Automatic Pancreas Segmentation in CT Images With Distance-Based Saliency-Aware DenseASPP Network

MOTC: Abdominal Multi-objective Segmentation Model with Parallel Fusion of Global and Local Information

Convolutional Neural Networks have been widely applied in medical image segmentation. However, the existence of local inductive bias in convolutional operations restricts the modeling of long-term dependencies. The introduction of Transformer enables the modeling of long-term dependencies and partially eliminates the local inductive bias in convolutional operations, thereby improving the accuracy of tasks such as segmentation and classification. Researchers have proposed various hybrid structures combining Transformer and Convolutional Neural Networks. One strategy is to stack Transformer blocks and convolutional blocks to concentrate on eliminating the accumulated local bias of convolutional operations. Another strategy is to nest convolutional blocks and Transformer blocks to eliminate bias within each nested block. However, due to the granularity of bias elimination operations, these two strategies cannot fully exploit the potential of Transformer. In this paper, a parallel hybrid model is proposed for segmentation, which includes a Transformer branch and a Convolutional Neural Network branch in encoder. After parallel feature extraction, inter-layer information fusion and exchange of complementary information are performed between the two branches, simultaneously extracting local and global features while eliminating the local bias generated by convolutional operations within the current layer. A pure convolutional operation is used in decoder to obtain final segmentation results. To validate the impact of the granularity of bias elimination operations on the effectiveness of local bias elimination, the experiments in this paper were conducted on Flare21 dataset and Amos22 dataset. The average Dice coefficient reached 92.65% on Flare21 dataset, and 91.61% on Amos22 dataset, surpassing comparative methods. The experimental results demonstrate that smaller granularity of bias elimination operations leads to better performance.

Boundary-Sensitive Loss Function With Location Constraint for Hard Region Segmentation

In computer-aided diagnosis and treatment planning, accurate segmentation of medical images plays an essential role, especially for some hard regions including boundaries, small objects and background interference. However, existing segmentation loss functions including distribution-, region- and boundary-based losses cannot achieve satisfactory performances on these hard regions. In this paper, a boundary-sensitive loss function with location constraint is proposed for hard region segmentation in medical images, which provides three advantages: i) our Boundary-Sensitive loss (BS-loss) can automatically pay more attention to the hard-to-segment boundaries (e.g., thin structures and blurred boundaries), thus obtaining finer object boundaries; ii) BS-loss also can adjust its attention to small objects during training to segment them more accurately; and iii) our location constraint can alleviate the negative impact of the background interference, through the distribution matching of pixels between prediction and Ground Truth (GT) along each axis. By resorting to the proposed BS-loss and location constraint, the hard regions in both foreground and background are considered. Experimental results on three public datasets demonstrate the superiority of our method. Specifically, compared to the second-best method tested in this study, our method improves performance on hard regions in terms of Dice similarity coefficient (DSC) and 95% Hausdorff distance (95%HD) of up to 4.17% and 73% respectively. In addition, it also achieves the best overall segmentation performance. Hence, we can conclude that our method can accurately segment these hard regions and improve the overall segmentation performance in medical images.

An End-to-End Data-Adaptive Pancreas Segmentation System with an Image Quality Control Toolbox

With the development of radiology and computer technology, diagnosis by medical imaging is heading toward precision and automation. Due to complex anatomy around the pancreatic tissue and high demands for clinical experience, the assisted pancreas segmentation system will greatly promote clinical efficiency. However, the existing segmentation model suffers from poor generalization among images from multiple hospitals. In this paper, we propose an end-to-end data-adaptive pancreas segmentation system to tackle the problems of lack of annotations and model generalizability. The system employs adversarial learning to transfer features from labeled domains to unlabeled domains, seeking a dynamic balance between domain discrimination and unsupervised segmentation. The image quality control toolbox is embedded in the system, which standardizes image quality in terms of intensity, field of view, and so on, to decrease heterogeneity among image domains. In addition, the system implements a data-adaptive process end-to-end without complex operations by doctors. The experiments are conducted on an annotated public dataset and an unannotated in-hospital dataset. The results indicate that after data adaptation, the segmentation performance measured by the dice similarity coefficient on unlabeled images improves from 58.79% to 75.43%, with a gain of 16.64%. Furthermore, the system preserves quantitatively structured information such as the pancreas’ size and volume, as well as objective and accurate visualized images, which assists clinicians in diagnosing and formulating treatment plans in a timely and accurate manner.

Extension-contraction transformation network for pancreas segmentation in abdominal CT scans

Accurate and automatic pancreas segmentation from abdominal computed tomography (CT) scans is crucial for the diagnosis and prognosis of pancreatic diseases. However, the pancreas accounts for a relatively small portion of the scan and presents high anatomical variability and low contrast, making traditional automated segmentation methods fail to generate satisfactory results. In this paper, we propose an extension-contraction transformation network (ECTN) and deploy it into a cascaded two-stage segmentation framework for accurate pancreas segmenting. This model can enhance the perception of 3D context by distinguishing and exploiting the extension and contraction transformation of the pancreas between slices. It consists of an encoder, a segmentation decoder, and an extension-contraction (EC) decoder. The EC decoder is responsible for predicting the inter-slice extension and contraction transformation of the pancreas by feeding the extension and contraction information generated by the segmentation decoder; meanwhile, its output is combined with the output of the segmentation decoder to reconstruct and refine the segmentation results. Quantitative evaluation is performed on NIH Pancreas Segmentation (Pancreas-CT) dataset using 4-fold cross-validation. We obtained average Precision of 86.59±6.14% , Recall of 85.11±5.96%, Dice similarity coefficient (DSC) of 85.58±3.98%. and Jaccard Index (JI) of 74.99±5.86%. The performance of our method outperforms several baseline and state-of-the-art methods.

Multiscale unsupervised domain adaptation for automatic pancreas segmentation in CT volumes using adversarial learning

PURPOSE

Computer-aided automatic pancreas segmentation is essential for early diagnosis and treatment of pancreatic diseases. However, the annotation of pancreas images requires professional doctors and considerable expenditure. Due to imaging differences among various institution population, scanning devices and imaging protocols etc., significant degradation in the performance of model inference results is prone to occur when models trained with domain-specific (usually institution-specific) datasets are directly applied to new (other centers/institutions) domain data. In this paper, we propose a novel unsupervised domain adaptation method based on adversarial learning to address pancreas segmentation challenges with the lack of annotations and domain shift interference.

METHODS

A 3D semantic segmentation model with attention module and residual module is designed as the backbone pancreas segmentation model. In both segmentation model and domain adaptation discriminator network, a multiscale progressively weighted structure is introduced to acquire different field of views. Features of labeled data and unlabeled data are fed in pairs into the proposed multiscale discriminator to learn domain-specific characteristics. Then the unlabeled data features with pseudo-domain label are fed to the discriminator to acquire domain-ambiguous information. With this adversarial learning strategy, the performance of the segmentation network is enhanced to segment unseen unlabeled data.

RESULTS

Experiments were conducted on two public annotated datasets as source datasets respectively and one private dataset as target dataset, where annotations were not used for the training process but only for evaluation. The 3D segmentation model achieves comparative performance with state-of-the-art pancreas segmentation methods on source domain. After implementing our domain adaptation architecture, the average Dice Similarity Coefficient(DSC) of the segmentation model trained on the NIH-TCIA source dataset increases from 58.79% to 72.73% on the local hospital dataset, while the performance of the target domain segmentation model transferred from the MSD source dataset rises from 62.34% to 71.17%.

CONCLUSIONS

Correlation of features across data domains are utilized to train the pancreas segmentation model on unlabeled data domain, improving the generalization of the model. Our results demonstrate that the proposed method enables the segmentation model to make meaningful segmentation for unseen data of the training set. In the future, the proposed method has the potential to apply segmentation model trained on public dataset to clinical unannotated CT images from local hospital, effectively assisting radiologists in clinical practice. This article is protected by copyright. All rights reserved.

AX-Unet: A Deep Learning Framework for Image Segmentation to Assist Pancreatic Tumor Diagnosis

Image segmentation plays an essential role in medical imaging analysis such as tumor boundary extraction. Recently, deep learning techniques have dramatically improved performance for image segmentation. However, an important factor preventing deep neural networks from going further is the information loss during the information propagation process. In this article, we present AX-Unet, a deep learning framework incorporating a modified atrous spatial pyramid pooling module to learn the location information and to extract multi-level contextual information to reduce information loss during downsampling. We also introduce a special group convolution operation on the feature map at each level to achieve information decoupling between channels. In addition, we propose an explicit boundary-aware loss function to tackle the blurry boundary problem. We evaluate our model on two public Pancreas-CT datasets, NIH Pancreas-CT dataset, and the pancreas part in medical segmentation decathlon (MSD) medical dataset. The experimental results validate that our model can outperform the state-of-the-art methods in pancreas CT image segmentation. By comparing the extracted feature output of our model, we find that the pancreatic region of normal people and patients with pancreatic tumors shows significant differences. This could provide a promising and reliable way to assist physicians for the screening of pancreatic tumors.

Accurate pancreas segmentation using multi-level pyramidal pooling residual U-Net with adversarial mechanism

Background

A novel multi-level pyramidal pooling residual U-Net with adversarial mechanism was proposed for organ segmentation from medical imaging, and was conducted on the challenging NIH Pancreas-CT dataset.

Methods

The 82 pancreatic contrast-enhanced abdominal CT volumes were split via four-fold cross validation to test the model performance. In order to achieve accurate segmentation, we firstly involved residual learning into an adversarial U-Net to achieve a better gradient information flow for improving segmentation performance. Then, we introduced a multi-level pyramidal pooling module (MLPP), where a novel pyramidal pooling was involved to gather contextual information for segmentation, then four groups of structures consisted of a different number of pyramidal pooling blocks were proposed to search for the structure with the optimal performance, and two types of pooling blocks were applied in the experimental section to further assess the robustness of MLPP for pancreas segmentation. For evaluation, Dice similarity coefficient (DSC) and recall were used as the metrics in this work.

Results

The proposed method preceded the baseline network 5.30% and 6.16% on metrics DSC and recall, and achieved competitive results compared with the-state-of-art methods.

Conclusions

Our algorithm showed great segmentation performance even on the particularly challenging pancreas dataset, this indicates that the proposed model is a satisfactory and promising segmentor.

A Semiautomated Deep Learning Approach for Pancreas Segmentation

Accurate pancreas segmentation from 3D CT volumes is important for pancreas diseases therapy. It is challenging to accurately delineate the pancreas due to the poor intensity contrast and intrinsic large variations in volume, shape, and location. In this paper, we propose a semiautomated deformable U-Net, i.e., DUNet for the pancreas segmentation. The key innovation of our proposed method is a deformable convolution module, which adaptively adds learned offsets to each sampling position of 2D convolutional kernel to enhance feature representation. Combining deformable convolution module with U-Net enables our DUNet to flexibly capture pancreatic features and improve the geometric modeling capability of U-Net. Moreover, a nonlinear Dice-based loss function is designed to tackle the class-imbalanced problem in the pancreas segmentation. Experimental results show that our proposed method outperforms all comparison methods on the same NIH dataset.