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

Conditional Random Fields as Recurrent Neural Networks

Pixel-level labelling tasks, such as semantic segmentation, play a central role in image understanding. Recent approaches have attempted to harness the capabilities of deep learning techniques for image recognition to tackle pixel-level labelling tasks. One central issue in this methodology is the limited capacity of deep learning techniques to delineate visual objects. To solve this problem, we introduce a new form of convolutional neural network that combines the strengths of Convolutional Neural Networks (CNNs) and Conditional Random Fields (CRFs)-based probabilistic graphical modelling. To this end, we formulate mean-field approximate inference for the Conditional Random Fields with Gaussian pairwise potentials as Recurrent Neural Networks. This network, called CRF-RNN, is then plugged in as a part of a CNN to obtain a deep network that has desirable properties of both CNNs and CRFs. Importantly, our system fully integrates CRF modelling with CNNs, making it possible to train the whole deep network end-to-end with the usual back-propagation algorithm, avoiding offline post-processing methods for object delineation. We apply the proposed method to the problem of semantic image segmentation, obtaining top results on the challenging Pascal VOC 2012 segmentation benchmark.Comment: This paper is published in IEEE ICCV 201

SEGCloud: Semantic Segmentation of 3D Point Clouds

3D semantic scene labeling is fundamental to agents operating in the real world. In particular, labeling raw 3D point sets from sensors provides fine-grained semantics. Recent works leverage the capabilities of Neural Networks (NNs), but are limited to coarse voxel predictions and do not explicitly enforce global consistency. We present SEGCloud, an end-to-end framework to obtain 3D point-level segmentation that combines the advantages of NNs, trilinear interpolation(TI) and fully connected Conditional Random Fields (FC-CRF). Coarse voxel predictions from a 3D Fully Convolutional NN are transferred back to the raw 3D points via trilinear interpolation. Then the FC-CRF enforces global consistency and provides fine-grained semantics on the points. We implement the latter as a differentiable Recurrent NN to allow joint optimization. We evaluate the framework on two indoor and two outdoor 3D datasets (NYU V2, S3DIS, KITTI, Semantic3D.net), and show performance comparable or superior to the state-of-the-art on all datasets.Comment: Accepted as a spotlight at the International Conference of 3D Vision (3DV 2017