A Mathematical Morphology Approach to Cell Shape Analysis

This contribution aims to apply mathematical morphology operators to quantify the shape of round-objects which present irregularities from an ideal circular pattern. More specifically we illustrate, on the one hand, the application of morphological granulometries for size/shape multi-scale description and on the other hand, the radial/angular decompo- sitions using skeletons in polar-logarithmic representation. We discuss also the aspects related to the properties of invariance of these tools, which is important to describe cell shapes acquired under different magnifications, orientations, etc

Polar contour shape descriptors in the template matching approach to object recognition

The paper provides a review of contour polar shape descriptors used in recognition of objects based on their silhouettes. The process of recognition in the template matching approach has to be based on so called descriptors, assigned to object features, e.g. shape, texture, color, luminance, context of the information and movement. Amongst them very special attention is paid to the shape, because in many applications it is the most relevant and the less changeable feature that can be used.The shape in the digital image processing has usually a form of binary object. One of the representations uses the boundary, contour of a silhouette. The most important advantage of such approach is a small number of pixels to consider.Amongst several dozen shape descriptors special properties can be found in the polar ones, which use the transformation from the Cartesian to the polar coordinates. The most important is invariance to translation of the object points. The rotation becomes a circular shift what can be easily solved in further processing. Owing to the normalization the descriptors can be also invariant to scaling. Some of the methods are also robust to some level of noise and occlusion

Biologically inspired composite image sensor for deep field target tracking

The use of nonuniform image sensors in mobile based computer vision applications can be an effective solution when computational burden is problematic. Nonuniform image sensors are still in their infancy and as such have not been fully investigated for their unique qualities nor have they been extensively applied in practice. In this dissertation a system has been developed that can perform vision tasks in both the far field and the near field. In order to accomplish this, a new and novel image sensor system has been developed. Inspired by the biological aspects of the visual systems found in both falcons and primates, a composite multi-camera sensor was constructed. The sensor provides for expandable visual range, excellent depth of field, and produces a single compact output image based on the log-polar retinal-cortical mapping that occurs in primates. This mapping provides for scale and rotational tolerant processing which, in turn, supports the mitigation of perspective distortion found in strict Cartesian based sensor systems. Furthermore, the scale-tolerant representation of objects moving on trajectories parallel to the sensor\u27s optical axis allows for fast acquisition and tracking of objects moving at high rates of speed. In order to investigate how effective this combination would be for object detection and tracking at both near and far field, the system was tuned for the application of vehicle detection and tracking from a moving platform. Finally, it was shown that the capturing of license plate information in an autonomous fashion could easily be accomplished from the extraction of information contained in the mapped log-polar representation space. The novel composite log-polar deep-field image sensor opens new horizons for computer vision. This current work demonstrates features that can benefit applications beyond the high-speed vehicle tracking for drivers assistance and license plate capture. Some of the future applications envisioned include obstacle detection for high-speed trains, computer assisted aircraft landing, and computer assisted spacecraft docking

NMR DIFFUSION MEASUREMENTS OF COMPARTMENTALIZED AND MULTICOMPONENT BIOLOGICAL SYSTEMS: Studies of Tropoelastin, the Self Association of N Methylacetamide, and q-Space Analysis of Real and Model Cell Suspensions

Molecular diffusion is an inherent feature of all fluid systems. The processes and interactions that characterize these systems are in some way dependent upon the mobility of the component molecules. Pulsed field-gradient spin-echo nuclear magnetic resonance (PGSE NMR) is a powerful tool for the study of molecular diffusion; for heterogeneous systems, such as those typically found in biology, this technique is unsurpassed in the diversity of systems that yield to its probing. The aim of the work presented in this thesis was to use an integrated NMR-based approach, in conjunction with computer modeling, for the study of molecular diffusion in compartmentalized and multicomponent biological systems. Erythrocyte suspensions provided an ideal experimental system for the study of compartmentalized diffusion in cells. Water exchanges rapidly between the intra- and extracellular regions and, as the major constituent of the cell, provides a strong and predominant proton NMR signal. In addition, the cells are known to align in the strong static magnetic field of the spectrometer. As a consequence of these two properties, the signal intensity from a suitably designed series of PGSE NMR experiments exhibits a series of maxima and minima when graphed as a function of the magnitude of the spatial wave number vector q. The apparently periodic phenomenon is mathematically analogous to optical diffraction and interference and is referred to here as diffusion-coherence. It is the characterization of this phenomenon, with the aid of computer-based models, which was the focus of a major section of the work described herein. Two quite distinct molecular systems formed the basis of the work in which I investigated diffusion in multicomponent systems. Both systems involved molecules that undergo self-association such that at equilibrium a population distribution of different oligomeric species is present. The first of these was tropoelastin, the monomeric subunit of elastin, which under certain conditions aggregates to form a coacervate. The second system was N-methylacetamide (NMA) which also undergoes extensive self-association. NMA oligomers have previously been studied as peptide analogues due to the presence in the monomer of a peptide linkage. In this work the aim was to use PGSE NMR diffusion measurements, in a manner that is in many ways analogous to analytical ultracentrifugation, to obtain estimates of hydrodynamic and thermodynamic parameters. Computer modeling was also used extensively in this section of work for the interpretation of the experimental data

NMR DIFFUSION MEASUREMENTS OF COMPARTMENTALIZED AND MULTICOMPONENT BIOLOGICAL SYSTEMS: Studies of Tropoelastin, the Self Association of N Methylacetamide, and q-Space Analysis of Real and Model Cell Suspensions

Molecular diffusion is an inherent feature of all fluid systems. The processes and interactions that characterize these systems are in some way dependent upon the mobility of the component molecules. Pulsed field-gradient spin-echo nuclear magnetic resonance (PGSE NMR) is a powerful tool for the study of molecular diffusion; for heterogeneous systems, such as those typically found in biology, this technique is unsurpassed in the diversity of systems that yield to its probing. The aim of the work presented in this thesis was to use an integrated NMR-based approach, in conjunction with computer modeling, for the study of molecular diffusion in compartmentalized and multicomponent biological systems. Erythrocyte suspensions provided an ideal experimental system for the study of compartmentalized diffusion in cells. Water exchanges rapidly between the intra- and extracellular regions and, as the major constituent of the cell, provides a strong and predominant proton NMR signal. In addition, the cells are known to align in the strong static magnetic field of the spectrometer. As a consequence of these two properties, the signal intensity from a suitably designed series of PGSE NMR experiments exhibits a series of maxima and minima when graphed as a function of the magnitude of the spatial wave number vector q. The apparently periodic phenomenon is mathematically analogous to optical diffraction and interference and is referred to here as diffusion-coherence. It is the characterization of this phenomenon, with the aid of computer-based models, which was the focus of a major section of the work described herein. Two quite distinct molecular systems formed the basis of the work in which I investigated diffusion in multicomponent systems. Both systems involved molecules that undergo self-association such that at equilibrium a population distribution of different oligomeric species is present. The first of these was tropoelastin, the monomeric subunit of elastin, which under certain conditions aggregates to form a coacervate. The second system was N-methylacetamide (NMA) which also undergoes extensive self-association. NMA oligomers have previously been studied as peptide analogues due to the presence in the monomer of a peptide linkage. In this work the aim was to use PGSE NMR diffusion measurements, in a manner that is in many ways analogous to analytical ultracentrifugation, to obtain estimates of hydrodynamic and thermodynamic parameters. Computer modeling was also used extensively in this section of work for the interpretation of the experimental data

High Pressure and Micro-spectroscopic Studies of Single Living Erythrocytes and the Intraerythrocytic Multplication Cycle of Plasmodium Falciparum

A novel experimental approach for micro-absorption spectroscopy and high-pressure microscopy of single cells is developed and applied to the investigation of morphological, volume, and spectroscopic changes in healthy red blood cells (RBCs) and erythrocytes infected with the malaria parasite Plasmodium falciparum. Through real-time optical imaging of individual erythrocytes (size ~ 7[micrometer]) we determine the change in volume over the pressure range from 0.1 to 210 MPa. The lateral diameter of healthy RBCs decreases reversibly with pressure with an approximate slope of 0.015 [micrometer] / MPa. In infected cells, clear differences in the deformability and between the compression and decompression curves are observed. The results are discussed with respect to the elasticity of the phospholipid membrane and the spectrin molecular network. Employing micro-absorption spectroscopy with spatial resolution of 1.4 [micrometer] in the lateral and 3.6 [micrometer] in the axial direction the visible absorption spectrum of hemoglobin in a single red blood cell is measured under physiological conditions. The spectra of cells infected with the malaria parasite show changes in peak positions and relative intensities in the Soret and [alpha]- and [beta]- bands. These indicate hemoglobin degradation that can be correlated with the stages of the parasite multiplication cycle and can be used as a potential diagnostic marker. The research is further extended towards the understanding of pressure effects on the ligand binding kinetics to heme proteins. For a well characterized reaction at ambient pressure, CO binding to myoglobin in solution, we investigate the transient absorption following laser flash photolysis over eight decades in time at variable pressure and temperature. The data demonstrate that pressure significantly affects the amplitudes (not just the rates) of the component processes. The amplitude of the geminate process increases with pressure corresponding to a smaller escape fraction of ligands into the solvent and a smaller inner barrier

Investigation of the biophysical basis for cell organelle morphology

It is known that fission yeast Schizosaccharomyces pombe maintains its nuclear envelope during mitosis and it undergoes an interesting shape change during cell division - from a spherical via an ellipsoidal and a peanut-like to a dumb-bell shape. However, the biomechanical system behind this amazing transformation is still not understood. What we know is, that the shape must change due to forces acting on the membrane surrounding the nucleus and the microtubule based mitotic spindle is thought to play a key role. To estimate the locations and directions of the forces, the shape of the nucleus was recorded by confocal light microscopy. But such data is often inhomogeneously labeled with gaps in the boundary, making classical segmentation impractical. In order to accurately determine the shape we developed a global parametric shape description method, based on a Fourier coordinate expansion. The method implicitly assumes a closed and smooth surface. We will calculate the geometrical properties of the 2-dimensional shape and extend it to 3-dimensional properties, assuming rotational symmetry. Using a mechanical model for the lipid bilayer and the so called Helfrich-Canham free energy we want to calculate the minimum energy shape while respecting system-specific constraints to the surface and the enclosed volume. Comparing it with the observed shape leads to the forces. This provides the needed research tools to study forces based on images

Coarse-grained modelling of blood cell mechanics

This thesis concerns development of mechanically realistic in silico representations of human blood cells using coarse-grained molecular dynamics (CGMD), ultimately building a new model for a lymphocyte-class white blood cell (WBC). This development is approached successively, evaluated through simulation of experimental testing methods common to past in vitro studies on blood cell mechanics. Considering both their biophysical simplicity and the extensive associated literature, the red blood cell (RBC) is first considered. As a foundation, I thus used the CGMD RBC model of Fu et al. [Lennard-Jones type pair-potential method for coarse-grained lipid bilayer membrane simulations in LAMMPS, Fu et al., Comput. Phys. Commun., 210, 193-203 (2017)]. Chapter 3 establishes implementation of this model, and in silico implementations of the three chosen testing methods. In doing so, the first quantitative assessment of the "miniature cell" approach is conducted - being the down-scaling of the physical cell size to make feasible simulation times, as was done in the original article presenting the model. The RBC model is then used as a foundation from which to develop a new whole-cell WBC lymphocyte model. This is approached sequentially. Firstly (Chapter 4), the morphology and mechanics relevant to the existing RBC model are adapted to those of a lymphocyte. As such, a quasi-spherical morphology is induced, and elastic membrane-associated parameters brought in line with the literature on isolated lymphocytes in vitro. A semi-rigid nucleus is then added to the cell interior, again parameterised to produce elastic properties consistent with the literature. These developments produce a cell having macroscopic mechanical properties much more consistent with a WBC, with an "optimal" parameterisation established. After the membrane and nucleus, the entity most influential to the mechanics of nucleated cells (such as WBC) is their complex intracellular actin-based cytoskeleton (CSK). Therefore, Chapter 5 attempts to represent such a system within our new lymphocyte model. This is approached in three successive stages, assessed against recognised CSK mechanical properties, in particular those also common to soft glassy materials. As such, a novel CSK representation is developed, inspired as a discretisation of soft glassy rheology (SGR). It is proposed that the resulting system has characteristics comparable to having undergone a glass-like transition, as relatable to a real CSK. Therefore, the resulting lymphocyte model may lay a foundation for future development towards mechanically accurate representations of other cells - in particular, a circulating tumour cell

Particles at Membranes and Interfaces

Soft surfaces experience morphological changes upon interaction with objects at various length scales. Two important classes of soft surfaces are membranes and interfaces. In presence of particles, through surface-mediated interactions soft surfaces exhibit diverse phenomena in nature. A fluid membrane which acts as a protective periphery enclosing cellular material can be described as a two dimensional mathematical surface characterized by `bending elasticity' and `membrane tension'. Similarly, interfaces at the boundary of two liquid phases or a liquid and a gas phase are characterized by their interface tension. Interestingly, a close interplay of the deformation energy of these soft surfaces and the geometry and form of the particles allows the particles to interact. Thus, the study of interactions of particles with membranes and interfaces forms the basis of this work. The mechanistic aspects of cellular entry via membrane wrapping for particles of various geometries are studied theoretically and numerically. Such systems are characterized by the membrane bending rigidity, the membrane tension, and the adhesion strength. The different wrapping states exhibited are ``non wrapped", ``partially wrapped" (with low and high wrapping fraction), and ``completely wrapped". There are two kinds of phase boundaries: a continuous binding transition and a discontinuous transition either between two partially-wrapped states or from a partially-wrapped to a completely wrapped state. The theoretical analysis predicts stable partially wrapped states for nonspherical particles. Nonspherical particles having flat sides can show preferential initial binding though the decisive factor for encapsulation is the ratio of the width to the length of the particles and the softness of its edges. Wrapping energy contributions of the erythrocyte membrane to the invasion energetics for a malarial merozoite that has an asymmetric ``egg-like'' shape is assessed. Furthermore cell adhesion to nanopatterned substrates is characterized to predict optimal shapes of 3D nanoelectrodes for efficient coupling to cells using deformation energy calculations. For a fluid interface dominated by an interfacial tension, self-assembly via capillary interactions for micron-sized nonspherical particles is reported. A nonspherical particle can induce interface distortion due to an undulating contact line creating excess interfacial area. Neighboring particles interact to minimize the excess area via long-range interface-mediated capillary forces. The particle-induced interface distortion due to single ellipsoidal or cuboidal particles are calculated. The near-field nature of the capillary interactions between a pair of particles in different relative orientations is characterized using power-law fits

Лексичний мінімум з наукового стилю мовлення. Інженерний, медично-біологічний, економічний профілі

Даний лексичний мінімум, репрезентований як перекладний українсько-англійський словник, містить більше 5000 слів та словосполучень з наукового стилю мовлення. Призначений для студентів підготовчих факультетів інженерного, медично-біологічного і економічного профілів навчання, а також може використовуватись студентами основних курсів