arXiv subjects

Nassir Navab

Publications and source records attributed to Nassir Navab.

571 records · Page 32Linked to original sources

arXiv2016

Deeper Depth Prediction with Fully Convolutional Residual Networks

This paper addresses the problem of estimating the depth map of a scene given a single RGB image. We propose a fully convolutional architecture, encompassing residual learning, to model the ambiguous mapping between monocular images and depth maps. In order to improve the output resolution, we present a novel way to efficiently learn feature map up-sampling within the network. For optimization, we introduce the reverse Huber loss that is particularly suited for the task at hand and driven by the value distributions commonly present in depth maps. Our model is composed of a single architecture that is trained end-to-end and does not rely on post-processing techniques, such as CRFs or other additional refinement steps. As a result, it runs in real-time on images or videos. In the evaluation, we show that the proposed model contains fewer parameters and requires fewer training data than the current state of the art, while outperforming all approaches on depth estimation. Code and models are publicly available.

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arXiv2016

A Deep Metric for Multimodal Registration

Multimodal registration is a challenging problem in medical imaging due the high variability of tissue appearance under different imaging modalities. The crucial component here is the choice of the right similarity measure. We make a step towards a general learning-based solution that can be adapted to specific situations and present a metric based on a convolutional neural network. Our network can be trained from scratch even from a few aligned image pairs. The metric is validated on intersubject deformable registration on a dataset different from the one used for training, demonstrating good generalization. In this task, we outperform mutual information by a significant margin.

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arXiv2016

An Octree-Based Approach towards Efficient Variational Range Data Fusion

Volume-based reconstruction is usually expensive both in terms of memory consumption and runtime. Especially for sparse geometric structures, volumetric representations produce a huge computational overhead. We present an efficient way to fuse range data via a variational Octree-based minimization approach by taking the actual range data geometry into account. We transform the data into Octree-based truncated signed distance fields and show how the optimization can be conducted on the newly created structures. The main challenge is to uphold speed and a low memory footprint without sacrificing the solutions' accuracy during optimization. We explain how to dynamically adjust the optimizer's geometric structure via joining/splitting of Octree nodes and how to define the operators. We evaluate on various datasets and outline the suitability in terms of performance and geometric accuracy.

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arXiv2016

Mitosis Detection in Intestinal Crypt Images with Hough Forest and Conditional Random Fields

Intestinal enteroendocrine cells secrete hormones that are vital for the regulation of glucose metabolism but their differentiation from intestinal stem cells is not fully understood. Asymmetric stem cell divisions have been linked to intestinal stem cell homeostasis and secretory fate commitment. We monitored cell divisions using 4D live cell imaging of cultured intestinal crypts to characterize division modes by means of measurable features such as orientation or shape. A statistical analysis of these measurements requires annotation of mitosis events, which is currently a tedious and time-consuming task that has to be performed manually. To assist data processing, we developed a learning based method to automatically detect mitosis events. The method contains a dual-phase framework for joint detection of dividing cells (mothers) and their progeny (daughters). In the first phase we detect mother and daughters independently using Hough Forest whilst in the second phase we associate mother and daughters by modelling their joint probability as Conditional Random Field (CRF). The method has been evaluated on 32 movies and has achieved an AUC of 72%, which can be used in conjunction with manual correction and dramatically speed up the processing pipeline.

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arXiv2016

Towards MRI-Based Autonomous Robotic US Acquisitions: A First Feasibility Study

Robotic ultrasound has the potential to assist and guide physicians during interventions. In this work, we present a set of methods and a workflow to enable autonomous MRI-guided ultrasound acquisitions. Our approach uses a structured-light 3D scanner for patient-to-robot and image-to-patient calibration, which in turn is used to plan 3D ultrasound trajectories. These MRI-based trajectories are followed autonomously by the robot and are further refined online using automatic MRI/US registration. Despite the low spatial resolution of structured light scanners, the initial planned acquisition path can be followed with an accuracy of 2.46 +/- 0.96 mm. This leads to a good initialization of the MRI/US registration: the 3D-scan-based alignment for planning and acquisition shows an accuracy (distance between planned ultrasound and MRI) of 4.47 mm, and 0.97 mm after an online-update of the calibration based on a closed loop registration.

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arXiv2016

Deep Learning of Local RGB-D Patches for 3D Object Detection and 6D Pose Estimation

We present a 3D object detection method that uses regressed descriptors of locally-sampled RGB-D patches for 6D vote casting. For regression, we employ a convolutional auto-encoder that has been trained on a large collection of random local patches. During testing, scene patch descriptors are matched against a database of synthetic model view patches and cast 6D object votes which are subsequently filtered to refined hypotheses. We evaluate on three datasets to show that our method generalizes well to previously unseen input data, delivers robust detection results that compete with and surpass the state-of-the-art while being scalable in the number of objects.

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arXiv2016

Hashmod: A Hashing Method for Scalable 3D Object Detection

We present a scalable method for detecting objects and estimating their 3D poses in RGB-D data. To this end, we rely on an efficient representation of object views and employ hashing techniques to match these views against the input frame in a scalable way. While a similar approach already exists for 2D detection, we show how to extend it to estimate the 3D pose of the detected objects. In particular, we explore different hashing strategies and identify the one which is more suitable to our problem. We show empirically that the complexity of our method is sublinear with the number of objects and we enable detection and pose estimation of many 3D objects with high accuracy while outperforming the state-of-the-art in terms of runtime.

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arXiv2016

Deep Active Contours

We propose a method for interactive boundary extraction which combines a deep, patch-based representation with an active contour framework. We train a class-specific convolutional neural network which predicts a vector pointing from the respective point on the evolving contour towards the closest point on the boundary of the object of interest. These predictions form a vector field which is then used for evolving the contour by the Sobolev active contour framework proposed by Sundaramoorthi et al. The resulting interactive segmentation method is very efficient in terms of required computational resources and can even be trained on comparatively small graphics cards. We evaluate the potential of the proposed method on both medical and non-medical challenge data sets, such as the STACOM data set and the PASCAL VOC 2012 data set.

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arXiv2016

A Taxonomy and Library for Visualizing Learned Features in Convolutional Neural Networks

Over the last decade, Convolutional Neural Networks (CNN) saw a tremendous surge in performance. However, understanding what a network has learned still proves to be a challenging task. To remedy this unsatisfactory situation, a number of groups have recently proposed different methods to visualize the learned models. In this work we suggest a general taxonomy to classify and compare these methods, subdividing the literature into three main categories and providing researchers with a terminology to base their works on. Furthermore, we introduce the FeatureVis library for MatConvNet: an extendable, easy to use open source library for visualizing CNNs. It contains implementations from each of the three main classes of visualization methods and serves as a useful tool for an enhanced understanding of the features learned by intermediate layers, as well as for the analysis of why a network might fail for certain examples.

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arXiv2016

V-Net: Fully Convolutional Neural Networks for Volumetric Medical Image Segmentation

Convolutional Neural Networks (CNNs) have been recently employed to solve problems from both the computer vision and medical image analysis fields. Despite their popularity, most approaches are only able to process 2D images while most medical data used in clinical practice consists of 3D volumes. In this work we propose an approach to 3D image segmentation based on a volumetric, fully convolutional, neural network. Our CNN is trained end-to-end on MRI volumes depicting prostate, and learns to predict segmentation for the whole volume at once. We introduce a novel objective function, that we optimise during training, based on Dice coefficient. In this way we can deal with situations where there is a strong imbalance between the number of foreground and background voxels. To cope with the limited number of annotated volumes available for training, we augment the data applying random non-linear transformations and histogram matching. We show in our experimental evaluation that our approach achieves good performances on challenging test data while requiring only a fraction of the processing time needed by other previous methods.

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arXiv2016

Hough-CNN: Deep Learning for Segmentation of Deep Brain Regions in MRI and Ultrasound

In this work we propose a novel approach to perform segmentation by leveraging the abstraction capabilities of convolutional neural networks (CNNs). Our method is based on Hough voting, a strategy that allows for fully automatic localisation and segmentation of the anatomies of interest. This approach does not only use the CNN classification outcomes, but it also implements voting by exploiting the features produced by the deepest portion of the network. We show that this learning-based segmentation method is robust, multi-region, flexible and can be easily adapted to different modalities. In the attempt to show the capabilities and the behaviour of CNNs when they are applied to medical image analysis, we perform a systematic study of the performances of six different network architectures, conceived according to state-of-the-art criteria, in various situations. We evaluate the impact of both different amount of training data and different data dimensionality (2D, 2.5D and 3D) on the final results. We show results on both MRI and transcranial US volumes depicting respectively 26 regions of the basal ganglia and the midbrain.

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arXiv2015

Semi-Automatic Segmentation of Autosomal Dominant Polycystic Kidneys using Random Forests

This paper presents a method for 3D segmentation of kidneys from patients with autosomal dominant polycystic kidney disease (ADPKD) and severe renal insufficiency, using computed tomography (CT) data. ADPKD severely alters the shape of the kidneys due to non-uniform formation of cysts. As a consequence, fully automatic segmentation of such kidneys is very challenging. We present a segmentation method with minimal user interaction based on a random forest classifier. One of the major novelties of the proposed approach is the usage of geodesic distance volumes as additional source of information. These volumes contain the intensity weighted distance to a manual outline of the respective kidney in only one slice (for each kidney) of the CT volume. We evaluate our method qualitatively and quantitatively on 55 CT acquisitions using ground truth annotations from clinical experts.

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arXiv2015

Robust Optimization for Deep Regression

Convolutional Neural Networks (ConvNets) have successfully contributed to improve the accuracy of regression-based methods for computer vision tasks such as human pose estimation, landmark localization, and object detection. The network optimization has been usually performed with L2 loss and without considering the impact of outliers on the training process, where an outlier in this context is defined by a sample estimation that lies at an abnormal distance from the other training sample estimations in the objective space. In this work, we propose a regression model with ConvNets that achieves robustness to such outliers by minimizing Tukey's biweight function, an M-estimator robust to outliers, as the loss function for the ConvNet. In addition to the robust loss, we introduce a coarse-to-fine model, which processes input images of progressively higher resolutions for improving the accuracy of the regressed values. In our experiments, we demonstrate faster convergence and better generalization of our robust loss function for the tasks of human pose estimation and age estimation from face images. We also show that the combination of the robust loss function with the coarse-to-fine model produces comparable or better results than current state-of-the-art approaches in four publicly available human pose estimation datasets.

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