Pathological lung segmentation in chest CT images based on improved random walker

Study on lung CT image segmentation algorithm based on threshold-gradient combination and improved convex hull method

Lung images often have the characteristics of strong noise, uneven grayscale distribution, and complex pathological structures, which makes lung image segmentation a challenging task. To solve this problems, this paper proposes an initial lung mask extraction algorithm that combines threshold and gradient. The gradient used in the algorithm is obtained by the time series feature extraction method based on differential memory (TFDM), which is obtained by the grayscale threshold and image grayscale features. At the same time, we also proposed a lung contour repair algorithm based on the improved convex hull method to solve the contour loss caused by solid nodules and other lesions. Experimental results show that on the COVID-19 CT segmentation dataset, the advanced lung segmentation algorithm proposed in this article achieves better segmentation results and greatly improves the consistency and accuracy of lung segmentation. Our method can obtain more lung information, resulting in ideal segmentation effects with improved accuracy and robustness.

Kidney, ureter, and urinary bladder segmentation based on non-contrast enhanced computed tomography images using modified U-Net

This study was performed to segment the urinary system as the basis for diagnosing urinary system diseases on non-contrast computed tomography (CT). This study was conducted with images obtained between January 2016 and December 2020. During the study period, non-contrast abdominopelvic CT scans of patients and diagnosed and treated with urinary stones at the emergency departments of two institutions were collected. Region of interest extraction was first performed, and urinary system segmentation was performed using a modified U-Net. Thereafter, fivefold cross-validation was performed to evaluate the robustness of the model performance. In fivefold cross-validation results of the segmentation of the urinary system, the average dice coefficient was 0.8673, and the dice coefficients for each class (kidney, ureter, and urinary bladder) were 0.9651, 0.7172, and 0.9196, respectively. In the test dataset, the average dice coefficient of best performing model in fivefold cross validation for whole urinary system was 0.8623, and the dice coefficients for each class (kidney, ureter, and urinary bladder) were 0.9613, 0.7225, and 0.9032, respectively. The segmentation of the urinary system using the modified U-Net proposed in this study could be the basis for the detection of kidney, ureter, and urinary bladder lesions, such as stones and tumours, through machine learning.

Linear semantic transformation for semi-supervised medical image segmentation

Medical image segmentation is a focus research and foundation in developing intelligent medical systems. Recently, deep learning for medical image segmentation has become a standard process and succeeded significantly, promoting the development of reconstruction, and surgical planning of disease diagnosis. However, semantic learning is often inefficient owing to the lack of supervision of feature maps, resulting in that high-quality segmentation models always rely on numerous and accurate data annotations. Learning robust semantic representation in latent spaces remains a challenge. In this paper, we propose a novel semi-supervised learning framework to learn vital attributes in medical images, which constructs generalized representation from diverse semantics to realize medical image segmentation. We first build a self-supervised learning part that achieves context recovery by reconstructing space and intensity of medical images, which conduct semantic representation for feature maps. Subsequently, we combine semantic-rich feature maps and utilize simple linear semantic transformation to convert them into image segmentation. The proposed framework was tested using five medical segmentation datasets. Quantitative assessments indicate the highest scores of our method on IXI (73.78%), ScaF (47.50%), COVID-19-Seg (50.72%), PC-Seg (65.06%), and Brain-MR (72.63%) datasets. Finally, we compared our method with the latest semi-supervised learning methods and obtained 77.15% and 75.22% DSC values, respectively, ranking first on two representative datasets. The experimental results not only proved that the proposed linear semantic transformation was effectively applied to medical image segmentation, but also presented its simplicity and ease-of-use to pursue robust segmentation in semi-supervised learning. Our code is now open at: https://github.com/QingYunA/Linear-Semantic-Transformation-for-Semi-Supervised-Medical-Image-Segmentation.

Deep Learning Framework for Liver Segmentation from T1-Weighted MRI Images

The human liver exhibits variable characteristics and anatomical information, which is often ambiguous in radiological images. Machine learning can be of great assistance in automatically segmenting the liver in radiological images, which can be further processed for computer-aided diagnosis. Magnetic resonance imaging (MRI) is preferred by clinicians for liver pathology diagnosis over volumetric abdominal computerized tomography (CT) scans, due to their superior representation of soft tissues. The convenience of Hounsfield unit (HoU) based preprocessing in CT scans is not available in MRI, making automatic segmentation challenging for MR images. This study investigates multiple state-of-the-art segmentation networks for liver segmentation from volumetric MRI images. Here, T1-weighted (in-phase) scans are investigated using expert-labeled liver masks from a public dataset of 20 patients (647 MR slices) from the Combined Healthy Abdominal Organ Segmentation grant challenge (CHAOS). The reason for using T1-weighted images is that it demonstrates brighter fat content, thus providing enhanced images for the segmentation task. Twenty-four different state-of-the-art segmentation networks with varying depths of dense, residual, and inception encoder and decoder backbones were investigated for the task. A novel cascaded network is proposed to segment axial liver slices. The proposed framework outperforms existing approaches reported in the literature for the liver segmentation task (on the same test set) with a dice similarity coefficient (DSC) score and intersect over union (IoU) of 95.15% and 92.10%, respectively.

All answers are in the images: A review of deep learning for cerebrovascular segmentation

Cerebrovascular imaging is a common examination. Its accurate cerebrovascular segmentation become an important auxiliary method for the diagnosis and treatment of cerebrovascular diseases, which has received extensive attention from researchers. Deep learning is a heuristic method that encourages researchers to derive answers from the images by driving datasets. With the continuous development of datasets and deep learning theory, it has achieved important success for cerebrovascular segmentation. Detailed survey is an important reference for researchers. To comprehensively analyze the newest cerebrovascular segmentation, we have organized and discussed researches centered on deep learning. This survey comprehensively reviews deep learning for cerebrovascular segmentation since 2015, it mainly includes sliding window based models, U-Net based models, other CNNs based models, small-sample based models, semi-supervised or unsupervised models, fusion based models, Transformer based models, and graphics based models. We organize the structures, improvement, and important parameters of these models, as well as analyze development trends and quantitative assessment. Finally, we have discussed the challenges and opportunities of possible research directions, hoping that our survey can provide researchers with convenient reference.

BPCN: bilateral progressive compensation network for lung infection image segmentation

Lung infection image segmentation is a key technology for autonomous understanding of the potential illness. However, current approaches usually lose the low-level details, which leads to a considerable accuracy decrease for lung infection areas with varied shapes and sizes. In this paper, we propose bilateral progressive compensation network (BPCN), a bilateral progressive compensation network to improve the accuracy of lung lesion segmentation through complementary learning of spatial and semantic features. The proposed BPCN are mainly composed of two deep branches. One branch is the multi-scale progressive fusion for main region features. The other branch is a flow-field based adaptive body-edge aggregation operations to explicitly learn detail features of lung infection areas which is supplement to region features. In addition, we propose a bilateral spatial-channel down-sampling to generate a hierarchical complementary feature which avoids losing discriminative features caused by pooling operations. Experimental results show that our proposed network outperforms state-of-the-art segmentation methods in lung infection segmentation on two public image datasets with or without a pseudo-label training strategy.

An Intelligent Breast Ultrasound System for Diagnosis and 3D Visualization

Background: Ultrasonography is the main examination method for breast diseases. Ultrasound imaging is currently relied upon by doctors to form statements of characteristics and locations of lesions, which severely limits the completeness and effectiveness of ultrasound image information. Moreover, analyzing ultrasonography requires experienced ultrasound doctors, which are not common in hospitals. Thus, this work proposes a 3D-based breast ultrasound system, which can automatically diagnose ultrasound images of the breasts and generate a representative 3D breast lesion model through typical ultrasonography. Methods: In this system, we use a weighted ensemble method to combine three different neural networks and explore different combinations of the neural networks. On this basis, a breast locator was designed to measure and transform the spatial position of lesions. The breast ultrasound software generates a 3D visualization report through the selection and geometric transformation of the nodular model. Results: The ensemble neural network improved in all metrics compared with the classical neural network (DenseNet, AlexNet, GoogLeNet, etc.). It proved that the ensemble neural network proposed in this work can be used for intelligent diagnosis of breast ultrasound images. For 3D visualization, magnetic resonance imaging (MRI) scans were performed to achieve their 3D reconstructions. By comparing two types of visualized results (MRI and our 3D model), we determined that models generated by the 3D-based breast ultrasound system have similar nodule characteristics and spatial relationships with the MRI. Conclusions: In summary, this system implements automatic diagnosis of ultrasound images and presents lesions through 3D models, which can obtain complete and accurate ultrasound image information. Thus, it has clinical potential.

A Saliency Prediction Model Based on Re-Parameterization and Channel Attention Mechanism

Deep saliency models can effectively imitate the attention mechanism of human vision, and they perform considerably better than classical models that rely on handcrafted features. However, deep models also require higher-level information, such as context or emotional content, to further approach human performance. Therefore, this study proposes a multilevel saliency prediction network that aims to use a combination of spatial and channel information to find possible high-level features, further improving the performance of a saliency model. Firstly, we use a VGG style network with an identity block as the primary network architecture. With the help of re-parameterization, we can obtain rich features similar to multiscale networks and effectively reduce computational cost. Secondly, a subnetwork with a channel attention mechanism is designed to find potential saliency regions and possible high-level semantic information in an image. Finally, image spatial features and a channel enhancement vector are combined after quantization to improve the overall performance of the model. Compared with classical models and other deep models, our model exhibits superior overall performance.

AI-driven quantification of ground glass opacities in lungs of COVID-19 patients using 3D computed tomography imaging

Objectives

Ground-glass opacity (GGO)—a hazy, gray appearing density on computed tomography (CT) of lungs—is one of the hallmark features of SARS-CoV-2 in COVID-19 patients. This AI-driven study is focused on segmentation, morphology, and distribution patterns of GGOs.

Method

We use an AI-driven unsupervised machine learning approach called PointNet++ to detect and quantify GGOs in CT scans of COVID-19 patients and to assess the severity of the disease. We have conducted our study on the “MosMedData”, which contains CT lung scans of 1110 patients with or without COVID-19 infections. We quantify the morphologies of GGOs using Minkowski tensors and compute the abnormality score of individual regions of segmented lung and GGOs.

Results

PointNet++ detects GGOs with the highest evaluation accuracy (98%), average class accuracy (95%), and intersection over union (92%) using only a fraction of 3D data. On average, the shapes of GGOs in the COVID-19 datasets deviate from sphericity by 15% and anisotropies in GGOs are dominated by dipole and hexapole components. These anisotropies may help to quantitatively delineate GGOs of COVID-19 from other lung diseases.

Conclusion

The PointNet++ and the Minkowski tensor based morphological approach together with abnormality analysis will provide radiologists and clinicians with a valuable set of tools when interpreting CT lung scans of COVID-19 patients. Implementation would be particularly useful in countries severely devastated by COVID-19 such as India, where the number of cases has outstripped available resources creating delays or even breakdowns in patient care. This AI-driven approach synthesizes both the unique GGO distribution pattern and severity of the disease to allow for more efficient diagnosis, triaging and conservation of limited resources.

Towards Machine Learning-Aided Lung Cancer Clinical Routines: Approaches and Open Challenges

Advancements in the development of computer-aided decision (CAD) systems for clinical routines provide unquestionable benefits in connecting human medical expertise with machine intelligence, to achieve better quality healthcare. Considering the large number of incidences and mortality numbers associated with lung cancer, there is a need for the most accurate clinical procedures; thus, the possibility of using artificial intelligence (AI) tools for decision support is becoming a closer reality. At any stage of the lung cancer clinical pathway, specific obstacles are identified and "motivate" the application of innovative AI solutions. This work provides a comprehensive review of the most recent research dedicated toward the development of CAD tools using computed tomography images for lung cancer-related tasks. We discuss the major challenges and provide critical perspectives on future directions. Although we focus on lung cancer in this review, we also provide a more clear definition of the path used to integrate AI in healthcare, emphasizing fundamental research points that are crucial for overcoming current barriers.

Symmetry GAN Detection Network: An Automatic One-Stage High-Accuracy Detection Network for Various Types of Lesions on CT Images

Computed tomography (CT) is the first modern slice-imaging modality. Recent years have witnessed its widespread application and improvement in detecting and diagnosing related lesions. Nonetheless, there are several difficulties in detecting lesions in CT images: (1) image quality degrades as the radiation dose is reduced to decrease radiational injury to the human body; (2) image quality is frequently hampered by noise interference; (3) because of the complicated circumstances of diseased tissue, lesion pictures typically show complex shapes; (4) the difference between the orientated object and the background is not discernible. This paper proposes a symmetry GAN detection network based on a one-stage detection network to tackle the challenges mentioned above. This paper employs the DeepLesion dataset, containing 10,594 CT scans (studies) of 4427 unique patients. The symmetry GANs proposed in this research consist of two distinct GAN models that serve different functions. A generative model is introduced ahead of the backbone to increase the input CT image series to address the typical problem of small sample size in medical datasets. Afterward, GAN models are added to the attention extraction module to generate attention masks. Furthermore, experimental data indicate that this strategy has significantly improved the model’s robustness. Eventually, the proposed method reaches 0.9720, 0.9858, and 0.9833 on P, R, and mAP, on the validation set. The experimental outcome shows that the suggested model outperforms other comparison models. In addition to this innovation, we are inspired by the innovation of the ResNet model in terms of network depth. Thus, we propose parallel multi-activation functions, an optimization method in the network width. It is theoretically proven that by adding coefficients to each base activation function and performing a softmax function on all coefficients, parallel multi-activation functions can express a single activation function, which is a unique ability compared to others. Ultimately, our model outperforms all comparison models in terms of P, R, and mAP, achieving 0.9737, 0.9845, and 0.9841. In addition, we encapsulate the model and build a related iOS application to make the model more applicable. The suggested model also won the second prize in the 2021 Chinese Collegiate Computing Competition.

DW-UNet: Loss Balance under Local-Patch for 3D Infection Segmentation from COVID-19 CT Images

(1) Background: COVID-19 has been global epidemic. This work aims to extract 3D infection from COVID-19 CT images; (2) Methods: Firstly, COVID-19 CT images are processed with lung region extraction and data enhancement. In this strategy, gradient changes of voxels in different directions respond to geometric characteristics. Due to the complexity of tubular tissues in lung region, they are clustered to the lung parenchyma center based on their filtered possibility. Thus, infection is improved after data enhancement. Then, deep weighted UNet is established to refining 3D infection texture, and weighted loss function is introduced. It changes cost calculation of different samples, causing target samples to dominate convergence direction. Finally, the trained network effectively extracts 3D infection from CT images by adjusting driving strategy of different samples. (3) Results: Using Accuracy, Precision, Recall and Coincidence rate, 20 subjects from a private dataset and eight subjects from Kaggle Competition COVID-19 CT dataset tested this method in hold-out validation framework. This work achieved good performance both in the private dataset (99.94-00.02%, 60.42-11.25%, 70.79-09.35% and 63.15-08.35%) and public dataset (99.73-00.12%, 77.02-06.06%, 41.23-08.61% and 52.50-08.18%). We also applied some extra indicators to test data augmentation and different models. The statistical tests have verified the significant difference of different models. (4) Conclusions: This study provides a COVID-19 infection segmentation technology, which provides an important prerequisite for the quantitative analysis of COVID-19 CT images.

CSR-Net: Cross-Scale Residual Network for multi-objective scaphoid fracture segmentation

The scaphoid is located in the carpals. Owing to the body structure and location of the scaphoid, scaphoid fractures are common and it is difficult to heal. Three-dimensional reconstruction of scaphoid fracture can accurately display the fracture surface and provide important support for the surgical plan involving screw placement. To achieve this goal, in this study, the cross-scale residual network (CSR-Net) is proposed for scaphoid fracture segmentation. In the CSR-Net, the features of different layers are used to achieve fusion through cross-scale residual connection, which realizes scale and channel conversions between the features of different layers. It can establish close connections between different scale features. The structures of the output layer and channel are designed to establish the CSR-Net as a multi-objective architecture, which can realize scaphoid fracture and hand bone segmentations synchronously. In this study, 65 computed tomography images of scaphoid fracture are tested. Quantitative metrics are used for assessment, and the results obtained show that the CSR-Net achieves higher performance in hand bone and scaphoid fracture segmentations. In the visually detailed display, the fracture surface is clearer and more intuitive than those obtained from other methods. Therefore, the CSR-Net can achieve accurate and rapid scaphoid fracture segmentation. Its multi-objective design provides not only an accurate digital model, but also a prerequisite for navigation in the hand bone.

AI-DRIVEN QUANTIFICATION OF GROUND GLASS OPACITIES IN LUNGS OF COVID-19 PATIENTS USING 3D COMPUTED TOMOGRAPHY IMAGING

Objectives

Ground-glass opacity (GGO) - a hazy, gray appearing density on computed tomography (CT) of lungs - is one of the hallmark features of SARS-CoV-2 in COVID-19 patients. This AI-driven study is focused on segmentation, morphology, and distribution patterns of GGOs.

Method

We use an AI-driven unsupervised machine learning approach called PointNet++ to detect and quantify GGOs in CT scans of COVID-19 patients and to assess the severity of the disease. We have conducted our study on the "MosMedData", which contains CT lung scans of 1110 patients with or without COVID-19 infections. We quantify the morphologies of GGOs using Minkowski tensors and compute the abnormality score of individual regions of segmented lung and GGOs.

Results

PointNet++ detects GGOs with the highest evaluation accuracy (98%), average class accuracy (95%), and intersection over union (92%) using only a fraction of 3D data. On average, the shapes of GGOs in the COVID-19 datasets deviate from sphericity by 15% and anisotropies in GGOs are dominated by dipole and hexapole components. These anisotropies may help to quantitatively delineate GGOs of COVID-19 from other lung diseases.

Conclusion

The PointNet++ and the Minkowski tensor based morphological approach together with abnormality analysis will provide radiologists and clinicians with a valuable set of tools when interpreting CT lung scans of COVID-19 patients. Implementation would be particularly useful in countries severely devastated by COVID-19 such as India, where the number of cases has outstripped available resources creating delays or even breakdowns in patient care. This AI-driven approach synthesizes both the unique GGO distribution pattern and severity of the disease to allow for more efficient diagnosis, triaging and conservation of limited resources.

Key Points

Our approach to GGO analysis has four distinguishing features:We combine an unsupervised computer vision approach with convex hull and convex points algorithms to segment and preserve the actual structure of the lung.To the best of our knowledge, we are the first group to use PointNet++ architecture for 3D visualization, segmentation, classification, and pattern analysis of GGOs.We make abnormality predictions using a deep network and Cox proportional hazards model using lung CT images of COVID-19 patients.We quantify the shapes and sizes of GGOs using Minkowski tensors to understand the morphological variations of GGOs within the COVID-19 cohort.