New implementations of phase-contrast imaging

Phase-contrast imaging is a method of imaging widely used in biomedical research and applications. It is a label-free method that exploits intrinsic differences in the refractive index of different tissues to differentiate between biological structures under analysis. The basic principle of phase-contrast imaging has inspired a lot of implementations that are suited for different applications. This thesis explores multiple novel implementations of phase-contrast imaging in the following order. 1, We combined scanning Oblique Back-illumination Microscope (sOBM) and confocal microscope to produce phase and fluorescence contrast images in an endomicroscopy configuration. This dual-modality design provides co-registered, complementary labeled and unlabeled contrast of the sample. We further miniaturized the probe by dispensing the two optical fibers in our old design. And we presented proof of principle demonstrations with ex-vivo mouse colon tissue. 2, Then we explored sOBM-based phase and amplitude contrast imaging under different wavelengths. Hyperspectral imaging is achieved by multiplexing a wide-range supercontinuum laser with a Michaelson interferometer (similar to Fourier transform spectroscopy). It features simultaneous acquisition of hyperspectral phase and amplitude images with arbitrarily thick scattering biological samples. Proof-of-principle demonstrations are presented with chorioallantoic membrane of a chick embryo, illustrating the possibility of high-resolution hemodynamics imaging in thick tissue. 3, We focused on increasing the throughput of flow cytometry with principle of phase-contrast imaging and compressive sensing. By utilizing the linearity of scattered patterns under partially coherent illumination, our cytometer can detect multiple objects in the same field of view. By utilizing an optimized matched filter on pupil plane, it also provides increased information capacity of each measurement without sacrificing speed. We demonstrated a throughput of over 10,000 particles/s with accuracy over 91% in our results. 4, A fourth part, which describes the principle and preliminary results of a computational fluorescence endomicroscope is also included. It uses a numerical method to achieve sectioning effect and renders a pseudo-3D image stack with a single shot. The results are compared with true-3D image stack acquired with a confocal microscope

Automatic Change-based Diagnosis of Structures Using Spatiotemporal Data and As- Designed Model

abstract: Civil infrastructures undergo frequent spatial changes such as deviations between as-designed model and as-is condition, rigid body motions of the structure, and deformations of individual elements of the structure, etc. These spatial changes can occur during the design phase, the construction phase, or during the service life of a structure. Inability to accurately detect and analyze the impact of such changes may miss opportunities for early detections of pending structural integrity and stability issues. Commercial Building Information Modeling (BIM) tools could hardly track differences between as-designed and as-built conditions as they mainly focus on design changes and rely on project managers to manually update and analyze the impact of field changes on the project performance. Structural engineers collect detailed onsite data of a civil infrastructure to perform manual updates of the model for structural analysis, but such approach tends to become tedious and complicated while handling large civil infrastructures. Previous studies started collecting detailed geometric data generated by 3D laser scanners for defect detection and geometric change analysis of structures. However, previous studies have not yet systematically examined methods for exploring the correlation between the detected geometric changes and their relation to the behaviors of the structural system. Manually checking every possible loading combination leading to the observed geometric change is tedious and sometimes error-prone. The work presented in this dissertation develops a spatial change analysis framework that utilizes spatiotemporal data collected using 3D laser scanning technology and the as-designed models of the structures to automatically detect, classify, and correlate the spatial changes of a structure. The change detection part of the developed framework is computationally efficient and can automatically detect spatial changes between as-designed model and as-built data or between two sets of as-built data collected using 3D laser scanning technology. Then a spatial change classification algorithm automatically classifies the detected spatial changes as global (rigid body motion) and local deformations (tension, compression). Finally, a change correlation technique utilizes a qualitative shape-based reasoning approach for identifying correlated deformations of structure elements connected at joints that contradicts the joint equilibrium. Those contradicting deformations can help to eliminate improbable loading combinations therefore guiding the loading path analysis of the structure.Dissertation/ThesisDoctoral Dissertation Civil and Environmental Engineering 201

3D Reconstruction of Indoor Corridor Models Using Single Imagery and Video Sequences

In recent years, 3D indoor modeling has gained more attention due to its role in decision-making process of maintaining the status and managing the security of building indoor spaces. In this thesis, the problem of continuous indoor corridor space modeling has been tackled through two approaches. The first approach develops a modeling method based on middle-level perceptual organization. The second approach develops a visual Simultaneous Localisation and Mapping (SLAM) system with model-based loop closure. In the first approach, the image space was searched for a corridor layout that can be converted into a geometrically accurate 3D model. Manhattan rule assumption was adopted, and indoor corridor layout hypotheses were generated through a random rule-based intersection of image physical line segments and virtual rays of orthogonal vanishing points. Volumetric reasoning, correspondences to physical edges, orientation map and geometric context of an image are all considered for scoring layout hypotheses. This approach provides physically plausible solutions while facing objects or occlusions in a corridor scene. In the second approach, Layout SLAM is introduced. Layout SLAM performs camera localization while maps layout corners and normal point features in 3D space. Here, a new feature matching cost function was proposed considering both local and global context information. In addition, a rotation compensation variable makes Layout SLAM robust against cameras orientation errors accumulations. Moreover, layout model matching of keyframes insures accurate loop closures that prevent miss-association of newly visited landmarks to previously visited scene parts. The comparison of generated single image-based 3D models to ground truth models showed that average ratio differences in widths, heights and lengths were 1.8%, 3.7% and 19.2% respectively. Moreover, Layout SLAM performed with the maximum absolute trajectory error of 2.4m in position and 8.2 degree in orientation for approximately 318m path on RAWSEEDS data set. Loop closing was strongly performed for Layout SLAM and provided 3D indoor corridor layouts with less than 1.05m displacement errors in length and less than 20cm in width and height for approximately 315m path on York University data set. The proposed methods can successfully generate 3D indoor corridor models compared to their major counterpart

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

2D and 3D surface image processing algorithms and their applications

This doctoral dissertation work aims to develop algorithms for 2D image segmentation application of solar filament disappearance detection, 3D mesh simplification, and 3D image warping in pre-surgery simulation. Filament area detection in solar images is an image segmentation problem. A thresholding and region growing combined method is proposed and applied in this application. Based on the filament area detection results, filament disappearances are reported in real time. The solar images in 1999 are processed with this proposed system and three statistical results of filaments are presented. 3D images can be obtained by passive and active range sensing. An image registration process finds the transformation between each pair of range views. To model an object, a common reference frame in which all views can be transformed must be defined. After the registration, the range views should be integrated into a non-redundant model. Optimization is necessary to obtain a complete 3D model. One single surface representation can better fit to the data. It may be further simplified for rendering, storing and transmitting efficiently, or the representation can be converted to some other formats. This work proposes an efficient algorithm for solving the mesh simplification problem, approximating an arbitrary mesh by a simplified mesh. The algorithm uses Root Mean Square distance error metric to decide the facet curvature. Two vertices of one edge and the surrounding vertices decide the average plane. The simplification results are excellent and the computation speed is fast. The algorithm is compared with six other major simplification algorithms. Image morphing is used for all methods that gradually and continuously deform a source image into a target image, while producing the in-between models. Image warping is a continuous deformation of a: graphical object. A morphing process is usually composed of warping and interpolation. This work develops a direct-manipulation-of-free-form-deformation-based method and application for pre-surgical planning. The developed user interface provides a friendly interactive tool in the plastic surgery. Nose augmentation surgery is presented as an example. Displacement vector and lattices resulting in different resolution are used to obtain various deformation results. During the deformation, the volume change of the model is also considered based on a simplified skin-muscle model

Digital Holography Microscopy at Lab-on-a-Chip scale: novel algorithms and recording strategies

Il lavoro presentato è mirato allo sviluppo di nuove tecniche di microscopia olografica digitale (Digital Holography Microscopy, DHM), e di opportuni algoritmi numerici per lo studio di biomateriali in ambiente microfluidico. Nello specifico vengono affrontate due problematiche di imaging particolarmente rilevanti nello studio di sistemi Lab-on-a-Chip (LoC). Dapprima è stato studiato il problema della microscopia quantitativa di oggetti biologici osservati attraverso mezzi complessi, come soluzioni torbide e substrati diffondenti, dove la formazione dell’immagine è ostacolata da processi di scattering. Lo studio condotto è stato mirato all’analisi di processi di diffusione da layer statico e da mezzo liquido di tipo colloidale, in regime quasi-statico e dinamico. Sono stati sviluppati a tale scopo dei metodi di registrazione e nuovi algoritmi di ricostruzione dell’immagine olografica (Multi-Look Digital Holography, MLDH) che consentono di fornire un imaging quantitativo dei campioni in esame. Di particolare interesse è il caso di volumi di liquido costituiti da globuli rossi: nel lavoro presentato viene dimostrata la possibilità di studiare, mediante MLDH, processi di adesione cellulare di materiale biologico situato in presenza di flussi di globuli rossi ad alta concentrazione. La possibilità di visualizzare e analizzare quantitativamente materiale biologico all’interno di un capillare o una vena, compensando l’effetto di diffusione del sangue, potrebbe in futuro consentire di studiare la formazione all’interno del vaso di coaguli e placche di colesterolo, sintomatici dell’insorgere di malattie cardiache. La stessa tecnica è in grado di recuperare l’informazione distorta a causa della presenza all’interno del canale di ostacoli statici o quasi-statici (dovuti alla formazione di bio-film o sospensioni batteriche, o causata da processi di fabbricazione del canale microfluidico), aumentando così notevolmente la varietà dei processi biologici analizzabili su piattaforme LoC. Nel lavoro viene anche dimostrato come la presenza di un mezzo torbido possa essere sfruttata vantaggiosamente al fine di migliorare la qualità dell’immagine in sistemi di imaging basati su luce coerente. Parallelamente è stata messa a punto una tecnica interferometrica che, sfruttando il movimento dei campioni nei canali microfluidici, consente di sostituire un sensore convenzionale 2D con un sensore lineare, più compatto e integrabile a bordo del chip, e capace di fornire prestazioni superiori in termini di velocità di acquisizione. Il lavoro presentato descrive il processo di sintesi di un nuovo tipo di ologramma (Space-Time Digital Hologram, STDH), che consente di ottenere un Field-of-View (FoV) illimitato nella direzione del flusso e, quindi, di superare il trade-off esistente tra fattore di ingrandimento e FoV, comune ad ogni tecnica di microscopia convenzionale. Viene inoltre dimostrato che un STDH mantiene le caratteristiche e i vantaggi di un ologramma digitale standard, quali la focalizzazione numerica flessibile, che permette di analizzare contemporaneamente tutti gli oggetti presenti in un volume di liquido, e la possibilità di estrarre la segnatura di fase degli stessi

Low-rank Based Algorithms for Rectification, Repetition Detection and De-noising in Urban Images

In this thesis, we aim to solve the problem of automatic image rectification and repeated patterns detection on 2D urban images, using novel low-rank based techniques. Repeated patterns (such as windows, tiles, balconies and doors) are prominent and significant features in urban scenes. Detection of the periodic structures is useful in many applications such as photorealistic 3D reconstruction, 2D-to-3D alignment, facade parsing, city modeling, classification, navigation, visualization in 3D map environments, shape completion, cinematography and 3D games. However both of the image rectification and repeated patterns detection problems are challenging due to scene occlusions, varying illumination, pose variation and sensor noise. Therefore, detection of these repeated patterns becomes very important for city scene analysis. Given a 2D image of urban scene, we automatically rectify a facade image and extract facade textures first. Based on the rectified facade texture, we exploit novel algorithms that extract repeated patterns by using Kronecker product based modeling that is based on a solid theoretical foundation. We have tested our algorithms in a large set of images, which includes building facades from Paris, Hong Kong and New York