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Register a new user3D RoI-aware U-Net for Accurate and Efficient Colorectal Tumor Segmentation
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Added by
Yi-Jie Huang
Publication date
2018
fields
Informatics Engineering
and research's language is
English
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Segmentation of colorectal cancerous regions from 3D Magnetic Resonance (MR) images is a crucial procedure for radiotherapy which conventionally requires accurate delineation of tumour boundaries at an expense of labor, time and reproducibility. While deep learning based methods serve good baselines in 3D image segmentation tasks, small applicable patch size limits effective receptive field and degrades segmentation performance. In addition, Regions of interest (RoIs) localization from large whole volume 3D images serves as a preceding operation that brings about multiple benefits in terms of speed, target completeness, reduction of false positives. Distinct from sliding window or non-joint localization-segmentation based models, we propose a novel multitask framework referred to as 3D RoI-aware U-Net (3D RU-Net), for RoI localization and in-region segmentation where the two tasks share one backbone encoder network. With the region proposals from the encoder, we crop multi-level RoI in-region features from the encoder to form a GPU memory-efficient decoder for detailpreserving segmentation and therefore enlarged applicable volume size and effective receptive field. To effectively train the model, we designed a Dice formulated loss function for the global-to-local multi-task learning procedure. Based on the efficiency gains, we went on to ensemble models with different receptive fields to achieve even higher performance costing minor extra computational expensiveness. Extensive experiments were conducted on 64 cancerous cases with a four-fold cross-validation, and the results showed significant superiority in terms of accuracy and efficiency over conventional frameworks. In conclusion, the proposed method has a huge potential for extension to other 3D object segmentation tasks from medical images due to its inherent generalizability. The code for the proposed method is publicly available.
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We propose a novel, simple and effective method to integrate lesion prior and a 3D U-Net for improving brain tumor segmentation. First, we utilize the ground-truth brain tumor lesions from a group of patients to generate the heatmaps of different types of lesions. These heatmaps are used to create the volume-of-interest (VOI) map which contains prior information about brain tumor lesions. The VOI map is then integrated with the multimodal MR images and input to a 3D U-Net for segmentation. The proposed method is evaluated on a public benchmark dataset, and the experimental results show that the proposed feature fusion method achieves an improvement over the baseline methods. In addition, our proposed method also achieves a competitive performance compared to state-of-the-art methods.
Automatic and accurate tumor segmentation on medical images is in high demand to assist physicians with diagnosis and treatment. However, it is difficult to obtain massive amounts of annotated training data required by the deep-learning models as the manual delineation process is often tedious and expertise required. Although self-supervised learning (SSL) scheme has been widely adopted to address this problem, most SSL methods focus only on global structure information, ignoring the key distinguishing features of tumor regions: local intensity variation and large size distribution. In this paper, we propose Scale-Aware Restoration (SAR), a SSL method for 3D tumor segmentation. Specifically, a novel proxy task, i.e. scale discrimination, is formulated to pre-train the 3D neural network combined with the self-restoration task. Thus, the pre-trained model learns multi-level local representations through multi-scale inputs. Moreover, an adversarial learning module is further introduced to learn modality invariant representations from multiple unlabeled source datasets. We demonstrate the effectiveness of our methods on two downstream tasks: i) Brain tumor segmentation, ii) Pancreas tumor segmentation. Compared with the state-of-the-art 3D SSL methods, our proposed approach can significantly improve the segmentation accuracy. Besides, we analyze its advantages from multiple perspectives such as data efficiency, performance, and convergence speed.
Deep learning has quickly become the weapon of choice for brain lesion segmentation. However, few existing algorithms pre-configure any biological context of their chosen segmentation tissues, and instead rely on the neural networks optimizer to develop such associations de novo. We present a novel method for applying deep neural networks to the problem of glioma tissue segmentation that takes into account the structured nature of gliomas - edematous tissue surrounding mutually-exclusive regions of enhancing and non-enhancing tumor. We trained multiple deep neural networks with a 3D U-Net architecture in a tree structure to create segmentations for edema, non-enhancing tumor, and enhancing tumor regions. Specifically, training was configured such that the whole tumor region including edema was predicted first, and its output segmentation was fed as input into separate models to predict enhancing and non-enhancing tumor. Our method was trained and evaluated on the publicly available BraTS dataset, achieving Dice scores of 0.882, 0.732, and 0.730 for whole tumor, enhancing tumor and tumor core respectively.
The detection of 3D objects from LiDAR data is a critical component in most autonomous driving systems. Safe, high speed driving needs larger detection ranges, which are enabled by new LiDARs. These larger detection ranges require more efficient and accurate detection models. Towards this goal, we propose Range Sparse Net (RSN), a simple, efficient, and accurate 3D object detector in order to tackle real time 3D object detection in this extended detection regime. RSN predicts foreground points from range images and applies sparse convolutions on the selected foreground points to detect objects. The lightweight 2D convolutions on dense range images results in significantly fewer selected foreground points, thus enabling the later sparse convolutions in RSN to efficiently operate. Combining features from the range image further enhance detection accuracy. RSN runs at more than 60 frames per second on a 150m x 150m detection region on Waymo Open Dataset (WOD) while being more accurate than previously published detectors. As of 11/2020, RSN is ranked first in the WOD leaderboard based on the APH/LEVEL 1 metrics for LiDAR-based pedestrian and vehicle detection, while being several times faster than alternatives.
Many cultures around the world believe that palm reading can be used to predict the future life of a person. Palmistry uses features of the hand such as palm lines, hand shape, or fingertip position. However, the research on palm-line detection is still scarce, many of them applied traditional image processing techniques. In most real-world scenarios, images usually are not in well-conditioned, causing these methods to severely under-perform. In this paper, we propose an algorithm to extract principle palm lines from an image of a persons hand. Our method applies deep learning networks (DNNs) to improve performance. Another challenge of this problem is the lack of training data. To deal with this issue, we handcrafted a dataset from scratch. From this dataset, we compare the performance of readily available methods with ours. Furthermore, based on the UNet segmentation neural network architecture and the knowledge of attention mechanism, we propose a highly efficient architecture to detect palm-lines. We proposed the Context Fusion Module to capture the most important context feature, which aims to improve segmentation accuracy. The experimental results show that it outperforms the other methods with the highest F1 Score about 99.42% and mIoU is 0.584 for the same dataset.
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