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Register a new userCoarse-to-fine Airway Segmentation Using Multi information Fusion Network and CNN-based Region Growing
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Automatic airway segmentation from chest computed tomography (CT) scans plays an important role in pulmonary disease diagnosis and computer-assisted therapy. However, low contrast at peripheral branches and complex tree-like structures remain as two mainly challenges for airway segmentation. Recent research has illustrated that deep learning methods perform well in segmentation tasks. Motivated by these works, a coarse-to-fine segmentation framework is proposed to obtain a complete airway tree. Our framework segments the overall airway and small branches via the multi-information fusion convolution neural network (Mif-CNN) and the CNN-based region growing, respectively. In Mif-CNN, atrous spatial pyramid pooling (ASPP) is integrated into a u-shaped network, and it can expend the receptive field and capture multi-scale information. Meanwhile, boundary and location information are incorporated into semantic information. These information are fused to help Mif-CNN utilize additional context knowledge and useful features. To improve the performance of the segmentation result, the CNN-based region growing method is designed to focus on obtaining small branches. A voxel classification network (VCN), which can entirely capture the rich information around each voxel, is applied to classify the voxels into airway and non-airway. In addition, a shape reconstruction method is used to refine the airway tree.
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Performing coarse-to-fine abdominal multi-organ segmentation facilitates to extract high-resolution segmentation minimizing the lost of spatial contextual information. However, current coarse-to-refine approaches require a significant number of models to perform single organ refine segmentation corresponding to the extracted organ region of interest (ROI). We propose a coarse-to-fine pipeline, which starts from the extraction of the global prior context of multiple organs from 3D volumes using a low-resolution coarse network, followed by a fine phase that uses a single refined model to segment all abdominal organs instead of multiple organ corresponding models. We combine the anatomical prior with corresponding extracted patches to preserve the anatomical locations and boundary information for performing high-resolution segmentation across all organs in a single model. To train and evaluate our method, a clinical research cohort consisting of 100 patient volumes with 13 organs well-annotated is used. We tested our algorithms with 4-fold cross-validation and computed the Dice score for evaluating the segmentation performance of the 13 organs. Our proposed method using single auto-context outperforms the state-of-the-art on 13 models with an average Dice score 84.58% versus 81.69% (p<0.0001).
Food resources face severe damages under extraordinary situations of catastrophes such as earthquakes, cyclones, and tsunamis. Under such scenarios, speedy assessment of food resources from agricultural land is critical as it supports aid activity in the disaster hit areas. In this article, a deep learning approach is presented for the detection and segmentation of coconut tress in aerial imagery provided through the AI competition organized by the World Bank in collaboration with OpenAerialMap and WeRobotics. Maked Region-based Convolutional Neural Network approach was used identification and segmentation of coconut trees. For the segmentation task, Mask R-CNN model with ResNet50 and ResNet1010 based architectures was used. Several experiments with different configuration parameters were performed and the best configuration for the detection of coconut trees with more than 90% confidence factor was reported. For the purpose of evaluation, Microsoft COCO dataset evaluation metric namely mean average precision (mAP) was used. An overall 91% mean average precision for coconut trees detection was achieved.
Multi-class segmentation of cardiac magnetic resonance (CMR) images seeks a separation of data into anatomical components with known structure and configuration. The most popular CNN-based methods are optimised using pixel wise loss functions, ignorant of the spatially extended features that characterise anatomy. Therefore, whilst sharing a high spatial overlap with the ground truth, inferred CNN-based segmentations can lack coherence, including spurious connected components, holes and voids. Such results are implausible, violating anticipated anatomical topology. In response, (single-class) persistent homology-based loss functions have been proposed to capture global anatomical features. Our work extends these approaches to the task of multi-class segmentation. Building an enriched topological description of all class labels and class label pairs, our loss functions make predictable and statistically significant improvements in segmentation topology using a CNN-based post-processing framework. We also present (and make available) a highly efficient implementation based on cubical complexes and parallel execution, enabling practical application within high resolution 3D data for the first time. We demonstrate our approach on 2D short axis and 3D whole heart CMR segmentation, advancing a detailed and faithful analysis of performance on two publicly available datasets.
Semantic segmentation of remote sensing images plays an important role in a wide range of applications including land resource management, biosphere monitoring and urban planning. Although the accuracy of semantic segmentation in remote sensing images has been increased significantly by deep convolutional neural networks, several limitations exist in standard models. First, for encoder-decoder architectures such as U-Net, the utilization of multi-scale features causes the underuse of information, where low-level features and high-level features are concatenated directly without any refinement. Second, long-range dependencies of feature maps are insufficiently explored, resulting in sub-optimal feature representations associated with each semantic class. Third, even though the dot-product attention mechanism has been introduced and utilized in semantic segmentation to model long-range dependencies, the large time and space demands of attention impede the actual usage of attention in application scenarios with large-scale input. This paper proposed a Multi-Attention-Network (MANet) to address these issues by extracting contextual dependencies through multiple efficient attention modules. A novel attention mechanism of kernel attention with linear complexity is proposed to alleviate the large computational demand in attention. Based on kernel attention and channel attention, we integrate local feature maps extracted by ResNeXt-101 with their corresponding global dependencies and reweight interdependent channel maps adaptively. Numerical experiments on three large-scale fine resolution remote sensing images captured by different satellite sensors demonstrate the superior performance of the proposed MANet, outperforming the DeepLab V3+, PSPNet, FastFCN, DANet, OCRNet, and other benchmark approaches.
The purpose of this study was to develop a fully-automated segmentation algorithm, robust to various density enhancing lung abnormalities, to facilitate rapid quantitative analysis of computed tomography images. A polymorphic training approach is proposed, in which both specifically labeled left and right lungs of humans with COPD, and nonspecifically labeled lungs of animals with acute lung injury, were incorporated into training a single neural network. The resulting network is intended for predicting left and right lung regions in humans with or without diffuse opacification and consolidation. Performance of the proposed lung segmentation algorithm was extensively evaluated on CT scans of subjects with COPD, confirmed COVID-19, lung cancer, and IPF, despite no labeled training data of the latter three diseases. Lobar segmentations were obtained using the left and right lung segmentation as input to the LobeNet algorithm. Regional lobar analysis was performed using hierarchical clustering to identify radiographic subtypes of COVID-19. The proposed lung segmentation algorithm was quantitatively evaluated using semi-automated and manually-corrected segmentations in 87 COVID-19 CT images, achieving an average symmetric surface distance of $0.495 pm 0.309$ mm and Dice coefficient of $0.985 pm 0.011$. Hierarchical clustering identified four radiographical phenotypes of COVID-19 based on lobar fractions of consolidated and poorly aerated tissue. Lower left and lower right lobes were consistently more afflicted with poor aeration and consolidation. However, the most severe cases demonstrated involvement of all lobes. The polymorphic training approach was able to accurately segment COVID-19 cases with diffuse consolidation without requiring COVID-19 cases for training.
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