Left-ventricle myocardium segmentation using a coupled level-set with a priori knowledge

This paper presents a coupled level-set segmentation of the myocardium of the left ventricle of the heart using a priori information. From a fast marching initialisation, two fronts representing the endocardium and epicardium boundaries of the left ventricle are evolved as the zero level-set of a higher dimension function. We introduce a novel and robust stopping term using both gradient and region-based information. The segmentation is supervised both with a coupling function and using a probabilistic model built from training instances. The robustness of the segmentation scheme is evaluated by performing a segmentation on four unseen data-sets containing high variation and the performance of the segmentation is quantitatively assessed

Discrete Visual Perception

International audienceComputational vision and biomedical image have made tremendous progress of the past decade. This is mostly due the development of efficient learning and inference algorithms which allow better, faster and richer modeling of visual perception tasks. Graph-based representations are among the most prominent tools to address such perception through the casting of perception as a graph optimization problem. In this paper, we briefly introduce the interest of such representations, discuss their strength and limitations and present their application to address a variety of problems in computer vision and biomedical image analysis

Modeling the structure of multivariate manifolds: Shape maps

We propose a shape population metric that reflects the interdependencies between points observed in a set of examples. It provides a notion of topology for shape and appearance models that represents the behavior of individual observations in a metric space, in which distances between points correspond to their joint modeling properties. A Markov chain is learnt using the description lengths of models that describe sub sets of the entire data. The according diffusion map or shape map provides for the metric that reflects the behavior of the training population. With this metric functional clustering, deformation- or motion segmentation, sparse sampling and the treatment of outliers can be dealt with in a unified and transparent manner. We report experimental results on synthetic and real world data and compare the framework with existing specialized approaches. 1

EnzyNet: enzyme classification using 3D convolutional neural networks on spatial representation

During the past decade, with the significant progress of computational power as well as ever-rising data availability, deep learning techniques became increasingly popular due to their excellent performance on computer vision problems. The size of the Protein Data Bank has increased more than 15 fold since 1999, which enabled the expansion of models that aim at predicting enzymatic function via their amino acid composition. Amino acid sequence however is less conserved in nature than protein structure and therefore considered a less reliable predictor of protein function. This paper presents EnzyNet, a novel 3D-convolutional neural networks classifier that predicts the Enzyme Commission number of enzymes based only on their voxel-based spatial structure. The spatial distribution of biochemical properties was also examined as complementary information. The 2-layer architecture was investigated on a large dataset of 63,558 enzymes from the Protein Data Bank and achieved an accuracy of 78.4% by exploiting only the binary representation of the protein shape. Code and datasets are available at https://github.com/shervinea/enzynet.Comment: 11 pages, 6 figure

Customized design of hearing aids using statistical shape learning

3D shape modeling is a crucial component of rapid prototyping systems that customize shapes of implants and prosthetic devices to a patient’s anatomy. In this paper, we present a solution to the problem of customized 3D shape modeling using a statistical shape analysis framework. We design a novel method to learn the relationship between two classes of shapes, which are related by certain operations or transformation. The two associated shape classes are represented in a lower dimensional manifold, and the reduced set of parameters obtained in this subspace is utilized in an estimation, which is exemplified by a multivariate regression in this paper.We demonstrate our method with a felicitous application to estimation of customized hearing aid devices

Sub-cortical brain structure segmentation using F-CNN's

In this paper we propose a deep learning approach for segmenting sub-cortical structures of the human brain in Magnetic Resonance (MR) image data. We draw inspiration from a state-of-the-art Fully-Convolutional Neural Network (F-CNN) architecture for semantic segmentation of objects in natural images, and adapt it to our task. Unlike previous CNN-based methods that operate on image patches, our model is applied on a full blown 2D image, without any alignment or registration steps at testing time. We further improve segmentation results by interpreting the CNN output as potentials of a Markov Random Field (MRF), whose topology corresponds to a volumetric grid. Alpha-expansion is used to perform approximate inference imposing spatial volumetric homogeneity to the CNN priors. We compare the performance of the proposed pipeline with a similar system using Random Forest-based priors, as well as state-of-art segmentation algorithms, and show promising results on two different brain MRI datasets.Comment: ISBI 2016: International Symposium on Biomedical Imaging, Apr 2016, Prague, Czech Republi

A Variational Framework for the Simultaneous Segmentation and Object Behavior Classification of Image Sequences

In this paper, we advance the state of the art in variational image segmentation through the fusion of bottom-up segmentation and top-down classification of object behavior over an image sequence. Such an approach is beneficial for both tasks and is carried out through a joint optimization, which enables the two tasks to cooperate, such that knowledge relevant to each can aid in the resolution of the other, thereby enhancing the final result. In particular, classification offers dynamic probabilistic priors to guide segmentation, while segmentation supplies its results to classification, ensuring that they are consistent with prior knowledge. The prior models are learned from training data and updated dynamically, based on segmentations of earlier images in the sequence. We demonstrate the potential of our approach in a hand gesture recognition application, where the combined use of segmentation and classification improves robustness in the presence of occlusion and background complexity

Learning Grammars for Architecture-Specific Facade Parsing

International audienceParsing facade images requires optimal handcrafted grammar for a given class of buildings. Such a handcrafted grammar is often designed manually by experts. In this paper, we present a novel framework to learn a compact grammar from a set of ground-truth images. To this end, parse trees of ground-truth annotated images are obtained running existing inference algorithms with a simple, very general grammar. From these parse trees, repeated subtrees are sought and merged together to share derivations and produce a grammar with fewer rules. Furthermore, unsupervised clustering is performed on these rules, so that, rules corresponding to the same complex pattern are grouped together leading to a rich compact grammar. Experimental validation and comparison with the state-of-the-art grammar-based methods on four diff erent datasets show that the learned grammar helps in much faster convergence while producing equal or more accurate parsing results compared to handcrafted grammars as well as grammars learned by other methods. Besides, we release a new dataset of facade images from Paris following the Art-deco style and demonstrate the general applicability and extreme potential of the proposed framework