Accurate 3D Cell Segmentation using Deep Feature and CRF Refinement

We consider the problem of accurately identifying cell boundaries and labeling individual cells in confocal microscopy images, specifically, 3D image stacks of cells with tagged cell membranes. Precise identification of cell boundaries, their shapes, and quantifying inter-cellular space leads to a better understanding of cell morphogenesis. Towards this, we outline a cell segmentation method that uses a deep neural network architecture to extract a confidence map of cell boundaries, followed by a 3D watershed algorithm and a final refinement using a conditional random field. In addition to improving the accuracy of segmentation compared to other state-of-the-art methods, the proposed approach also generalizes well to different datasets without the need to retrain the network for each dataset. Detailed experimental results are provided, and the source code is available on GitHub.Comment: 5 pages, 5 figures, 3 table

A Survey on Deep Learning-based Architectures for Semantic Segmentation on 2D images

Semantic segmentation is the pixel-wise labelling of an image. Since the problem is defined at the pixel level, determining image class labels only is not acceptable, but localising them at the original image pixel resolution is necessary. Boosted by the extraordinary ability of convolutional neural networks (CNN) in creating semantic, high level and hierarchical image features; excessive numbers of deep learning-based 2D semantic segmentation approaches have been proposed within the last decade. In this survey, we mainly focus on the recent scientific developments in semantic segmentation, specifically on deep learning-based methods using 2D images. We started with an analysis of the public image sets and leaderboards for 2D semantic segmantation, with an overview of the techniques employed in performance evaluation. In examining the evolution of the field, we chronologically categorised the approaches into three main periods, namely pre-and early deep learning era, the fully convolutional era, and the post-FCN era. We technically analysed the solutions put forward in terms of solving the fundamental problems of the field, such as fine-grained localisation and scale invariance. Before drawing our conclusions, we present a table of methods from all mentioned eras, with a brief summary of each approach that explains their contribution to the field. We conclude the survey by discussing the current challenges of the field and to what extent they have been solved.Comment: Updated with new studie

Semantic Video CNNs through Representation Warping

In this work, we propose a technique to convert CNN models for semantic segmentation of static images into CNNs for video data. We describe a warping method that can be used to augment existing architectures with very little extra computational cost. This module is called NetWarp and we demonstrate its use for a range of network architectures. The main design principle is to use optical flow of adjacent frames for warping internal network representations across time. A key insight of this work is that fast optical flow methods can be combined with many different CNN architectures for improved performance and end-to-end training. Experiments validate that the proposed approach incurs only little extra computational cost, while improving performance, when video streams are available. We achieve new state-of-the-art results on the CamVid and Cityscapes benchmark datasets and show consistent improvements over different baseline networks. Our code and models will be available at http://segmentation.is.tue.mpg.deComment: ICCV 201

End-to-End Learning of Semantic Grid Estimation Deep Neural Network with Occupancy Grids

International audienceWe propose semantic grid, a spatial 2D map of the environment around an autonomous vehicle consisting of cells which represent the semantic information of the corresponding region such as car, road, vegetation, bikes, etc. It consists of an integration of an occupancy grid, which computes the grid states with a Bayesian filter approach, and semantic segmentation information from monocular RGB images, which is obtained with a deep neural network. The network fuses the information and can be trained in an end-to-end manner. The output of the neural network is refined with a conditional random field. The proposed method is tested in various datasets (KITTI dataset, Inria-Chroma dataset and SYNTHIA) and different deep neural network architectures are compared