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

Beyond KernelBoost

In this Technical Report we propose a set of improvements with respect to the KernelBoost classifier presented in [Becker et al., MICCAI 2013]. We start with a scheme inspired by Auto-Context, but that is suitable in situations where the lack of large training sets poses a potential problem of overfitting. The aim is to capture the interactions between neighboring image pixels to better regularize the boundaries of segmented regions. As in Auto-Context [Tu et al., PAMI 2009] the segmentation process is iterative and, at each iteration, the segmentation results for the previous iterations are taken into account in conjunction with the image itself. However, unlike in [Tu et al., PAMI 2009], we organize our recursion so that the classifiers can progressively focus on difficult-to-classify locations. This lets us exploit the power of the decision-tree paradigm while avoiding over-fitting. In the context of this architecture, KernelBoost represents a powerful building block due to its ability to learn on the score maps coming from previous iterations. We first introduce two important mechanisms to empower the KernelBoost classifier, namely pooling and the clustering of positive samples based on the appearance of the corresponding ground-truth. These operations significantly contribute to increase the effectiveness of the system on biomedical images, where texture plays a major role in the recognition of the different image components. We then present some other techniques that can be easily integrated in the KernelBoost framework to further improve the accuracy of the final segmentation. We show extensive results on different medical image datasets, including some multi-label tasks, on which our method is shown to outperform state-of-the-art approaches. The resulting segmentations display high accuracy, neat contours, and reduced noise

On Rendering Synthetic Images for Training an Object Detector

We propose a novel approach to synthesizing images that are effective for training object detectors. Starting from a small set of real images, our algorithm estimates the rendering parameters required to synthesize similar images given a coarse 3D model of the target object. These parameters can then be reused to generate an unlimited number of training images of the object of interest in arbitrary 3D poses, which can then be used to increase classification performances. A key insight of our approach is that the synthetically generated images should be similar to real images, not in terms of image quality, but rather in terms of features used during the detector training. We show in the context of drone, plane, and car detection that using such synthetically generated images yields significantly better performances than simply perturbing real images or even synthesizing images in such way that they look very realistic, as is often done when only limited amounts of training data are available

Learning to Reconstruct Texture-less Deformable Surfaces from a Single View

Recent years have seen the development of mature solutions for reconstructing deformable surfaces from a single image, provided that they are relatively well-textured. By contrast, recovering the 3D shape of texture-less surfaces remains an open problem, and essentially relates to Shape-from-Shading. In this paper, we introduce a data-driven approach to this problem. We introduce a general framework that can predict diverse 3D representations, such as meshes, normals, and depth maps. Our experiments show that meshes are ill-suited to handle texture-less 3D reconstruction in our context. Furthermore, we demonstrate that our approach generalizes well to unseen objects, and that it yields higher-quality reconstructions than a state-of-the-art SfS technique, particularly in terms of normal estimates. Our reconstructions accurately model the fine details of the surfaces, such as the creases of a T-Shirt worn by a person.Comment: Accepted to 3DV 201

Introducing Geometry in Active Learning for Image Segmentation

We propose an Active Learning approach to training a segmentation classifier that exploits geometric priors to streamline the annotation process in 3D image volumes. To this end, we use these priors not only to select voxels most in need of annotation but to guarantee that they lie on 2D planar patch, which makes it much easier to annotate than if they were randomly distributed in the volume. A simplified version of this approach is effective in natural 2D images. We evaluated our approach on Electron Microscopy and Magnetic Resonance image volumes, as well as on natural images. Comparing our approach against several accepted baselines demonstrates a marked performance increase

Deep Occlusion Reasoning for Multi-Camera Multi-Target Detection

People detection in single 2D images has improved greatly in recent years. However, comparatively little of this progress has percolated into multi-camera multi-people tracking algorithms, whose performance still degrades severely when scenes become very crowded. In this work, we introduce a new architecture that combines Convolutional Neural Nets and Conditional Random Fields to explicitly model those ambiguities. One of its key ingredients are high-order CRF terms that model potential occlusions and give our approach its robustness even when many people are present. Our model is trained end-to-end and we show that it outperforms several state-of-art algorithms on challenging scenes