The LONI QC System: A Semi-Automated, Web-Based and Freely-Available Environment for the Comprehensive Quality Control of Neuroimaging Data.

Quantifying, controlling, and monitoring image quality is an essential prerequisite for ensuring the validity and reproducibility of many types of neuroimaging data analyses. Implementation of quality control (QC) procedures is the key to ensuring that neuroimaging data are of high-quality and their validity in the subsequent analyses. We introduce the QC system of the Laboratory of Neuro Imaging (LONI): a web-based system featuring a workflow for the assessment of various modality and contrast brain imaging data. The design allows users to anonymously upload imaging data to the LONI-QC system. It then computes an exhaustive set of QC metrics which aids users to perform a standardized QC by generating a range of scalar and vector statistics. These procedures are performed in parallel using a large compute cluster. Finally, the system offers an automated QC procedure for structural MRI, which can flag each QC metric as being 'good' or 'bad.' Validation using various sets of data acquired from a single scanner and from multiple sites demonstrated the reproducibility of our QC metrics, and the sensitivity and specificity of the proposed Auto QC to 'bad' quality images in comparison to visual inspection. To the best of our knowledge, LONI-QC is the first online QC system that uniquely supports the variety of functionality where we compute numerous QC metrics and perform visual/automated image QC of multi-contrast and multi-modal brain imaging data. The LONI-QC system has been used to assess the quality of large neuroimaging datasets acquired as part of various multi-site studies such as the Transforming Research and Clinical Knowledge in Traumatic Brain Injury (TRACK-TBI) Study and the Alzheimer's Disease Neuroimaging Initiative (ADNI). LONI-QC's functionality is freely available to users worldwide and its adoption by imaging researchers is likely to contribute substantially to upholding high standards of brain image data quality and to implementing these standards across the neuroimaging community

3D Face Reconstruction by Learning from Synthetic Data

Fast and robust three-dimensional reconstruction of facial geometric structure from a single image is a challenging task with numerous applications. Here, we introduce a learning-based approach for reconstructing a three-dimensional face from a single image. Recent face recovery methods rely on accurate localization of key characteristic points. In contrast, the proposed approach is based on a Convolutional-Neural-Network (CNN) which extracts the face geometry directly from its image. Although such deep architectures outperform other models in complex computer vision problems, training them properly requires a large dataset of annotated examples. In the case of three-dimensional faces, currently, there are no large volume data sets, while acquiring such big-data is a tedious task. As an alternative, we propose to generate random, yet nearly photo-realistic, facial images for which the geometric form is known. The suggested model successfully recovers facial shapes from real images, even for faces with extreme expressions and under various lighting conditions.Comment: The first two authors contributed equally to this wor

Towards a digital model of zebrafish embryogenesis. Integration of Cell Tracking and Gene Expression Quantification

We elaborate on a general framework composed of a set of computational tools to accurately quantificate cellular position and gene expression levels throughout early zebrafish embryogenesis captured over a time-lapse series of in vivo 3D images. Our modeling strategy involves nuclei detection, cell geometries extraction, automatic gene levels quantification and cell tracking to reconstruct cell trajectories and lineage tree which describe the animal development. Each cell in the embryo is then precisely described at each given time t by a vector composed of the cell 3D spatial coordinates (x; y; z) along with its gene expression level g. This comprehensive description of the embryo development is used to assess the general connection between genetic expression and cell movement. We also investigate genetic expression propagation between a cell and its progeny in the lineage tree. More to the point, this paper focuses on the evolution of the expression pattern of transcriptional factor goosecoid (gsc) through the gastrulation process between 6 and 9 hours post fertilization (hpf

Navigace mobilních robotů v neznámém prostředí s využitím měření vzdáleností

The ability of a robot to navigate itself in the environment is a crucial step towards its autonomy. Navigation as a subtask of the development of autonomous robots is the subject of this thesis, focusing on the development of a method for simultaneous localization an mapping (SLAM) of mobile robots in six degrees of freedom (DOF). As a part of this research, a platform for 3D range data acquisition based on a continuously inclined laser rangefinder was developed. This platform is presented, evaluating the measurements and also presenting the robotic equipment on which the platform can be fitted. The localization and mapping task is equal to the registration of multiple 3D images into a common frame of reference. For this purpose, a method based on the Iterative Closest Point (ICP) algorithm was developed. First, the originally implemented SLAM method is presented, focusing on the time-wise performance and the registration quality issues introduced by the implemented algorithms. In order to accelerate and improve the quality of the time-demanding 6DOF image registration, an extended method was developed. The major extension is the introduction of a factorized registration, extracting 2D representations of vertical objects called leveled maps from the 3D point sets, ensuring these representations are 3DOF invariant. The extracted representations are registered in 3DOF using ICP algorithm, allowing pre-alignment of the 3D data for the subsequent robust 6DOF ICP based registration. The extended method is presented, showing all important modifications to the original method. The developed registration method was evaluated using real 3D data acquired in different indoor environments, examining the benefits of the factorization and other extensions as well as the performance of the original ICP based method. The factorization gives promising results compared to a single phase 6DOF registration in vertically structured environments. Also, the disadvantages of the method are discussed, proposing possible solutions. Finally, the future prospects of the research are presented.Schopnost lokalizace a navigace je podmínkou autonomního provozu mobilních robotů. Předmětem této disertační práce jsou navigační metody se zaměřením na metodu pro simultánní lokalizaci a mapování (SLAM) mobilních robotů v šesti stupních volnosti (6DOF). Nedílnou součástí tohoto výzkumu byl vývoj platformy pro sběr 3D vzdálenostních dat s využitím kontinuálně naklápěného laserového řádkového scanneru. Tato platforma byla vyvinuta jako samostatný modul, aby mohla být umístěna na různé šasi mobilních robotů. Úkol lokalizace a mapování je ekvivalentní registraci více 3D obrazů do společného souřadného systému. Pro tyto účely byla vyvinuta metoda založená na algoritmu Iterative Closest Point Algorithm (ICP). Původně implementovaná verze navigační metody využívá ICP s akcelerací pomocí kd-stromů přičemž jsou zhodnoceny její kvalitativní a výkonnostní aspekty. Na základě této analýzy byly vyvinuty rozšíření původní metody založené na ICP. Jednou z hlavních modifikací je faktorizace registračního procesu, kdy tato faktorizace je založena na redukci dat: vytvoření 2D „leveled“ map (ve smyslu jednoúrovňových map) ze 3D vzdálenostních obrazů. Pro tuto redukci je technologicky i algoritmicky zajištěna invariantnost těchto map vůči třem stupňům volnosti. Tyto redukované mapy jsou registrovány pomocí ICP ve zbylých třech stupních volnosti, přičemž získaná transformace je aplikována na 3D data za účelem před-registrace 3D obrazů. Následně je provedena robustní 6DOF registrace. Rozšířená metoda je v disertační práci v popsána spolu se všemi podstatnými modifikacemi. Vyvinutá metoda byla otestována a zhodnocena s využitím skutečných 3D vzdálenostních dat naměřených v různých vnitřních prostředích. Jsou zhodnoceny přínosy faktorizace a jiných modifikací ve srovnání s původní jednofázovou 6DOF registrací, také jsou zmíněny nevýhody implementované metody a navrženy způsoby jejich řešení. Nakonec následuje návrh budoucího výzkumu a diskuse o možnostech dalšího rozvoje.