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Register a new userRecurrent convolutional neural networks for mandible segmentation from computed tomography
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Recently, accurate mandible segmentation in CT scans based on deep learning methods has attracted much attention. However, there still exist two major challenges, namely, metal artifacts among mandibles and large variations in shape or size among individuals. To address these two challenges, we propose a recurrent segmentation convolutional neural network (RSegCNN) that embeds segmentation convolutional neural network (SegCNN) into the recurrent neural network (RNN) for robust and accurate segmentation of the mandible. Such a design of the system takes into account the similarity and continuity of the mandible shapes captured in adjacent image slices in CT scans. The RSegCNN infers the mandible information based on the recurrent structure with the embedded encoder-decoder segmentation (SegCNN) components. The recurrent structure guides the system to exploit relevant and important information from adjacent slices, while the SegCNN component focuses on the mandible shapes from a single CT slice. We conducted extensive experiments to evaluate the proposed RSegCNN on two head and neck CT datasets. The experimental results show that the RSegCNN is significantly better than the state-of-the-art models for accurate mandible segmentation.
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Quantitative lung measures derived from computed tomography (CT) have been demonstrated to improve prognostication in coronavirus disease (COVID-19) patients, but are not part of the clinical routine since required manual segmentation of lung lesions is prohibitively time-consuming. We propose a new fully automated deep learning framework for rapid quantification and differentiation between lung lesions in COVID-19 pneumonia from both contrast and non-contrast CT images using convolutional Long Short-Term Memory (ConvLSTM) networks. Utilizing the expert annotations, model training was performed 5 times with separate hold-out sets using 5-fold cross-validation to segment ground-glass opacity and high opacity (including consolidation and pleural effusion). The performance of the method was evaluated on CT data sets from 197 patients with positive reverse transcription polymerase chain reaction test result for SARS-CoV-2. Strong agreement between expert manual and automatic segmentation was obtained for lung lesions with a Dice score coefficient of 0.876 $pm$ 0.005; excellent correlations of 0.978 and 0.981 for ground-glass opacity and high opacity volumes. In the external validation set of 67 patients, there was dice score coefficient of 0.767 $pm$ 0.009 as well as excellent correlations of 0.989 and 0.996 for ground-glass opacity and high opacity volumes. Computations for a CT scan comprising 120 slices were performed under 2 seconds on a personal computer equipped with NVIDIA Titan RTX graphics processing unit. Therefore, our deep learning-based method allows rapid fully-automated quantitative measurement of pneumonia burden from CT and may generate results with an accuracy similar to the expert readers.
Ischemic stroke lesion segmentation from Computed Tomography Perfusion (CTP) images is important for accurate diagnosis of stroke in acute care units. However, it is challenged by low image contrast and resolution of the perfusion parameter maps, in addition to the complex appearance of the lesion. To deal with this problem, we propose a novel framework based on synthesized pseudo Diffusion-Weighted Imaging (DWI) from perfusion parameter maps to obtain better image quality for more accurate segmentation. Our framework consists of three components based on Convolutional Neural Networks (CNNs) and is trained end-to-end. First, a feature extractor is used to obtain both a low-level and high-level compact representation of the raw spatiotemporal Computed Tomography Angiography (CTA) images. Second, a pseudo DWI generator takes as input the concatenation of CTP perfusion parameter maps and our extracted features to obtain the synthesized pseudo DWI. To achieve better synthesis quality, we propose a hybrid loss function that pays more attention to lesion regions and encourages high-level contextual consistency. Finally, we segment the lesion region from the synthesized pseudo DWI, where the segmentation network is based on switchable normalization and channel calibration for better performance. Experimental results showed that our framework achieved the top performance on ISLES 2018 challenge and: 1) our method using synthesized pseudo DWI outperformed methods segmenting the lesion from perfusion parameter maps directly; 2) the feature extractor exploiting additional spatiotemporal CTA images led to better synthesized pseudo DWI quality and higher segmentation accuracy; and 3) the proposed loss functions and network structure improved the pseudo DWI synthesis and lesion segmentation performance.
Colorectal cancer is the third most common cancer-related death after lung cancer and breast cancer worldwide. The risk of developing colorectal cancer could be reduced by early diagnosis of polyps during a colonoscopy. Computer-aided diagnosis systems have the potential to be applied for polyp screening and reduce the number of missing polyps. In this paper, we compare the performance of different deep learning architectures as feature extractors, i.e. ResNet, DenseNet, InceptionV3, InceptionResNetV2 and SE-ResNeXt in the encoder part of a U-Net architecture. We validated the performance of presented ensemble models on the CVC-Clinic (GIANA 2018) dataset. The DenseNet169 feature extractor combined with U-Net architecture outperformed the other counterparts and achieved an accuracy of 99.15%, Dice similarity coefficient of 90.87%, and Jaccard index of 83.82%.
Segmentation of mandibles in CT scans during virtual surgical planning is crucial for 3D surgical planning in order to obtain a detailed surface representation of the patients bone. Automatic segmentation of mandibles in CT scans is a challenging task due to large variation in their shape and size between individuals. In order to address this challenge we propose a convolutional neural network approach for mandible segmentation in CT scans by considering the continuum of anatomical structures through different planes. The proposed convolutional neural network adopts the architecture of the U-Net and then combines the resulting 2D segmentations from three different planes into a 3D segmentation. We implement such a segmentation approach on 11 neck CT scans and then evaluate the performance. We achieve an average dice coefficient of $ 0.89 $ on two testing mandible segmentation. Experimental results show that our proposed approach for mandible segmentation in CT scans exhibits high accuracy.
Spine-related diseases have high morbidity and cause a huge burden of social cost. Spine imaging is an essential tool for noninvasively visualizing and assessing spinal pathology. Segmenting vertebrae in computed tomography (CT) images is the basis of quantitative medical image analysis for clinical diagnosis and surgery planning of spine diseases. Current publicly available annotated datasets on spinal vertebrae are small in size. Due to the lack of a large-scale annotated spine image dataset, the mainstream deep learning-based segmentation methods, which are data-driven, are heavily restricted. In this paper, we introduce a large-scale spine CT dataset, called CTSpine1K, curated from multiple sources for vertebra segmentation, which contains 1,005 CT volumes with over 11,100 labeled vertebrae belonging to different spinal conditions. Based on this dataset, we conduct several spinal vertebrae segmentation experiments to set the first benchmark. We believe that this large-scale dataset will facilitate further research in many spine-related image analysis tasks, including but not limited to vertebrae segmentation, labeling, 3D spine reconstruction from biplanar radiographs, image super-resolution, and enhancement.
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