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.
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.
@cite_38 @cite_33 @cite_8 @cite_41 @cite_16 @cite_24 @cite_19 @cite_0 @cite_15 @cite_34 @cite_17
2611197392 2291422229 2963794428 2963881378
Training deep fully convolutional neural networks (F-CNNs) for semantic image segmentation requires access to abundant labeled data. While large datasets of unlabeled image data are available in medical applications, access to manually labeled data is very limited. We propose to automatically create auxiliary labels on initially unlabeled data with existing tools and to use them for pre-training. For the subsequent fine-tuning of the network with manually labeled data, we introduce error corrective boosting (ECB), which emphasizes parameter updates on classes with lower accuracy. Furthermore, we introduce SkipDeconv-Net (SD-Net), a new F-CNN architecture for brain segmentation that combines skip connections with the unpooling strategy for upsampling. The SD-Net addresses challenges of severe class imbalance and errors along boundaries. With application to whole-brain MRI T1 scan segmentation, we generate auxiliary labels on a large dataset with FreeSurfer and fine-tune on two datasets with manual annotations. Our results show that the inclusion of auxiliary labels and ECB yields significant improvements. SD-Net segments a 3D scan in 7 secs in comparison to 30 hours for the closest multi-atlas segmentation method, while reaching similar performance. It also outperforms the latest state-of-the-art F-CNN models. Recently, deep convolutional neural networks (DCNNs) have significantly promoted the development of semantic image segmentation. However, previous works on learning the segmentation network often rely on a large number of ground-truths with pixel-level annotations, which usually require considerable human effort. In this paper, we explore a more challenging problem by learning to segment under image-level annotations. Specifically, our framework consists of two components. First, reliable hypotheses based localization maps are generated by incorporating the hypotheses-aware classification and cross-image contextual refinement. Second, the segmentation network can be trained in a supervised manner by these generated localization maps. We explore two network training strategies for achieving good segmentation performance. For the first strategy, a novel multi-label cross-entropy loss is proposed to train the network by directly using multiple localization maps for all classes, where each pixel contributes to each class with different weights. For the second strategy, the rough segmentation mask can be inferred from the localization maps, and then the network is optimized based on the single-label cross-entropy loss with the produced masks. We evaluate our methods on the PASCAL VOC 2012 segmentation benchmark. Extensive experimental results demonstrate the effectiveness of the proposed methods compared with the state-of-the-arts. HighlightsLocalization map generation is proposed by using the hypothesis-based classification.A novel multi-label loss is proposed to train the network based on localization maps.An effective method is proposed to predict the rough mask of the given training image.Our methods achieve new state-of-the-art results on PASCAL VOC 2012 benchmark. Fully convolutional neural networks (F-CNNs) have set the state-of-the-art in image segmentation for a plethora of applications. Architectural innovations within F-CNNs have mainly focused on improving spatial encoding or network connectivity to aid gradient flow. In this paper, we explore an alternate direction of recalibrating the feature maps adaptively, to boost meaningful features, while suppressing weak ones. We draw inspiration from the recently proposed squeeze & excitation (SE) module for channel recalibration of feature maps for image classification. Towards this end, we introduce three variants of SE modules for image segmentation, (i) squeezing spatially and exciting channel-wise (cSE), (ii) squeezing channel-wise and exciting spatially (sSE) and (iii) concurrent spatial and channel squeeze & excitation (scSE). We effectively incorporate these SE modules within three different state-of-the-art F-CNNs (DenseNet, SD-Net, U-Net) and observe consistent improvement of performance across all architectures, while minimally effecting model complexity. Evaluations are performed on two challenging applications: whole brain segmentation on MRI scans and organ segmentation on whole body contrast enhanced CT scans. 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 .