Parallel unfolding and visualization of curved surfaces extracted from large three-dimensional volumes

Although many three-dimensional (3D) medical imaging visualization methods exist, 3D volume slicing remains the most commonly used technique for visualizing medical data from modalities such as CT, MRI, and PET. We propose to extend the possibilities of oblique slicing to developable curved surfaces that can be flattened and displayed in two dimensions without deformation. Such surfaces can be used to follow curved anatomical structures while preserving distance metrics at visualization time. They may also be useful for the staging of tumors, i.e., to evaluate the spatial extension of a tumor. We propose an out of core algorithm that runs in parallel on a multi-PC architecture and is able to extract surfaces from very large 3D datasets such as the visible human data set (man: 13 GB, woman: 49 GB). Experimental performance results are presented which demonstrate that parallel surface extraction is scalable and has a reasonable overhead compared with traditional oblique planar slicing. Surface extraction is made available to the public as one of the services offered by EPFLs visible human web server (http://visiblehuman.epfl.ch

A variational approach for viewpoint-based visibility maximization

We present a variational method for unfolding of the cortex based on a user-chosen point of view as an alternative to more traditional global flattening methods, which incur more distortion around the region of interest. Our approach involves three novel contributions. The first is an energy function and its corresponding gradient flow to measure the average visibility of a region of interest of a surface from a given viewpoint. The second is an additional energy function and flow designed to preserve the 3D topology of the evolving surface. This latter contribution receives significant focus in this thesis as it is crucial to obtain the desired unfolding effect derived from the first energy functional and flow. Without it, the resulting topology changes render the unconstrained evolution uninteresting for the purpose of cortical visualization, exploration, and inspection. The third is a method that dramatically improves the computational speed of the 3D topology-preservation approach by creating a tree structure of the triangulated surface and using a recursion technique.Ph.D.Committee Chair: Allen R. Tannenbaum; Committee Member: Anthony J. Yezzi; Committee Member: Gregory Turk; Committee Member: Joel R. Jackson; Committee Member: Patricio A. Vel

Computerized Analysis of Magnetic Resonance Images to Study Cerebral Anatomy in Developing Neonates

The study of cerebral anatomy in developing neonates is of great importance for the understanding of brain development during the early period of life. This dissertation therefore focuses on three challenges in the modelling of cerebral anatomy in neonates during brain development. The methods that have been developed all use Magnetic Resonance Images (MRI) as source data. To facilitate study of vascular development in the neonatal period, a set of image analysis algorithms are developed to automatically extract and model cerebral vessel trees. The whole process consists of cerebral vessel tracking from automatically placed seed points, vessel tree generation, and vasculature registration and matching. These algorithms have been tested on clinical Time-of- Flight (TOF) MR angiographic datasets. To facilitate study of the neonatal cortex a complete cerebral cortex segmentation and reconstruction pipeline has been developed. Segmentation of the neonatal cortex is not effectively done by existing algorithms designed for the adult brain because the contrast between grey and white matter is reversed. This causes pixels containing tissue mixtures to be incorrectly labelled by conventional methods. The neonatal cortical segmentation method that has been developed is based on a novel expectation-maximization (EM) method with explicit correction for mislabelled partial volume voxels. Based on the resulting cortical segmentation, an implicit surface evolution technique is adopted for the reconstruction of the cortex in neonates. The performance of the method is investigated by performing a detailed landmark study. To facilitate study of cortical development, a cortical surface registration algorithm for aligning the cortical surface is developed. The method first inflates extracted cortical surfaces and then performs a non-rigid surface registration using free-form deformations (FFDs) to remove residual alignment. Validation experiments using data labelled by an expert observer demonstrate that the method can capture local changes and follow the growth of specific sulcus

Industrial product design by using two-dimensional material in the context of origamic structure and integrity

Thesis (Master)--Izmir Institute of Technology, Izmir, 2004Includes bibliographical references (leaves: 115)Text in English; Abstract: Turkish and English.xiii, 118 leavesThroughout the history of industrial product design, there have always been attempts to shape everyday objects from a single piece of semi-finished industrial materials such as plywood, sheet metal, plastic sheet and paper-based sheet. One of the ways to form these two-dimensional materials into three-dimensional products is bending following cutting. Similar concepts of this spatial transformation are encountered in the origami form, which has a planar surface in unfolded state, then transforms to a three-dimensional state by folding or by folding following cutting. If so, conceptually it may be useful to think of one-axis bending, which is a manufacturing technique, is somewhat similar to folding paper.In this regard, the studies in the scope of computational origami, which light the way for real-world problems such as how sheets of material will behave under stress, have applications especially in .manufacturing phase. of industrial product design.Besides manufacturing phase, origami design is also used as a product design tool either in .concept creating phase. (in the context of its concepts) or in 'form creating phase' (in the context of its design principles).In this thesis, the designing of industrial products, which are made from sheet material, is presented in a framework that considers the origami design. In the theoretical framework, evolutionary progression of origami design is discussed briefly in order to comprehend the situation of origami design in distinct application fields.Moreover, the elements, principles, basics of origami design and origamic structures are generally introduced. The theoretical framework is completed with the descriptions of the concepts on origami design and origamic structures. In the practical framework, typical applications that have origamic structures in distinct industrial product fields are exemplified. Furthermore, sheet materials and their bending process are taken up separately. By means of its excessive advantages, sheet metal bending is particularly emphasized. The practical framework is completed with several case studies base on sheet metal bending. Finally, the study is concluded with the evaluation of the origamic-structured product in respect of good design principles. Furthermore, designing by considering origami design is recommended to designer to design a good industrial product

A four-dimensional probabilistic atlas of the human brain

The authors describe the development of a four-dimensional atlas and reference system that includes both macroscopic and microscopic information on structure and function of the human brain in persons between the ages of 18 and 90 years. Given the presumed large but previously unquantified degree of structural and functional variance among normal persons in the human population, the basis for this atlas and reference system is probabilistic. Through the efforts of the International Consortium for Brain Mapping (ICBM), 7,000 subjects will be included in the initial phase of database and atlas development. For each subject, detailed demographic, clinical, behavioral, and imaging information is being collected. In addition, 5,800 subjects will contribute DNA for the purpose of determining genotype-phenotype-behavioral correlations. The process of developing the strategies, algorithms, data collection methods, validation approaches, database structures, and distribution of results is described in this report. Examples of applications of the approach are described for the normal brain in both adults and children as well as in patients with schizophrenia. This project should provide new insights into the relationship between microscopic and macroscopic structure and function in the human brain and should have important implications in basic neuroscience, clinical diagnostics, and cerebral disorders

Author response

Many pathogenic bacteria produce pore-forming toxins to attack and kill human cells. We have determined the 4.5 Å structure of the ~2.2 MDa pore complex of pneumolysin, the main virulence factor of Streptococcus pneumoniae, by cryoEM. The pneumolysin pore is a 400 Å ring of 42 membrane-inserted monomers. Domain 3 of the soluble toxin refolds into two ~85 Å β-hairpins that traverse the lipid bilayer and assemble into a 168-strand β-barrel. The pore complex is stabilized by salt bridges between β-hairpins of adjacent subunits and an internal α-barrel. The apolar outer barrel surface with large sidechains is immersed in the lipid bilayer, while the inner barrel surface is highly charged. Comparison of the cryoEM pore complex to the prepore structure obtained by electron cryo-tomography and the x-ray structure of the soluble form reveals the detailed mechanisms by which the toxin monomers insert into the lipid bilayer to perforate the target membrane

Visual analytics of movement: An overview of methods, tools and procedures

Analysis of movement is currently a hot research topic in visual analytics. A wide variety of methods and tools for analysis of movement data has been developed in recent years. They allow analysts to look at the data from different perspectives and fulfil diverse analytical tasks. Visual displays and interactive techniques are often combined with computational processing, which, in particular, enables analysis of a larger number of data than would be possible with purely visual methods. Visual analytics leverages methods and tools developed in other areas related to data analytics, particularly statistics, machine learning and geographic information science. We present an illustrated structured survey of the state of the art in visual analytics concerning the analysis of movement data. Besides reviewing the existing works, we demonstrate, using examples, how different visual analytics techniques can support our understanding of various aspects of movement

A four-dimensional probabilistic atlas of the human brain

The authors describe the development of a four-dimensional atlas and reference system that includes both macroscopic and microscopic information on structure and function of the human brain in persons between the ages of 18 and 90 years. Given the presumed large but previously unquantified degree of structural and functional variance among normal persons in the human population, the basis for this atlas and reference system is probabilistic. Through the efforts of the International Consortium for Brain Mapping (ICBM), 7,000 subjects will be included in the initial phase of database and atlas development. For each subject, detailed demographic, clinical, behavioral, and imaging information is being collected. In addition, 5,800 subjects will contribute DNA for the purpose of determining genotype– phenotype–behavioral correlations. The process of developing the strategies, algorithms, data collection methods, validation approaches, database structures, and distribution of results is described in this report. Examples of applications of the approach are described for the normal brain in both adults and children as well as in patients with schizophrenia. This project should provide new insights into the relationship between microscopic and macroscopic structure and function in the human brain and should have important implications in basic neuroscience, clinical diagnostics, and cerebral disorders

Sub-pixel Registration In Computational Imaging And Applications To Enhancement Of Maxillofacial Ct Data

In computational imaging, data acquired by sampling the same scene or object at different times or from different orientations result in images in different coordinate systems. Registration is a crucial step in order to be able to compare, integrate and fuse the data obtained from different measurements. Tomography is the method of imaging a single plane or slice of an object. A Computed Tomography (CT) scan, also known as a CAT scan (Computed Axial Tomography scan), is a Helical Tomography, which traditionally produces a 2D image of the structures in a thin section of the body. It uses X-ray, which is ionizing radiation. Although the actual dose is typically low, repeated scans should be limited. In dentistry, implant dentistry in specific, there is a need for 3D visualization of internal anatomy. The internal visualization is mainly based on CT scanning technologies. The most important technological advancement which dramatically enhanced the clinician\u27s ability to diagnose, treat, and plan dental implants has been the CT scan. Advanced 3D modeling and visualization techniques permit highly refined and accurate assessment of the CT scan data. However, in addition to imperfections of the instrument and the imaging process, it is not uncommon to encounter other unwanted artifacts in the form of bright regions, flares and erroneous pixels due to dental bridges, metal braces, etc. Currently, removing and cleaning up the data from acquisition backscattering imperfections and unwanted artifacts is performed manually, which is as good as the experience level of the technician. On the other hand the process is error prone, since the editing process needs to be performed image by image. We address some of these issues by proposing novel registration methods and using stonecast models of patient\u27s dental imprint as reference ground truth data. Stone-cast models were originally used by dentists to make complete or partial dentures. The CT scan of such stone-cast models can be used to automatically guide the cleaning of patients\u27 CT scans from defects or unwanted artifacts, and also as an automatic segmentation system for the outliers of the CT scan data without use of stone-cast models. Segmented data is subsequently used to clean the data from artifacts using a new proposed 3D inpainting approach

Development of fluorescence lifetime measurement techniques for use in microfluidic channels

Fluorescence lifetime measurements are a powerful tool in biomedical research and advances in detection technology make them ideally suited for the study of biomolecular interactions. Time-resolved techniques, compared to more conventional methods, provide improved precision and contrast in the monitoring of complex biological processes. Fluorescence lifetimes are extracted by using time-correlated single-photon counting, which offers single photon sensitivity, high temporal resolution and excellent signal to noise ratio. Furthermore, combining this technique with microfluidics offers unprecedented advantages. For example, in analytical applications, apart from the high sensitivity required, the study of analytes often demands low sample consumption and short mixing times to allow for the monitoring of quick reactions. These parameters can nicely be achieved with the use of microfluidics. Hydrodynamic focusing within 3-inlet 1-outlet continuous flow microfluidic devices can be used as a molecular confinement mechanism to improve the detection efficiency as well as a means to enhance mixing within microchannels for the study of fast reaction kinetics. In this work, a powerful combination of confocal microscopy and microfluidics was used to perform fluorescence lifetime measurements on freely diffusing and freely flowing molecules. For this purpose, a home-built scanning confocal system was developed to ensure sufficient reduction in background levels, enabling the detection of fluorescence signal that arises from single molecules. Fluorescence lifetime imaging along with a maximum likelihood estimator adapted from single molecule studies was performed to visualise hydrodynamic focusing and characterise mixing within microfluidic devices. Time-resolved methods were also employed to detect single molecules freely flowing within microchannels. A novel fluorescence lifetime approach was developed to perform Förster resonance energy transfer measurements on freely diffusing molecules and subsequently applied for the study of streptavidin-biotin binding and protein conformational changes upon unfolding