Extracting 3D parametric curves from 2D images of Helical objects

Helical objects occur in medicine, biology, cosmetics, nanotechnology, and engineering. Extracting a 3D parametric curve from a 2D image of a helical object has many practical applications, in particular being able to extract metrics such as tortuosity, frequency, and pitch. We present a method that is able to straighten the image object and derive a robust 3D helical curve from peaks in the object boundary. The algorithm has a small number of stable parameters that require little tuning, and the curve is validated against both synthetic and real-world data. The results show that the extracted 3D curve comes within close Hausdorff distance to the ground truth, and has near identical tortuosity for helical objects with a circular profile. Parameter insensitivity and robustness against high levels of image noise are demonstrated thoroughly and quantitatively

Extracting 3D parametric curves from 2D images of helical objects

Helical objects occur in medicine, biology, cosmetics, nanotechnology, and engineering. Extracting a 3D parametric curve from a 2D image of a helical object has many practical applications, in particular being able to extract metrics such as tortuosity, frequency, and pitch. We present a method that is able to straighten the image object and derive a robust 3D helical curve from peaks in the object boundary. The algorithm has a small number of stable parameters that require little tuning, and the curve is validated against both synthetic and real-world data. The results show that the extracted 3D curve comes within close Hausdorff distance to the ground truth, and has near identical tortuosity for helical objects with a circular profile. Parameter insensitivity and robustness against high levels of image noise are demonstrated thoroughly and quantitatively

Modeling Of The Interaction Between Colon And Colonoscope During A Colonoscopy

University of Minnesota M.S.M.E. thesis. May 2018. Major: Mechanical Engineering. Advisor: Debao Zhou. 1 computer file (PDF); x, 78 pages.One of the main complications in completing a colonoscopy is that the colonoscope causes patient pain during the procedure. To reduce patient pain, small-caliber (SC) colonoscopes have been developed. To evaluate the efficacy of SC colonoscopes in reducing patient pain with that of traditional standard colonoscope (SDC), several randomized control trials (RCTs) were conducted and showed varying results, with some showed benefits whereas others did not. Among these RCTs, patient characteristics, including gender, age, and region were varied and further assumed to be responsible for the varied results. However, the influence of patient characteristics on the efficacy of SC colonoscopes in terms of reducing patient pain is still unclear due to many unavoidable disturbing factors in RCTs, including endoscopists’ skills, bowel preparation methods, and other new beneficial features of colonoscopes (passive bending and high force transmission shaft). Therefore, to explore the influence of gender, age, and region of patients on the efficacy of SC colonoscopes in terms of reducing patient pain, a numerical model could overcome the limitations of RCTs and provide such insight is developed in our work. As a first step, the structural differences of the human colon with respect to gender, age, and region were analyzed and summarized, which further functions as the basis of the development of colon models and their boundary conditions. As a result, three normalized colon segments were selected and modelled, including rectosigmoid junction (RCJ), rectum-splenic flexure (RSF), and transverse-hepatic flexure (THF) models. The colonoscope was modelled as a thin and flexible cylinder with a hemisphere tip. Three different diameters were applied to colonoscope models, including 9.2mm for ultrathin colonoscope (UTC), 11.3mm for pediatric colonoscope (PDC), and 12.8mm for standard colonoscope (SDC). UTC and PDC were classified as SC colonoscopes. In the stage of insertion simulation, a comparison between implicit and explicit finite element solution method was conducted, and then an explicit solver ANSYS-LSDYNA was selected to simulate the insertion process of colonoscopes in colon models. An uni-axial tension test was carried out to provide the experimental data of a porcine colon, and then an optimization procedure with the use of ANSYS and Optislang programs was performed to provide the necessary parameters of the constitutive material model of the colonic tissue. By comparing colon deformation during the insertion simulation, patient pain induced by colonoscopes were further predicted. The model developed in this research serves as a starting point in understanding the efficacy of SC colonoscopes in reducing patient pain considering the effects of patient characteristics, including gender, age, and region. This model may also provide scientific guidelines for the selection of patient specified colonoscop

Spatiotemporal models and simulations reveal the physical mechanisms that migrating cells sense and self-adapt to heterogeneous extracellular microenvironments

Cell migration plays essential roles in many normal physiological and pathological processes, such as embryonic morphogenesis, wound healing, tissue renewal, nervous system development, cancer metastasis and autoimmune disorders. Both single cell migration and collective cell migration are powered by the actin-based lamellipodia, filopodia or invadopodia protrusions at their leading edges to migrate through extremely heterogeneous extracellular microenvironments. Although extensive experimental studies about cell migration have been conducted, it is unknown of the intracellular physical mechanisms of how migrating cells sense and adapt to the highly varying extracellular mechanical microenvironments. To address this, we construct the predictive spatiotemporal model of the lamellipodial branched actin network through simulating its realistic selfassembling process by encompassing key proteins and their highly dynamic interactions. Then, using finite element simulations, we quantitatively demonstrate the mechanical roles of individual intracellular proteins in regulating the elastic properties of the self-assembling network during cell migration. More importantly, we reveal a resistance-adaptive intracellular physical mechanism of cell migration: the lamellipodial branched actin network can sense the variations of immediate extracellular resistance through the bending deformations of actin filaments, and then adapt to the resistance by self-regulating its elastic properties sensitively through Arp2/3 nucleating, remodelling with F-actin, filamin-A and α-actinin and altering the filament orientations. Such resistance-adaptive behaviours are versatile and essential in driving cells to over-come the highly varying extracellular confinements. Additionally, it is deciphered that the actin filament bending deformation and anisotropic Poisson’s ratio effect of the branched actin network and Arp2/3 branching preference jointly determine why lamellipodium grows into a sheet-like structure and protrudes against resistance persistently. Our predictions Abstract IV are confirmed by published pioneering experiments. The revealed mechanism also can be applied to endocytosis and intracellular pathogens motion. The propulsive force of cell migration is based on actin filament polymerization. We propose a theoretical ‘bending-straightening elastic ratchet’ (BSER) model, which is based on geometrical nonlinearity deformation of continuum solid mechanics. Then, we develop the self-assembling spatiotemporal mathematical model of the polymerizing lamellipodial branched actin filaments propelling the leading edge protrusion under heterogeneous extracellular microenvironment, and perform large-scale spatial and temporal simulations by applying the BSER theoretical model. Our simulation realistically encompasses the stochastic actin filament polymerization, Arp2/3 complex branching, capping proteins inhibiting actin polymerization, curved LE membrane, rupture of molecular linkers and varying extracellular mechanical microenvironment. Strikingly, our model for the first time systematically predicts all important leading-edge behaviours of a migrating cell. More importantly, we reveal two very fundamental biophysical mechanisms that migrating cells sense and adapt their protruding force to varying immediate extracellular physical constraints, and that how migrating cells navigate their migratory path to in highly heterogeneous and complex extracellular microenvironments. Additionally, our BSER theoretical model and the underlying physical mechanism revealed here are also applicable to the propulsion systems of endocytosis, intracellular pathogen transport and dendritic spine formation in cortical neurons, which are powered by polymerization of branched actin filaments as well. Filopodia and invadopodia protrusions are the other two types of cell migration behaviours at their leading edges. Through three-dimensional assembling model of filopodial/invadopodial F-actin bundles and finite element simulations, we quantitatively identify how the highly dynamic assembling and disassembling actin filaments and binding and unbinding of crosslinking proteins, i.e., α-actinin and fascin, regulate Young’s modulus and buckling behaviours of Abstract V filopodia/invadopodia, respectively and combinedly. In addition, thermal induced undulation of actin filaments has an important influence on the buckling behaviours of filopodia/invadopodia. Compared with sheet-like lamellipodia, the finger-like filopodia/invadopodia have a much larger stiffness to protrude in extracellular microenvironment. Thus, they can cooperate with lamellipodia to complementarily split a channel in extracellular microenvironment and drive cell migration through the channel

Development of a Physical Simulation of the Human Defecatory System for the Investigation of Continence Mechanisms

Faecal incontinence is a highly debilitating condition, prevalent across the population worldwide. Coupled with a large unmet need for clinically viable treatment options, a paucity of research into the biomechanics of continence inhibits the development of treatments which address multi-faceted challenges associated with the condition. Consequently, this thesis presents a method to fabricate, measure and control a physical simulation of the human defecatory system to investigate individual and combined effects of anorectal angle and sphincter pressure on continence. To illustrate the capabilities and clinical relevance of the work, the influence of a passive-assistive artificial anal sphincter (FENIX) is evaluated. A model rectum and associated soft tissues, based on geometry from an anonymised computerised tomography dataset, was fabricated from silicone and showed behavioural realism in terms of their morphology to the biological system and ex-vivo tissue. Simulated stool matter with similar rheological properties to human faeces was developed. Instrumentation and control hardware were used to regulate injection of simulated stool into the system, define the anorectal angle and monitor stool flow rate, intra-rectal pressure, anal canal pressure and puborectalis force. Studies were conducted to examine the response of anorectal angles at 80°, 90° and 100° with simulated stool. Tests were then repeated with the inclusion of a FENIX device. Stool leakage was reduced as the anorectal angle became more acute. Conversely, intra-rectal pressure increased. Overall inclusion of the FENIX reduced faecal leakage, while combined effects of the FENIX and an acute anorectal angle showed the greatest resistance to faecal leakage. These data demonstrate that the anorectal angle and sphincter pressure are fundamental in maintaining continence. Furthermore it demonstrates that use of the FENIX can increase resistance to faecal leakage and reduce anorectal angles required to maintain continence. The physical simulation of the defecatory system is an insightful tool to better understand, in a quantitative manner, the effects of the anorectal angle and sphincter pressure on continence. This work is valuable in helping improve our understanding of the physical behaviour of the continence mechanism and facilitating improved technologies to treat severe faecal incontinence