Computerized Analysis of Magnetic Resonance Images to Study Cerebral Anatomy in Developing Neonates

The study of cerebral anatomy in developing neonates is of great importance for the understanding of brain development during the early period of life. This dissertation therefore focuses on three challenges in the modelling of cerebral anatomy in neonates during brain development. The methods that have been developed all use Magnetic Resonance Images (MRI) as source data. To facilitate study of vascular development in the neonatal period, a set of image analysis algorithms are developed to automatically extract and model cerebral vessel trees. The whole process consists of cerebral vessel tracking from automatically placed seed points, vessel tree generation, and vasculature registration and matching. These algorithms have been tested on clinical Time-of- Flight (TOF) MR angiographic datasets. To facilitate study of the neonatal cortex a complete cerebral cortex segmentation and reconstruction pipeline has been developed. Segmentation of the neonatal cortex is not effectively done by existing algorithms designed for the adult brain because the contrast between grey and white matter is reversed. This causes pixels containing tissue mixtures to be incorrectly labelled by conventional methods. The neonatal cortical segmentation method that has been developed is based on a novel expectation-maximization (EM) method with explicit correction for mislabelled partial volume voxels. Based on the resulting cortical segmentation, an implicit surface evolution technique is adopted for the reconstruction of the cortex in neonates. The performance of the method is investigated by performing a detailed landmark study. To facilitate study of cortical development, a cortical surface registration algorithm for aligning the cortical surface is developed. The method first inflates extracted cortical surfaces and then performs a non-rigid surface registration using free-form deformations (FFDs) to remove residual alignment. Validation experiments using data labelled by an expert observer demonstrate that the method can capture local changes and follow the growth of specific sulcus

Modeling Brain Circuitry over a Wide Range of Scales

If we are ever to unravel the mysteries of brain function at its most fundamental level, we will need a precise understanding of how its component neurons connect to each other. Electron Microscopes (EM) can now provide the nanometer resolution that is needed to image synapses, and therefore connections, while Light Microscopes (LM) see at the micrometer resolution required to model the 3D structure of the dendritic network. Since both the topology and the connection strength are integral parts of the brain's wiring diagram, being able to combine these two modalities is critically important. In fact, these microscopes now routinely produce high-resolution imagery in such large quantities that the bottleneck becomes automated processing and interpretation, which is needed for such data to be exploited to its full potential. In this paper, we briefly review the Computer Vision techniques we have developed at EPFL to address this need. They include delineating dendritic arbors from LM imagery, segmenting organelles from EM, and combining the two into a consistent representation

CNN-SLAM: Real-time dense monocular SLAM with learned depth prediction

Given the recent advances in depth prediction from Convolutional Neural Networks (CNNs), this paper investigates how predicted depth maps from a deep neural network can be deployed for accurate and dense monocular reconstruction. We propose a method where CNN-predicted dense depth maps are naturally fused together with depth measurements obtained from direct monocular SLAM. Our fusion scheme privileges depth prediction in image locations where monocular SLAM approaches tend to fail, e.g. along low-textured regions, and vice-versa. We demonstrate the use of depth prediction for estimating the absolute scale of the reconstruction, hence overcoming one of the major limitations of monocular SLAM. Finally, we propose a framework to efficiently fuse semantic labels, obtained from a single frame, with dense SLAM, yielding semantically coherent scene reconstruction from a single view. Evaluation results on two benchmark datasets show the robustness and accuracy of our approach.Comment: 10 pages, 6 figures, IEEE Computer Society Conference on Computer Vision and Pattern Recognition (CVPR), Hawaii, USA, June, 2017. The first two authors contribute equally to this pape

Bi-Plane X-ray coronary 3D reconstruction for flow velocity assessment

In coronary angiography the coronary blood flow velocity can be assessed by tracking a contrast agent in an image sequence. The contrast agent flow velocity is used to estimate the functional behavior of the coronary arteries using TIMI frame count (TFC). In this paper we descibe the 3D reconstruction algorithm used in our method towards the automation of TFC. The method creates a two dimensional map of the contrast agent in which the opacification of the vessel centerline is plotted against time. This map is used to find the velocity of the contrast agent and subsequently the TFC. The vessel centerline is obtained using the Fast Marching Method to find the minimum cost path between\ud the catheter point and the end of the vessel. The determination of the start and endpoint is estimated using a 3D model reconstructed from bi-plane 2D image\ud data. The final reconstructed coronary model only includes the segments matching our error criterion

Structure Preserving Large Imagery Reconstruction

With the explosive growth of web-based cameras and mobile devices, billions of photographs are uploaded to the internet. We can trivially collect a huge number of photo streams for various goals, such as image clustering, 3D scene reconstruction, and other big data applications. However, such tasks are not easy due to the fact the retrieved photos can have large variations in their view perspectives, resolutions, lighting, noises, and distortions. Fur-thermore, with the occlusion of unexpected objects like people, vehicles, it is even more challenging to find feature correspondences and reconstruct re-alistic scenes. In this paper, we propose a structure-based image completion algorithm for object removal that produces visually plausible content with consistent structure and scene texture. We use an edge matching technique to infer the potential structure of the unknown region. Driven by the estimated structure, texture synthesis is performed automatically along the estimated curves. We evaluate the proposed method on different types of images: from highly structured indoor environment to natural scenes. Our experimental results demonstrate satisfactory performance that can be potentially used for subsequent big data processing, such as image localization, object retrieval, and scene reconstruction. Our experiments show that this approach achieves favorable results that outperform existing state-of-the-art techniques

In-loop Feature Tracking for Structure and Motion with Out-of-core Optimization

In this paper, a novel and approach for obtaining 3D models from video sequences captured with hand-held cameras is addressed. We define a pipeline that robustly deals with different types of sequences and acquiring devices. Our system follows a divide and conquer approach: after a frame decimation that pre-conditions the input sequence, the video is split into short-length clips. This allows to parallelize the reconstruction step which translates into a reduction in the amount of computational resources required. The short length of the clips allows an intensive search for the best solution at each step of reconstruction which robustifies the system. The process of feature tracking is embedded within the reconstruction loop for each clip as opposed to other approaches. A final registration step, merges all the processed clips to the same coordinate fram

Data Fusion of Objects Using Techniques Such as Laser Scanning, Structured Light and Photogrammetry for Cultural Heritage Applications

In this paper we present a semi-automatic 2D-3D local registration pipeline capable of coloring 3D models obtained from 3D scanners by using uncalibrated images. The proposed pipeline exploits the Structure from Motion (SfM) technique in order to reconstruct a sparse representation of the 3D object and obtain the camera parameters from image feature matches. We then coarsely register the reconstructed 3D model to the scanned one through the Scale Iterative Closest Point (SICP) algorithm. SICP provides the global scale, rotation and translation parameters, using minimal manual user intervention. In the final processing stage, a local registration refinement algorithm optimizes the color projection of the aligned photos on the 3D object removing the blurring/ghosting artefacts introduced due to small inaccuracies during the registration. The proposed pipeline is capable of handling real world cases with a range of characteristics from objects with low level geometric features to complex ones

Contour Generator Points for Threshold Selection and a Novel Photo-Consistency Measure for Space Carving

Space carving has emerged as a powerful method for multiview scene reconstruction. Although a wide variety of methods have been proposed, the quality of the reconstruction remains highly-dependent on the photometric consistency measure, and the threshold used to carve away voxels. In this paper, we present a novel photo-consistency measure that is motivated by a multiset variant of the chamfer distance. The new measure is robust to high amounts of within-view color variance and also takes into account the projection angles of back-projected pixels. Another critical issue in space carving is the selection of the photo-consistency threshold used to determine what surface voxels are kept or carved away. In this paper, a reliable threshold selection technique is proposed that examines the photo-consistency values at contour generator points. Contour generators are points that lie on both the surface of the object and the visual hull. To determine the threshold, a percentile ranking of the photo-consistency values of these generator points is used. This improved technique is applicable to a wide variety of photo-consistency measures, including the new measure presented in this paper. Also presented in this paper is a method to choose between photo-consistency measures, and voxel array resolutions prior to carving using receiver operating characteristic (ROC) curves