: MR cholangiography at 3.0 T shows a trend toward higher CNR without improving image quality significantly.

Use of a 3D perfusion bioreactor with osteoblasts and osteoblast/endothelial cell co-cultures to improve tissue-engineered bone

The delivery of oxygen, nutrients, and the removal of waste are essential for cellular survival. Culture systems for 3D bone tissue engineering have addressed this issue by utilizing perfusion flow bioreactors that stimulate osteogenic activity through the delivery of oxygen and nutrients by low-shear fluid flow. It is also well established that bone responds to mechanical stimulation, but may desensitize under continuous loading. While perfusion flow and mechanical stimulation are used to increase cellular survival in vitro, 3D tissue-engineered constructs face additional limitations upon in vivo implantation. As it requires significant amounts of time for vascular infiltration by the host, implants are subject to an increased risk of necrosis. One solution is to introduce tissue-engineered bone that has been pre-vascularized through the co-culture of osteoblasts and endothelial cells on 3D constructs. It is unclear from previous studies: 1) how 3D bone tissue constructs will respond to partitioned mechanical stimulation, 2) how gene expression compares in 2D and in 3D, 3) how co-cultures will affect osteoblast activity, and 4) how perfusion flow will affect co-cultures of osteoblasts and endothelial cells. We have used an integrated approach to address these questions by utilizing mechanical stimulation, perfusion flow, and a co-culture technique to increase the success of 3D bone tissue engineering. We measured gene expression of several osteogenic and angiogenic genes in both 2D and 3D (static culture and mechanical stimulation), as well as in 3D cultures subjected to perfusion flow, mechanical stimulation and partitioned mechanical stimulation. Finally, we co-cultured osteoblasts and endothelial cells on 3D scaffolds and subjected them to long-term incubation in either static culture or under perfusion flow to determine changes in gene expression as well as histological measures of osteogenic and angiogenic activity. We discovered that 2D and 3D osteoblast cultures react differently to shear stress, and that partitioning mechanical stimulation does not affect gene expression in our model. Furthermore, our results suggest that perfusion flow may rescue 3D tissue-engineered constructs from hypoxic-like conditions by reducing hypoxia-specific gene expression and increasing histological indices of both osteogenic and angiogenic activity. Future research to elucidate the mechanisms behind these results may contribute to a more mature bone-like structure that integrates more quickly into host tissue, increasing the potential of bone tissue engineering.

Semi-automatic segmentation of fetal cardiac cavities: progress towards an automated fetal echocardiogram

OBJECTIVE: To develop a novel application of a tool for semi-automatic volume segmentation and adapt it for analysis of fetal cardiac cavities and vessels from heart volume datasets. METHODS: We studied retrospectively virtual cardiac volume cycles obtained with spatiotemporal image correlation (STIC) from six fetuses with postnatally confirmed diagnoses: four with normal hearts between 19 and 29 completed gestational weeks, one with d-transposition of the great arteries and one with hypoplastic left heart syndrome. The volumes were analyzed offline using a commercially available segmentation algorithm designed for ovarian folliculometry. Using this software, individual 'cavities' in a static volume are selected and assigned individual colors in cross-sections and in 3D-rendered views, and their dimensions (diameters and volumes) can be calculated. RESULTS: Individual segments of fetal cardiac cavities could be separated, adjacent segments merged and the resulting electronic casts studied in their spatial context. Volume measurements could also be performed. Exemplary images and interactive videoclips showing the segmented digital casts were generated. CONCLUSION: The approach presented here is an important step towards an automated fetal volume echocardiogram. It has the potential both to help in obtaining a correct structural diagnosis, and to generate exemplary visual displays of cardiac anatomy in normal and structurally abnormal cases for consultation and teaching.

A system for 3-D reconstruction of a patient-specific surface model from calibrated X-ray images

This paper presents a system for 3-D reconstruction of a patient-specific surface model from calibrated X-ray images. Our system requires two X-ray images of a patient with one acquired from the anterior-posterior direction and the other from the axial direction. A custom-designed cage is utilized in our system to calibrate both images. Starting from bone contours that are interactively identified from the X-ray images, our system constructs a patient-specific surface model of the proximal femur based on a statistical model based 2D/3D reconstruction algorithm. In this paper, we present the design and validation of the system with 25 bones. An average reconstruction error of 0.95 mm was observed.

High-resolution three-dimensional 3 T magnetic resonance angiography for the evaluation of experimental aneurysm in the rabbit

OBJECTIVE: The standard technique of two-dimensional intra-arterial digital subtraction angiography (2D-DSA) for the imaging of experimental rabbit aneurysms is invasive and has considerable surgical risks. Therefore, minimally invasive techniques ideally providing three-dimensional imaging for intervention planning and follow-up are needed. This study evaluates the feasibility and quality of three-dimensional 3-T magnetic resonance angiography (3D-3T-MRA) and compares 3D-3T-MRA with 2D-DSA in experimental aneurysms in the rabbit. METHOD: Three microsurgically created aneurysms in three rabbits were evaluated using 2D-DSA and 3D-3T-MRA. Imaging of the aneurysms was performed 2 weeks after creation using 2D-DSA and contrast-enhanced (CE) MRA. Measurements included aneurysm dome (length and width) and aneurysm neck. Aneurysm volumes were determined using CE-MRA. RESULTS: The measurements of the aneurysms' dimensions and the evaluation of vicinity vessels with both techniques showed a good correlation. The mean aneurysm length, aneurysm width and neck width measured with DSA (6.9, 4.1 and 2.8 mm, respectively) correlated with the measurements performed in 3D-3T-MRA (6.9, 4 and 2.5 mm, respectively). The mean aneurysm volumes measured with CE-MRA was 46.7 mm(3). CONCLUSION: 3D-3T CE-MRA is feasible and less invasive and is a safer imaging alternative to DSA for experimental aneurysm. Additionally, aneurysm technique this precise offers the possibility of repetitive 3D aneurysm volumetry for long-term follow-up studies after endovascular aneurysm occlusion.

Tackling Software Navigation Issues of the Smalltalk IDE

The IDE used in most Smalltalk dialects such as Pharo, Squeak or Cincom Smalltalk did not evolve significantly over the last years, if not to say decades. For other languages, for instance Java, the available IDEs made tremendous progress as Eclipse or NetBeans illustrate. While the Smalltalk IDE served as an exemplar for many years, other IDEs caught up or even overtook the erstwhile leader in terms of feature-richness, usability, or code navigation facilities. In this paper we first analyze the difficulty of software navigation in the Smalltalk IDE and second illustrate with concrete examples the features we added to the Smalltalk IDE to fill the gap to modern IDEs and to provide novel, improved means to navigate source space. We show that thanks to the agility and dynamics of Smalltalk, we are able to extend and enhance with reasonable effort the Smalltalk IDE to better support software navigation, program comprehension, and software maintenance in general. One such support is the integration of dynamic information into the static source views we are familiar with. Other means include easing the access to static information (for instance by better arranging important packages) or helping developers re-locating artifacts of interest (for example with a categorization system such as smart groups).