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.
In this section we give an overview of existing approaches that employ CNNs to solve problems from both computer vision and medical imaging domain. In the last few years CNNs became very popular tools among the computer vision community. Classification problems such as image categorisation @cite_36 @cite_35 , object detection @cite_21 and face recognition @cite_15 as well as regression problems such as human pose estimation @cite_10 , and depth prediction from RGB data @cite_14 have been addressed using CNNs and unprecedented results have been reported. In order to cope with the challenges present in natural images, such as scale changes, occlusions, deformations different illumination settings and viewpoint changes, these methods needed to be trained on very large annotated datasets and required several weeks to be built even when powerful GPUs were employed. In medical imaging, however, it is difficult to obtain even a fraction of this amount of resources, both in terms of computational means and amount of annotated training data.
@cite_35 @cite_14 @cite_36 @cite_21 @cite_15 @cite_10
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Remarkable progress has been made in image recognition, primarily due to the availability of large-scale annotated datasets and deep convolutional neural networks (CNNs). CNNs enable learning data-driven, highly representative, hierarchical image features from sufficient training data. However, obtaining datasets as comprehensively annotated as ImageNet in the medical imaging domain remains a challenge. There are currently three major techniques that successfully employ CNNs to medical image classification: training the CNN from scratch, using off-the-shelf pre-trained CNN features, and conducting unsupervised CNN pre-training with supervised fine-tuning. Another effective method is transfer learning, i.e., fine-tuning CNN models pre-trained from natural image dataset to medical image tasks. In this paper, we exploit three important, but previously understudied factors of employing deep convolutional neural networks to computer-aided detection problems. We first explore and evaluate different CNN architectures. The studied models contain 5 thousand to 160 million parameters, and vary in numbers of layers. We then evaluate the influence of dataset scale and spatial image context on performance. Finally, we examine when and why transfer learning from pre-trained ImageNet (via fine-tuning) can be useful. We study two specific computer-aided detection (CADe) problems, namely thoraco-abdominal lymph node (LN) detection and interstitial lung disease (ILD) classification. We achieve the state-of-the-art performance on the mediastinal LN detection, and report the first five-fold cross-validation classification results on predicting axial CT slices with ILD categories. Our extensive empirical evaluation, CNN model analysis and valuable insights can be extended to the design of high performance CAD systems for other medical imaging tasks. Convolutional neural networks (CNNs) have been successfully used for fast and accurate estimation of dense correspondences between images in computer vision applications. However, much of their success is based on the availability of large training datasets with dense ground truth correspondences, which are only rarely available in medical applications. In this paper, we, therefore, address the problem of CNNs learning from few training data for medical image registration. Our contributions are threefold: (1) We present a novel approach for learning highly expressive appearance models from few training samples, (2) we show that this approach can be used to synthesize huge amounts of realistic ground truth training data for CNN-based medical image registration, and (3) we adapt the FlowNet architecture for CNN-based optical flow estimation to the medical image registration problem. This pipeline is applied to two medical data sets with less than 40 training images. We show that CNNs learned from the proposed generative model outperform those trained on random deformations or displacement fields estimated via classical image registration. In real-world face detection, large visual variations, such as those due to pose, expression, and lighting, demand an advanced discriminative model to accurately differentiate faces from the backgrounds. Consequently, effective models for the problem tend to be computationally prohibitive. To address these two conflicting challenges, we propose a cascade architecture built on convolutional neural networks (CNNs) with very powerful discriminative capability, while maintaining high performance. The proposed CNN cascade operates at multiple resolutions, quickly rejects the background regions in the fast low resolution stages, and carefully evaluates a small number of challenging candidates in the last high resolution stage. To improve localization effectiveness, and reduce the number of candidates at later stages, we introduce a CNN-based calibration stage after each of the detection stages in the cascade. The output of each calibration stage is used to adjust the detection window position for input to the subsequent stage. The proposed method runs at 14 FPS on a single CPU core for VGA-resolution images and 100 FPS using a GPU, and achieves state-of-the-art detection performance on two public face detection benchmarks. Convolutional neural networks (CNN) have recently shown outstanding image classification performance in the large- scale visual recognition challenge (ILSVRC2012). The suc- cess of CNNs is attributed to their ability to learn rich mid- level image representations as opposed to hand-designed low-level features used in other image classification meth- ods. Learning CNNs, however, amounts to estimating mil- lions of parameters and requires a very large number of annotated image samples. This property currently prevents application of CNNs to problems with limited training data. In this work we show how image representations learned with CNNs on large-scale annotated datasets can be effi- ciently transferred to other visual recognition tasks with limited amount of training data. We design a method to reuse layers trained on the ImageNet dataset to compute mid-level image representation for images in the PASCAL VOC dataset. We show that despite differences in image statistics and tasks in the two datasets, the transferred rep- resentation leads to significantly improved results for object and action classification, outperforming the current state of the art on Pascal VOC 2007 and 2012 datasets. We also show promising results for object and action localization.