X-Ray image enhancement, along with many other medical image processing applications, requires the segmentation of images into bone, soft tissue, and open beam regions. We apply a machine learning approach to this problem, presenting an end-to-end solution which results in robust and efficient inference. Since medical institutions frequently do not have the resources to process and label the large quantity of X-Ray images usually needed for neural network training, we design an end-to-end solution for small datasets, while achieving state-of-the-art results. Our implementation produces an overall accuracy of 92 , F1 score of 0.92, and an AUC of 0.98, surpassing classical image processing techniques, such as clustering and entropy based methods, while improving upon the output of existing neural networks used for segmentation in non-medical contexts. The code used for this project is available online.
@cite_38: There is large consent that successful training of deep networks requires many thousand annotated training samples. In this paper, we present a network and training strategy that relies on the strong use of data augmentation to use the available annotated samples more efficiently. The architecture consists of a contracting path to capture context and a symmetric expanding path that enables precise localization. We show that such a network can be trained end-to-end from very few images and outperforms the prior best method (a sliding-window convolutional network) on the ISBI challenge for segmentation of neuronal structures in electron microscopic stacks. Using the same network trained on transmitted light microscopy images (phase contrast and DIC) we won the ISBI cell tracking challenge 2015 in these categories by a large margin. Moreover, the network is fast. Segmentation of a 512x512 image takes less than a second on a recent GPU. The full implementation (based on Caffe) and the trained networks are available at this http URL .
@cite_33: 
@cite_8: Convolutional networks are powerful visual models that yield hierarchies of features. We show that convolutional networks by themselves, trained end-to-end, pixels-to-pixels, exceed the state-of-the-art in semantic segmentation. Our key insight is to build “fully convolutional” networks that take input of arbitrary size and produce correspondingly-sized output with efficient inference and learning. We define and detail the space of fully convolutional networks, explain their application to spatially dense prediction tasks, and draw connections to prior models. We adapt contemporary classification networks (AlexNet [20], the VGG net [31], and GoogLeNet [32]) into fully convolutional networks and transfer their learned representations by fine-tuning [3] to the segmentation task. We then define a skip architecture that combines semantic information from a deep, coarse layer with appearance information from a shallow, fine layer to produce accurate and detailed segmentations. Our fully convolutional network achieves state-of-the-art segmentation of PASCAL VOC (20 relative improvement to 62.2 mean IU on 2012), NYUDv2, and SIFT Flow, while inference takes less than one fifth of a second for a typical image.
@cite_41: 
@cite_16: We aim to analyze how automatic segmentation performances translate in accuracy and precision to morphology and relaxometry in osteoarthritis compared with manual segmentations and increase the speed and accuracy of the work flow that uses quantitative MR imaging to study knee degenerative diseases.
@cite_24: 
@cite_19: We present a novel and practical deep fully convolutional neural network architecture for semantic pixel-wise segmentation termed SegNet. This core trainable segmentation engine consists of an encoder network, a corresponding decoder network followed by a pixel-wise classification layer. The architecture of the encoder network is topologically identical to the 13 convolutional layers in the VGG16 network [1] . The role of the decoder network is to map the low resolution encoder feature maps to full input resolution feature maps for pixel-wise classification. The novelty of SegNet lies is in the manner in which the decoder upsamples its lower resolution input feature map(s). Specifically, the decoder uses pooling indices computed in the max-pooling step of the corresponding encoder to perform non-linear upsampling. This eliminates the need for learning to upsample. The upsampled maps are sparse and are then convolved with trainable filters to produce dense feature maps. We compare our proposed architecture with the widely adopted FCN [2] and also with the well known DeepLab-LargeFOV [3] , DeconvNet [4] architectures. This comparison reveals the memory versus accuracy trade-off involved in achieving good segmentation performance. SegNet was primarily motivated by scene understanding applications. Hence, it is designed to be efficient both in terms of memory and computational time during inference. It is also significantly smaller in the number of trainable parameters than other competing architectures and can be trained end-to-end using stochastic gradient descent. We also performed a controlled benchmark of SegNet and other architectures on both road scenes and SUN RGB-D indoor scene segmentation tasks. These quantitative assessments show that SegNet provides good performance with competitive inference time and most efficient inference memory-wise as compared to other architectures. We also provide a Caffe implementation of SegNet and a web demo at http: mi.eng.cam.ac.uk projects segnet .
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@cite_15: 
@cite_34: 
@cite_17: We propose a novel deep architecture, SegNet, for semantic pixel wise image labelling. SegNet has several attractive properties; (i) it only requires forward evaluation of a fully learnt function to obtain smooth label predictions, (ii) with increasing depth, a larger context is considered for pixel labelling which improves accuracy, and (iii) it is easy to visualise the effect of feature activation(s) in the pixel label space at any depth. SegNet is composed of a stack of encoders followed by a corresponding decoder stack which feeds into a soft-max classification layer. The decoders help map low resolution feature maps at the output of the encoder stack to full input image size feature maps. This addresses an important drawback of recent deep learning approaches which have adopted networks designed for object categorization for pixel wise labelling. These methods lack a mechanism to map deep layer feature maps to input dimensions. They resort to ad hoc methods to upsample features, e.g. by replication. This results in noisy predictions and also restricts the number of pooling layers in order to avoid too much upsampling and thus reduces spatial context. SegNet overcomes these problems by learning to map encoder outputs to image pixel labels. We test the performance of SegNet on outdoor RGB scenes from CamVid, KITTI and indoor scenes from the NYU dataset. Our results show that SegNet achieves state-of-the-art performance even without use of additional cues such as depth, video frames or post-processing with CRF models.
Complete multi-class image segmentation is an active, high-growth area of research, most recently driven by autonomous vehicle development. Neural networks have been at the forefront of this research and take various forms including the encoder-decoder design similar to that presented in this paper @cite_19 @cite_33 @cite_24 @cite_34 @cite_41 , and fully connected networks @cite_8 . Several applications of these networks also utilise the technique of image augmentation to aid network generalisation and reduce the risk of overfitting. Similarly, Badrinarayanan, Handa and Cipolla @cite_17 present a simplified version of the widely applied SegNet architecture @cite_19 , showing improved performance on small datasets. Indeed, it is against this simplified network, known as @cite_17 , that we benchmark our network performance. It is noted that some networks have been specifically designed for the total segmentation of medical images, yet these applications have been largely constrained to the segmentation of cell structures @cite_38 @cite_15 @cite_0 . There have been examples of networks, such as U-Net @cite_38 , being applied to other segmentation tasks in the field of X-Ray image segmentation @cite_16 , but only in specific use cases.