Coronary Artery Segmentation and Motion Modelling

Conventional coronary artery bypass surgery requires invasive sternotomy and the use of a cardiopulmonary bypass, which leads to long recovery period and has high infectious potential. Totally endoscopic coronary artery bypass (TECAB) surgery based on image guided robotic surgical approaches have been developed to allow the clinicians to conduct the bypass surgery off-pump with only three pin holes incisions in the chest cavity, through which two robotic arms and one stereo endoscopic camera are inserted. However, the restricted field of view of the stereo endoscopic images leads to possible vessel misidentification and coronary artery mis-localization. This results in 20-30% conversion rates from TECAB surgery to the conventional approach. We have constructed patient-specific 3D + time coronary artery and left ventricle motion models from preoperative 4D Computed Tomography Angiography (CTA) scans. Through temporally and spatially aligning this model with the intraoperative endoscopic views of the patient's beating heart, this work assists the surgeon to identify and locate the correct coronaries during the TECAB precedures. Thus this work has the prospect of reducing the conversion rate from TECAB to conventional coronary bypass procedures. This thesis mainly focus on designing segmentation and motion tracking methods of the coronary arteries in order to build pre-operative patient-specific motion models. Various vessel centreline extraction and lumen segmentation algorithms are presented, including intensity based approaches, geometric model matching method and morphology-based method. A probabilistic atlas of the coronary arteries is formed from a group of subjects to facilitate the vascular segmentation and registration procedures. Non-rigid registration framework based on a free-form deformation model and multi-level multi-channel large deformation diffeomorphic metric mapping are proposed to track the coronary motion. The methods are applied to 4D CTA images acquired from various groups of patients and quantitatively evaluated

Camera Marker Networks for Pose Estimation and Scene Understanding in Construction Automation and Robotics.

The construction industry faces challenges that include high workplace injuries and fatalities, stagnant productivity, and skill shortage. Automation and Robotics in Construction (ARC) has been proposed in the literature as a potential solution that makes machinery easier to collaborate with, facilitates better decision-making, or enables autonomous behavior. However, there are two primary technical challenges in ARC: 1) unstructured and featureless environments; and 2) differences between the as-designed and the as-built. It is therefore impossible to directly replicate conventional automation methods adopted in industries such as manufacturing on construction sites. In particular, two fundamental problems, pose estimation and scene understanding, must be addressed to realize the full potential of ARC. This dissertation proposes a pose estimation and scene understanding framework that addresses the identified research gaps by exploiting cameras, markers, and planar structures to mitigate the identified technical challenges. A fast plane extraction algorithm is developed for efficient modeling and understanding of built environments. A marker registration algorithm is designed for robust, accurate, cost-efficient, and rapidly reconfigurable pose estimation in unstructured and featureless environments. Camera marker networks are then established for unified and systematic design, estimation, and uncertainty analysis in larger scale applications. The proposed algorithms' efficiency has been validated through comprehensive experiments. Specifically, the speed, accuracy and robustness of the fast plane extraction and the marker registration have been demonstrated to be superior to existing state-of-the-art algorithms. These algorithms have also been implemented in two groups of ARC applications to demonstrate the proposed framework's effectiveness, wherein the applications themselves have significant social and economic value. The first group is related to in-situ robotic machinery, including an autonomous manipulator for assembling digital architecture designs on construction sites to help improve productivity and quality; and an intelligent guidance and monitoring system for articulated machinery such as excavators to help improve safety. The second group emphasizes human-machine interaction to make ARC more effective, including a mobile Building Information Modeling and way-finding platform with discrete location recognition to increase indoor facility management efficiency; and a 3D scanning and modeling solution for rapid and cost-efficient dimension checking and concise as-built modeling.PHDCivil EngineeringUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/113481/1/cforrest_1.pd

Non-contact strain determination of cell traction effects

Irreversible tissue damage leading to organ failure is a common health problem in today's world. Regenerating these damaged tissues with the help of scaffolds is the solution offered by tissue engineering. In cases where the extra-cellular matrix (ECM) is to be replaced by an artificial substrate (scaffold) or matrix, cellular traction forces (CTF) are exerted by the cells on the scaffold surface. An ideal scaffold should exhibit mechanical characteristics similar to those of the ECM it is intended to replace. In other words, the capacity of a scaffold to withstand deformation should be comparable to that of a natural ECM. And with knowledge of those forces and deformations the properties of the scaffolds may be inferred. Digital Image Correlation (DIC), a non-contact image analysis technique enables us to measure point to point deformation of the scaffold by comparing a sequence of images captured during the process of scaffold deformation. This review discusses the methodology involved and implementation of DIC to measure displacements and strain.Irreversible tissue damage leading to organ failure is a common health problem in today's world. Regenerating these damaged tissues with the help of scaffolds is the solution offered by tissue engineering. In cases where the extra-cellular matrix (ECM) is to be replaced by an artificial substrate (scaffold) or matrix, cellular traction forces (CTF) are exerted by the cells on the scaffold surface. An ideal scaffold should exhibit mechanical characteristics similar to those of the ECM it is intended to replace. In other words, the capacity of a scaffold to withstand deformation should be comparable to that of a natural ECM. And with knowledge of those forces and deformations the properties of the scaffolds may be inferred. Digital Image Correlation (DIC), a non-contact image analysis technique enables us to measure point to point deformation of the scaffold by comparing a sequence of images captured during the process of scaffold deformation. This review discusses the methodology involved and implementation of DIC to measure displacements and strain

Integrasjon av et minimalistisk sett av sensorer for kartlegging og lokalisering av landbruksroboter

Robots have recently become ubiquitous in many aspects of daily life. For in-house applications there is vacuuming, mopping and lawn-mowing robots. Swarms of robots have been used in Amazon warehouses for several years. Autonomous driving cars, despite being set back by several safety issues, are undeniably becoming the standard of the automobile industry. Not just being useful for commercial applications, robots can perform various tasks, such as inspecting hazardous sites, taking part in search-and-rescue missions. Regardless of end-user applications, autonomy plays a crucial role in modern robots. The essential capabilities required for autonomous operations are mapping, localization and navigation. The goal of this thesis is to develop a new approach to solve the problems of mapping, localization, and navigation for autonomous robots in agriculture. This type of environment poses some unique challenges such as repetitive patterns, large-scale sparse features environments, in comparison to other scenarios such as urban/cities, where the abundance of good features such as pavements, buildings, road lanes, traffic signs, etc., exists. In outdoor agricultural environments, a robot can rely on a Global Navigation Satellite System (GNSS) to determine its whereabouts. It is often limited to the robot's activities to accessible GNSS signal areas. It would fail for indoor environments. In this case, different types of exteroceptive sensors such as (RGB, Depth, Thermal) cameras, laser scanner, Light Detection and Ranging (LiDAR) and proprioceptive sensors such as Inertial Measurement Unit (IMU), wheel-encoders can be fused to better estimate the robot's states. Generic approaches of combining several different sensors often yield superior estimation results but they are not always optimal in terms of cost-effectiveness, high modularity, reusability, and interchangeability. For agricultural robots, it is equally important for being robust for long term operations as well as being cost-effective for mass production. We tackle this challenge by exploring and selectively using a handful of sensors such as RGB-D cameras, LiDAR and IMU for representative agricultural environments. The sensor fusion algorithms provide high precision and robustness for mapping and localization while at the same time assuring cost-effectiveness by employing only the necessary sensors for a task at hand. In this thesis, we extend the LiDAR mapping and localization methods for normal urban/city scenarios to cope with the agricultural environments where the presence of slopes, vegetation, trees render the traditional approaches to fail. Our mapping method substantially reduces the memory footprint for map storing, which is important for large-scale farms. We show how to handle the localization problem in dynamic growing strawberry polytunnels by using only a stereo visual-inertial (VI) and depth sensor to extract and track only invariant features. This eliminates the need for remapping to deal with dynamic scenes. Also, for a demonstration of the minimalistic requirement for autonomous agricultural robots, we show the ability to autonomously traverse between rows in a difficult environment of zigzag-liked polytunnel using only a laser scanner. Furthermore, we present an autonomous navigation capability by using only a camera without explicitly performing mapping or localization. Finally, our mapping and localization methods are generic and platform-agnostic, which can be applied to different types of agricultural robots. All contributions presented in this thesis have been tested and validated on real robots in real agricultural environments. All approaches have been published or submitted in peer-reviewed conference papers and journal articles.Roboter har nylig blitt standard i mange deler av hverdagen. I hjemmet har vi støvsuger-, vaske- og gressklippende roboter. Svermer med roboter har blitt brukt av Amazons varehus i mange år. Autonome selvkjørende biler, til tross for å ha vært satt tilbake av sikkerhetshensyn, er udiskutabelt på vei til å bli standarden innen bilbransjen. Roboter har mer nytte enn rent kommersielt bruk. Roboter kan utføre forskjellige oppgaver, som å inspisere farlige områder og delta i leteoppdrag. Uansett hva sluttbrukeren velger å gjøre, spiller autonomi en viktig rolle i moderne roboter. De essensielle egenskapene for autonome operasjoner i landbruket er kartlegging, lokalisering og navigering. Denne type miljø gir spesielle utfordringer som repetitive mønstre og storskala miljø med få landskapsdetaljer, sammenlignet med andre steder, som urbane-/bymiljø, hvor det finnes mange landskapsdetaljer som fortau, bygninger, trafikkfelt, trafikkskilt, etc. I utendørs jordbruksmiljø kan en robot bruke Global Navigation Satellite System (GNSS) til å navigere sine omgivelser. Dette begrenser robotens aktiviteter til områder med tilgjengelig GNSS signaler. Dette vil ikke fungere i miljøer innendørs. I ett slikt tilfelle vil reseptorer mot det eksterne miljø som (RGB-, dybde-, temperatur-) kameraer, laserskannere, «Light detection and Ranging» (LiDAR) og propriopsjonære detektorer som treghetssensorer (IMU) og hjulenkodere kunne brukes sammen for å bedre kunne estimere robotens tilstand. Generisk kombinering av forskjellige sensorer fører til overlegne estimeringsresultater, men er ofte suboptimale med hensyn på kostnadseffektivitet, moduleringingsgrad og utbyttbarhet. For landbruksroboter så er det like viktig med robusthet for lang tids bruk som kostnadseffektivitet for masseproduksjon. Vi taklet denne utfordringen med å utforske og selektivt velge en håndfull sensorer som RGB-D kameraer, LiDAR og IMU for representative landbruksmiljø. Algoritmen som kombinerer sensorsignalene gir en høy presisjonsgrad og robusthet for kartlegging og lokalisering, og gir samtidig kostnadseffektivitet med å bare bruke de nødvendige sensorene for oppgaven som skal utføres. I denne avhandlingen utvider vi en LiDAR kartlegging og lokaliseringsmetode normalt brukt i urbane/bymiljø til å takle landbruksmiljø, hvor hellinger, vegetasjon og trær gjør at tradisjonelle metoder mislykkes. Vår metode reduserer signifikant lagringsbehovet for kartlagring, noe som er viktig for storskala gårder. Vi viser hvordan lokaliseringsproblemet i dynamisk voksende jordbær-polytuneller kan løses ved å bruke en stereo visuel inertiel (VI) og en dybdesensor for å ekstrahere statiske objekter. Dette eliminerer behovet å kartlegge på nytt for å klare dynamiske scener. I tillegg demonstrerer vi de minimalistiske kravene for autonome jordbruksroboter. Vi viser robotens evne til å bevege seg autonomt mellom rader i ett vanskelig miljø med polytuneller i sikksakk-mønstre ved bruk av kun en laserskanner. Videre presenterer vi en autonom navigeringsevne ved bruk av kun ett kamera uten å eksplisitt kartlegge eller lokalisere. Til slutt viser vi at kartleggings- og lokaliseringsmetodene er generiske og platform-agnostiske, noe som kan brukes med flere typer jordbruksroboter. Alle bidrag presentert i denne avhandlingen har blitt testet og validert med ekte roboter i ekte landbruksmiljø. Alle forsøk har blitt publisert eller sendt til fagfellevurderte konferansepapirer og journalartikler

畳み込みニューラルネットワークと時空間サポートベクター回帰に基づくギターの運指の自動評価システム

早大学位記番号:新7965早稲田大

Image Processing and Simulation Toolboxes of Microscopy Images of Bacterial Cells

Recent advances in microscopy imaging technology have allowed the characterization of the dynamics of cellular processes at the single-cell and single-molecule level. Particularly in bacterial cell studies, and using the E. coli as a case study, these techniques have been used to detect and track internal cell structures such as the Nucleoid and the Cell Wall and fluorescently tagged molecular aggregates such as FtsZ proteins, Min system proteins, inclusion bodies and all the different types of RNA molecules. These studies have been performed with using multi-modal, multi-process, time-lapse microscopy, producing both morphological and functional images. To facilitate the finding of relationships between cellular processes, from small-scale, such as gene expression, to large-scale, such as cell division, an image processing toolbox was implemented with several automatic and/or manual features such as, cell segmentation and tracking, intra-modal and intra-modal image registration, as well as the detection, counting and characterization of several cellular components. Two segmentation algorithms of cellular component were implemented, the first one based on the Gaussian Distribution and the second based on Thresholding and morphological structuring functions. These algorithms were used to perform the segmentation of Nucleoids and to identify the different stages of FtsZ Ring formation (allied with the use of machine learning algorithms), which allowed to understand how the temperature influences the physical properties of the Nucleoid and correlated those properties with the exclusion of protein aggregates from the center of the cell. Another study used the segmentation algorithms to study how the temperature affects the formation of the FtsZ Ring. The validation of the developed image processing methods and techniques has been based on benchmark databases manually produced and curated by experts. When dealing with thousands of cells and hundreds of images, these manually generated datasets can become the biggest cost in a research project. To expedite these studies in terms of time and lower the cost of the manual labour, an image simulation was implemented to generate realistic artificial images. The proposed image simulation toolbox can generate biologically inspired objects that mimic the spatial and temporal organization of bacterial cells and their processes, such as cell growth and division and cell motility, and cell morphology (shape, size and cluster organization). The image simulation toolbox was shown to be useful in the validation of three cell tracking algorithms: Simple Nearest-Neighbour, Nearest-Neighbour with Morphology and DBSCAN cluster identification algorithm. It was shown that the Simple Nearest-Neighbour still performed with great reliability when simulating objects with small velocities, while the other algorithms performed better for higher velocities and when there were larger clusters present

Advances in interferometric techniques for the analysis of the three-dimensional flow in a lid-driven cylindrical cavity

Abstract: In this work, a qualitative and quantitative characterization of the three-dimensional flow in a lid-driven cylindrical cavity with different optical techniques is presented. Mach–Zehnder interferometry and photographic techniques have been used for a qualitative description of some flow features. However, the real challenge is to obtain quantitative measurements, as the cavity dimensions and geometry prevent the application of 3D digital techniques for measuring the flow velocity in the whole cavity with enough spatial resolution. Digital in-line holography was applied to the measure of the vortex-breakdown bubble that appears near the cavity bottom at Re = 2000. A 22 × 22 × 80 mm3 volume was recorded, its longest dimension parallel to the camera optical axis. This large volume in a liquid fluid combined with a high particle density forces us to develop new analysis strategies. Holograms have been analyzed using a new method, called Adaptive Cross Correlation with Tracking From Beginning, which includes the use of the reconstructed complex amplitude for particle localization. Particle tracking is based on the three-dimensional cross correlation of three-dimensional interrogation windows. The particle set defined in the first hologram is always used to find the particle position in subsequent holograms. This method provides an accurate 3D velocity map and the vortex-breakdown bubble spatial structure. Experimental and numerical data show a very good agreement. A new criterion for determining the accuracy in the particle position along the optical axis is introduced, achieving a spatial resolution of 0.1 mm. This tracking method can be applied not only to laminar flows but also to turbulent flows

Full-field characterisation of epicardial deformation using three dimensional digital image correlation (3D-DIC)

Imaging of the heart provides valuable insight into its functionality and the progression of diseases affecting the cardiac muscle. Currently, ultrasound 2D speckle tracking echocardiography (US-2D-STE) is the most frequently used clinical technique to detect and monitor the progression of cardiovascular disease through changes in strain of the cardiac muscle. However, this imaging modality has several limitations, which reduce the accuracy and reproducibility of the measurement. As a result, the complex behaviour of heart deformation including contraction and twisting cannot be accurately detected by this technique. This thesis describes the development of an optical method based on 3D digital image correlation (3D-DIC) to enable full-field deformation analysis in the heart. The hypothesis of this project is that 3D measurement of local strain in experimental in vitro and ex vivo models of the heart will provide a detailed characterisation of the behaviour of the heart and provide reference measurements for comparison with clinical imaging modalities. The experimental method requires a robust stereo optical system ensuring high-quality and synchronised imaging during heart deformation. The developed methodology was validated through multiple experimental and numerical tests in a zero-strain configuration, which provided an estimate of the error in the reconstruction of strain on the cardiac surface (approximately 1%). Applications in experimental in vitro and ex vivo models of the heart are described. Moreover, a comparison of the performance of 3D-DIC and US-2D-STE under the same conditions of the heart is investigated, demonstrating the superiority of 3D-DIC for dynamic, high-resolution strain measurements (approximately 1.5 mm). However, being an optical technique, 3D-DIC is limited to only surface measurements on the epicardium and requires an effective speckle pattern to be applied on the heart surface, which may pose biocompatible problems and important challenges in its application in Vivo. This experimental work has led to the development of a robust tool for localised and detailed measurement of strain at a high temporal and spatial resolution, with the latter one order of magnitude improved with respect to existing optical techniques. Interpretation of the full-field results can be used to show the non-uniform and inhomogeneous strain distribution on the epicardial surface and identify changes in strain within ex vivo models of cardiac disease