Surface Reconstruction from Noisy and Sparse Data

We introduce a set of algorithms for registering, filtering and measuring the similarity of unorganized 3d point clouds, usually obtained from multiple views. We contribute a method for computing the similarity between point clouds that represent closed surfaces, specifically segmented tumors from CT scans. We obtain watertight surfaces and utilize volumetric overlap to determine similarity in a volumetric way. This similarity measure is used to quantify treatment variability based on target volume segmentation both prior to and following radiotherapy planning stages. We also contribute an algorithm for the drift-free registration of thin, non- rigid scans, where drift is the build-up of error caused by sequential pairwise registration, which is the alignment of each scan to its neighbor. We construct an average scan using mutual nearest neighbors, each scan is registered to this average scan, after which we update the average scan and continue this process until convergence. The use case herein is for merging scans of plants from multiple views and registering vascular scans together. Our final contribution is a method for filtering noisy point clouds, specif- ically those constructed from merged depth maps as obtained from a range scanner or multiple view stereo (MVS), applying techniques that have been utilized in finding outliers in clustered data, but not in MVS. We utilize ker- nel density estimation to obtain a probability density function over the space of observed points, utilizing variable bandwidths based on the nature of the neighboring points, Mahalanobis and reachability distances that is more dis- criminative than a classical Mahalanobis distance-based metric

Biological image analysis

In biological research images are extensively used to monitor growth, dynamics and changes in biological specimen, such as cells or plants. Many of these images are used solely for observation or are manually annotated by an expert. In this dissertation we discuss several methods to automate the annotating and analysis of bio-images. Two large clusters of methods have been investigated and developed. A first set of methods focuses on the automatic delineation of relevant objects in bio-images, such as individual cells in microscopic images. Since these methods should be useful for many different applications, e.g. to detect and delineate different objects (cells, plants, leafs, ...) in different types of images (different types of microscopes, regular colour photographs, ...), the methods should be easy to adjust. Therefore we developed a methodology relying on probability theory, where all required parameters can easily be estimated by a biologist, without requiring any knowledge on the techniques used in the actual software. A second cluster of investigated techniques focuses on the analysis of shapes. By defining new features that describe shapes, we are able to automatically classify shapes, retrieve similar shapes from a database and even analyse how an object deforms through time

Learning Instance Segmentation from Sparse Supervision

Instance segmentation is an important task in many domains of automatic image processing, such as self-driving cars, robotics and microscopy data analysis. Recently, deep learning-based algorithms have brought image segmentation close to human performance. However, most existing models rely on dense groundtruth labels for training, which are expensive, time consuming and often require experienced annotators to perform the labeling. Besides the annotation burden, training complex high-capacity neural networks depends upon non-trivial expertise in the choice and tuning of hyperparameters, making the adoption of these models challenging for researchers in other fields. The aim of this work is twofold. The first is to make the deep learning segmentation methods accessible to non-specialist. The second is to address the dense annotation problem by developing instance segmentation methods trainable with limited groundtruth data. In the first part of this thesis, I bring state-of-the-art instance segmentation methods closer to non-experts by developing PlantSeg: a pipeline for volumetric segmentation of light microscopy images of biological tissues into cells. PlantSeg comes with a large repository of pre-trained models and delivers highly accurate results on a variety of samples and image modalities. We exemplify its usefulness to answer biological questions in several collaborative research projects. In the second part, I tackle the dense annotation bottleneck by introducing SPOCO, an instance segmentation method, which can be trained from just a few annotated objects. It demonstrates strong segmentation performance on challenging natural and biological benchmark datasets at a very reduced manual annotation cost and delivers state-of-the-art results on the CVPPP benchmark. In summary, my contributions enable training of instance segmentation models with limited amounts of labeled data and make these methods more accessible for non-experts, speeding up the process of quantitative data analysis

Study of Computational Image Matching Techniques: Improving Our View of Biomedical Image Data

Image matching techniques are proven to be necessary in various fields of science and engineering, with many new methods and applications introduced over the years. In this PhD thesis, several computational image matching methods are introduced and investigated for improving the analysis of various biomedical image data. These improvements include the use of matching techniques for enhancing visualization of cross-sectional imaging modalities such as Computed Tomography (CT) and Magnetic Resonance Imaging (MRI), denoising of retinal Optical Coherence Tomography (OCT), and high quality 3D reconstruction of surfaces from Scanning Electron Microscope (SEM) images. This work greatly improves the process of data interpretation of image data with far reaching consequences for basic sciences research. The thesis starts with a general notion of the problem of image matching followed by an overview of the topics covered in the thesis. This is followed by introduction and investigation of several applications of image matching/registration in biomdecial image processing: a) registration-based slice interpolation, b) fast mesh-based deformable image registration and c) use of simultaneous rigid registration and Robust Principal Component Analysis (RPCA) for speckle noise reduction of retinal OCT images. Moving towards a different notion of image matching/correspondence, the problem of view synthesis and 3D reconstruction, with a focus on 3D reconstruction of microscopic samples from 2D images captured by SEM, is considered next. Starting from sparse feature-based matching techniques, an extensive analysis is provided for using several well-known feature detector/descriptor techniques, namely ORB, BRIEF, SURF and SIFT, for the problem of multi-view 3D reconstruction. This chapter contains qualitative and quantitative comparisons in order to reveal the shortcomings of the sparse feature-based techniques. This is followed by introduction of a novel framework using sparse-dense matching/correspondence for high quality 3D reconstruction of SEM images. As will be shown, the proposed framework results in better reconstructions when compared with state-of-the-art sparse-feature based techniques. Even though the proposed framework produces satisfactory results, there is room for improvements. These improvements become more necessary when dealing with higher complexity microscopic samples imaged by SEM as well as in cases with large displacements between corresponding points in micrographs. Therefore, based on the proposed framework, a new approach is proposed for high quality 3D reconstruction of microscopic samples. While in case of having simpler microscopic samples the performance of the two proposed techniques are comparable, the new technique results in more truthful reconstruction of highly complex samples. The thesis is concluded with an overview of the thesis and also pointers regarding future directions of the research using both multi-view and photometric techniques for 3D reconstruction of SEM images

Tracking-by-Assignment as a Probabilistic Graphical Model with Applications in Developmental Biology

This thesis presents a novel approach for tracking a varying number of divisible objects with similar appearance in the presence of a non-negligible number of false positive detections (more than 10%). It is applied to the reconstruction of cell lineages in developing zebrafish and fruit fly embryos from 3d time-lapse record- ings. The model takes the form of a chain graph—a mixed directed-undirected probabilistic graphical model—and a tracking is obtained simultaneously over all time slices from the maximum a-posteriori configuration. The tracking model is used as the second step in a two-step pipeline to produce digital embryos—maps of cell nuclei in an embryo and their ancestral fate; the first step being the segmentation of the fluorescently-stained cell nuclei in light sheet microscopy images. The pipeline is implemented as a software with an intuitive graphical user interface. It is the first freely available program of its kind and makes the presented methods accessible to a broad audience of users from the life sciences

3D exemplar-based image inpainting in electron microscopy

In electron microscopy (EM) a common problem is the non-availability of data, which causes artefacts in reconstructions. In this thesis the goal is to generate artificial data where missing in EM by using exemplar-based inpainting (EBI). We implement an accelerated 3D version tailored to applications in EM, which reduces reconstruction times from days to minutes. We develop intelligent sampling strategies to find optimal data as input for reconstruction methods. Further, we investigate approaches to reduce electron dose and acquisition time. Sparse sampling followed by inpainting is the most promising approach. As common evaluation measures may lead to misinterpretation of results in EM and falsify a subsequent analysis, we propose to use application driven metrics and demonstrate this in a segmentation task. A further application of our technique is the artificial generation of projections in tiltbased EM. EBI is used to generate missing projections, such that the full angular range is covered. Subsequent reconstructions are significantly enhanced in terms of resolution, which facilitates further analysis of samples. In conclusion, EBI proves promising when used as an additional data generation step to tackle the non-availability of data in EM, which is evaluated in selected applications. Enhancing adaptive sampling methods and refining EBI, especially considering the mutual influence, promotes higher throughput in EM using less electron dose while not lessening quality.Ein häufig vorkommendes Problem in der Elektronenmikroskopie (EM) ist die Nichtverfügbarkeit von Daten, was zu Artefakten in Rekonstruktionen führt. In dieser Arbeit ist es das Ziel fehlende Daten in der EM künstlich zu erzeugen, was durch Exemplar-basiertes Inpainting (EBI) realisiert wird. Wir implementieren eine auf EM zugeschnittene beschleunigte 3D Version, welche es ermöglicht, Rekonstruktionszeiten von Tagen auf Minuten zu reduzieren. Wir entwickeln intelligente Abtaststrategien, um optimale Datenpunkte für die Rekonstruktion zu erhalten. Ansätze zur Reduzierung von Elektronendosis und Aufnahmezeit werden untersucht. Unterabtastung gefolgt von Inpainting führt zu den besten Resultaten. Evaluationsmaße zur Beurteilung der Rekonstruktionsqualität helfen in der EM oft nicht und können zu falschen Schlüssen führen, weswegen anwendungsbasierte Metriken die bessere Wahl darstellen. Dies demonstrieren wir anhand eines Beispiels. Die künstliche Erzeugung von Projektionen in der neigungsbasierten Elektronentomographie ist eine weitere Anwendung. EBI wird verwendet um fehlende Projektionen zu generieren. Daraus resultierende Rekonstruktionen weisen eine deutlich erhöhte Auflösung auf. EBI ist ein vielversprechender Ansatz, um nicht verfügbare Daten in der EM zu generieren. Dies wird auf Basis verschiedener Anwendungen gezeigt und evaluiert. Adaptive Aufnahmestrategien und EBI können also zu einem höheren Durchsatz in der EM führen, ohne die Bildqualität merklich zu verschlechtern

Virtuaalse proovikabiini 3D kehakujude ja roboti juhtimisalgoritmide uurimine

Väitekirja elektrooniline versioon ei sisalda publikatsiooneVirtuaalne riiete proovimine on üks põhilistest teenustest, mille pakkumine võib suurendada rõivapoodide edukust, sest tänu sellele lahendusele väheneb füüsilise töö vajadus proovimise faasis ning riiete proovimine muutub kasutaja jaoks mugavamaks. Samas pole enamikel varem välja pakutud masinnägemise ja graafika meetoditel õnnestunud inimkeha realistlik modelleerimine, eriti terve keha 3D modelleerimine, mis vajab suurt kogust andmeid ja palju arvutuslikku ressurssi. Varasemad katsed on ebaõnnestunud põhiliselt seetõttu, et ei ole suudetud korralikult arvesse võtta samaaegseid muutusi keha pinnal. Lisaks pole varasemad meetodid enamasti suutnud kujutiste liikumisi realistlikult reaalajas visualiseerida. Käesolev projekt kavatseb kõrvaldada eelmainitud puudused nii, et rahuldada virtuaalse proovikabiini vajadusi. Välja pakutud meetod seisneb nii kasutaja keha kui ka riiete skaneerimises, analüüsimises, modelleerimises, mõõtmete arvutamises, orientiiride paigutamises, mannekeenidelt võetud 3D visuaalsete andmete segmenteerimises ning riiete mudeli paigutamises ja visualiseerimises kasutaja kehal. Selle projekti käigus koguti visuaalseid andmeid kasutades 3D laserskannerit ja Kinecti optilist kaamerat ning koostati nendest andmebaas. Neid andmeid kasutati välja töötatud algoritmide testimiseks, mis peamiselt tegelevad riiete realistliku visuaalse kujutamisega inimkehal ja suuruse pakkumise süsteemi täiendamisega virtuaalse proovikabiini kontekstis.Virtual fitting constitutes a fundamental element of the developments expected to rise the commercial prosperity of online garment retailers to a new level, as it is expected to reduce the load of the manual labor and physical efforts required. Nevertheless, most of the previously proposed computer vision and graphics methods have failed to accurately and realistically model the human body, especially, when it comes to the 3D modeling of the whole human body. The failure is largely related to the huge data and calculations required, which in reality is caused mainly by inability to properly account for the simultaneous variations in the body surface. In addition, most of the foregoing techniques cannot render realistic movement representations in real-time. This project intends to overcome the aforementioned shortcomings so as to satisfy the requirements of a virtual fitting room. The proposed methodology consists in scanning and performing some specific analyses of both the user's body and the prospective garment to be virtually fitted, modeling, extracting measurements and assigning reference points on them, and segmenting the 3D visual data imported from the mannequins. Finally, superimposing, adopting and depicting the resulting garment model on the user's body. The project is intended to gather sufficient amounts of visual data using a 3D laser scanner and the Kinect optical camera, to manage it in form of a usable database, in order to experimentally implement the algorithms devised. The latter will provide a realistic visual representation of the garment on the body, and enhance the size-advisor system in the context of the virtual fitting room under study