Multi-Task Siamese Network for Retinal Artery/Vein Separation via Deep Convolution Along Vessel

Automated tear film break-up time measurement for dry eye diagnosis using deep learning

In the realm of ophthalmology, precise measurement of tear film break-up time (TBUT) plays a crucial role in diagnosing dry eye disease (DED). This study aims to introduce an automated approach utilizing artificial intelligence (AI) to mitigate subjectivity and enhance the reliability of TBUT measurement. We employed a dataset of 47 slit lamp videos for development, while a test dataset of 20 slit lamp videos was used for evaluating the proposed approach. The multistep approach for TBUT estimation involves the utilization of a Dual-Task Siamese Network for classifying video frames into tear film breakup or non-breakup categories. Subsequently, a postprocessing step incorporates a Gaussian filter to smooth the instant breakup/non-breakup predictions effectively. Applying a threshold to the smoothed predictions identifies the initiation of tear film breakup. Our proposed method demonstrates on the evaluation dataset a precise breakup/non-breakup classification of video frames, achieving an Area Under the Curve of 0.870. At the video level, we observed a strong Pearson correlation coefficient (r) of 0.81 between TBUT assessments conducted using our approach and the ground truth. These findings underscore the potential of AI-based approaches in quantifying TBUT, presenting a promising avenue for advancing diagnostic methodologies in ophthalmology.

Semi-supervised point consistency network for retinal artery/vein classification

Recent deep learning methods with convolutional neural networks (CNNs) have boosted advance prosperity of medical image analysis and expedited the automatic retinal artery/vein (A/V) classification. However, it is challenging for these CNN-based approaches in two aspects: (1) specific tubular structures and subtle variations in appearance, contrast, and geometry, which tend to be ignored in CNNs with network layer increasing; (2) limited well-labeled data for supervised segmentation of retinal vessels, which may hinder the effectiveness of deep learning methods. To address these issues, we propose a novel semi-supervised point consistency network (SPC-Net) for retinal A/V classification. SPC-Net consists of an A/V classification (AVC) module and a multi-class point consistency (MPC) module. The AVC module adopts an encoder-decoder segmentation network to generate the prediction probability map of A/V for supervised learning. The MPC module introduces point set representations to adaptively generate point set classification maps of the arteriovenous skeleton, which enjoys its prediction flexibility and consistency (i.e. point consistency) to effectively alleviate arteriovenous confusion. In addition, we propose a consistency regularization between the predicted A/V classification probability maps and point set representations maps for unlabeled data to explore the inherent segmentation perturbation of the point consistency, reducing the need for annotated data. We validate our method on two typical public datasets (DRIVE, HRF) and a private dataset (TR280) with different resolutions. Extensive qualitative and quantitative experimental results demonstrate the effectiveness of our proposed method for supervised and semi-supervised learning.

Computer-aided diagnostic system for hypertensive retinopathy: A review

Hypertensive Retinopathy (HR) is a retinal disease caused by elevated blood pressure for a prolonged period. There are no obvious signs in the early stages of high blood pressure, but it affects various body parts over time, including the eyes. HR is a biomarker for several illnesses, including retinal diseases, atherosclerosis, strokes, kidney disease, and cardiovascular risks. Early microcirculation abnormalities in chronic diseases can be diagnosed through retinal examination prior to the onset of major clinical consequences. Computer-aided diagnosis (CAD) plays a vital role in the early identification of HR with improved diagnostic accuracy, which is time-efficient and demands fewer resources. Recently, numerous studies have been reported on the automatic identification of HR. This paper provides a comprehensive review of the automated tasks of Artery-Vein (A/V) classification, Arteriovenous ratio (AVR) computation, HR detection (Binary classification), and HR severity grading. The review is conducted using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) protocol. The paper discusses the clinical features of HR, the availability of datasets, existing methods used for A/V classification, AVR computation, HR detection, and severity grading, and performance evaluation metrics. The reviewed articles are summarized with classifiers details, adoption of different kinds of methodologies, performance comparisons, datasets details, their pros and cons, and computational platform. For each task, a summary and critical in-depth analysis are provided, as well as common research issues and challenges in the existing studies. Finally, the paper proposes future research directions to overcome challenges associated with data set availability, HR detection, and severity grading.

Deep Learning-Based Modified YOLACT Algorithm on Magnetic Resonance Imaging Images for Screening Common and Difficult Samples of Breast Cancer

Computer-aided methods have been extensively applied for diagnosing breast lesions with magnetic resonance imaging (MRI), but fully-automatic diagnosis using deep learning is rarely documented. Deep-learning-technology-based artificial intelligence (AI) was used in this work to classify and diagnose breast cancer based on MRI images. Breast cancer MRI images from the Rider Breast MRI public dataset were converted into processable joint photographic expert group (JPG) format images. The location and shape of the lesion area were labeled using the Labelme software. A difficult-sample mining mechanism was introduced to improve the performance of the YOLACT algorithm model as a modified YOLACT algorithm model. Diagnostic efficacy was compared with the Mask R-CNN algorithm model. The deep learning framework was based on PyTorch version 1.0. Four thousand and four hundred labeled data with corresponding lesions were labeled as normal samples, and 1600 images with blurred lesion areas as difficult samples. The modified YOLACT algorithm model achieved higher accuracy and better classification performance than the YOLACT model. The detection accuracy of the modified YOLACT algorithm model with the difficult-sample-mining mechanism is improved by nearly 3% for common and difficult sample images. Compared with Mask R-CNN, it is still faster in running speed, and the difference in recognition accuracy is not obvious. The modified YOLACT algorithm had a classification accuracy of 98.5% for the common sample test set and 93.6% for difficult samples. We constructed a modified YOLACT algorithm model, which is superior to the YOLACT algorithm model in diagnosis and classification accuracy.

Multi-task deep learning for medical image computing and analysis: A review

The renaissance of deep learning has provided promising solutions to various tasks. While conventional deep learning models are constructed for a single specific task, multi-task deep learning (MTDL) that is capable to simultaneously accomplish at least two tasks has attracted research attention. MTDL is a joint learning paradigm that harnesses the inherent correlation of multiple related tasks to achieve reciprocal benefits in improving performance, enhancing generalizability, and reducing the overall computational cost. This review focuses on the advanced applications of MTDL for medical image computing and analysis. We first summarize four popular MTDL network architectures (i.e., cascaded, parallel, interacted, and hybrid). Then, we review the representative MTDL-based networks for eight application areas, including the brain, eye, chest, cardiac, abdomen, musculoskeletal, pathology, and other human body regions. While MTDL-based medical image processing has been flourishing and demonstrating outstanding performance in many tasks, in the meanwhile, there are performance gaps in some tasks, and accordingly we perceive the open challenges and the perspective trends. For instance, in the 2018 Ischemic Stroke Lesion Segmentation challenge, the reported top dice score of 0.51 and top recall of 0.55 achieved by the cascaded MTDL model indicate further research efforts in high demand to escalate the performance of current models.

AV-casNet: Fully Automatic Arteriole-Venule Segmentation and Differentiation in OCT Angiography

Automatic segmentation and differentiation of retinal arteriole and venule (AV), defined as small blood vessels directly before and after the capillary plexus, are of great importance for the diagnosis of various eye diseases and systemic diseases, such as diabetic retinopathy, hypertension, and cardiovascular diseases. Optical coherence tomography angiography (OCTA) is a recent imaging modality that provides capillary-level blood flow information. However, OCTA does not have the colorimetric and geometric differences between AV as the fundus photography does. Various methods have been proposed to differentiate AV in OCTA, which typically needs the guidance of other imaging modalities. In this study, we propose a cascaded neural network to automatically segment and differentiate AV solely based on OCTA. A convolutional neural network (CNN) module is first applied to generate an initial segmentation, followed by a graph neural network (GNN) to improve the connectivity of the initial segmentation. Various CNN and GNN architectures are employed and compared. The proposed method is evaluated on multi-center clinical datasets, including 3 ×3 mm2 and 6 ×6 mm2 OCTA. The proposed method holds the potential to enrich OCTA image information for the diagnosis of various diseases.

3D Soma Detection in Large-Scale Whole Brain Images via a Two-Stage Neural Network

3D soma detection in whole brain images is a critical step for neuron reconstruction. However, existing soma detection methods are not suitable for whole mouse brain images with large amounts of data and complex structure. In this paper, we propose a two-stage deep neural network to achieve fast and accurate soma detection in large-scale and high-resolution whole mouse brain images (more than 1TB). For the first stage, a lightweight Multi-level Cross Classification Network (MCC-Net) is proposed to filter out images without somas and generate coarse candidate images by combining the advantages of the multi convolution layer's feature extraction ability. It can speed up the detection of somas and reduce the computational complexity. For the second stage, to further obtain the accurate locations of somas in the whole mouse brain images, the Scale Fusion Segmentation Network (SFS-Net) is developed to segment soma regions from candidate images. Specifically, the SFS-Net captures multi-scale context information and establishes a complementary relationship between encoder and decoder by combining the encoder-decoder structure and a 3D Scale-Aware Pyramid Fusion (SAPF) module for better segmentation performance. The experimental results on three whole mouse brain images verify that the proposed method can achieve excellent performance and provide the reconstruction of neurons with beneficial information. Additionally, we have established a public dataset named WBMSD, including 798 high-resolution and representative images ( 256 ×256 ×256 voxels) from three whole mouse brain images, dedicated to the research of soma detection, which will be released along with this paper.

Automated diagnosing primary open-angle glaucoma from fundus image by simulating human's grading with deep learning

Primary open-angle glaucoma (POAG) is a leading cause of irreversible blindness worldwide. Although deep learning methods have been proposed to diagnose POAG, it remains challenging to develop a robust and explainable algorithm to automatically facilitate the downstream diagnostic tasks. In this study, we present an automated classification algorithm, GlaucomaNet, to identify POAG using variable fundus photographs from different populations and settings. GlaucomaNet consists of two convolutional neural networks to simulate the human grading process: learning the discriminative features and fusing the features for grading. We evaluated GlaucomaNet on two datasets: Ocular Hypertension Treatment Study (OHTS) participants and the Large-scale Attention-based Glaucoma (LAG) dataset. GlaucomaNet achieved the highest AUC of 0.904 and 0.997 for POAG diagnosis on OHTS and LAG datasets. An ensemble of network architectures further improved diagnostic accuracy. By simulating the human grading process, GlaucomaNet demonstrated high accuracy with increased transparency in POAG diagnosis (comprehensiveness scores of 97% and 36%). These methods also address two well-known challenges in the field: the need for increased image data diversity and relying heavily on perimetry for POAG diagnosis. These results highlight the potential of deep learning to assist and enhance clinical POAG diagnosis. GlaucomaNet is publicly available on https://github.com/bionlplab/GlaucomaNet .

Deep learning for ultra-widefield imaging: a scoping review

PURPOSE

This article is a scoping review of published and peer-reviewed articles using deep-learning (DL) applied to ultra-widefield (UWF) imaging. This study provides an overview of the published uses of DL and UWF imaging for the detection of ophthalmic and systemic diseases, generative image synthesis, quality assessment of images, and segmentation and localization of ophthalmic image features.

METHODS

A literature search was performed up to August 31st, 2021 using PubMed, Embase, Cochrane Library, and Google Scholar. The inclusion criteria were as follows: (1) deep learning, (2) ultra-widefield imaging. The exclusion criteria were as follows: (1) articles published in any language other than English, (2) articles not peer-reviewed (usually preprints), (3) no full-text availability, (4) articles using machine learning algorithms other than deep learning. No study design was excluded from consideration.

RESULTS

A total of 36 studies were included. Twenty-three studies discussed ophthalmic disease detection and classification, 5 discussed segmentation and localization of ultra-widefield images (UWFIs), 3 discussed generative image synthesis, 3 discussed ophthalmic image quality assessment, and 2 discussed detecting systemic diseases via UWF imaging.

CONCLUSION

The application of DL to UWF imaging has demonstrated significant effectiveness in the diagnosis and detection of ophthalmic diseases including diabetic retinopathy, retinal detachment, and glaucoma. DL has also been applied in the generation of synthetic ophthalmic images. This scoping review highlights and discusses the current uses of DL with UWF imaging, and the future of DL applications in this field.

Multi-perspective label based deep learning framework for cerebral vasculature segmentation in whole-brain fluorescence images

The popularity of fluorescent labelling and mesoscopic optical imaging techniques enable the acquisition of whole mammalian brain vasculature images at capillary resolution. Segmentation of the cerebrovascular network is essential for analyzing the cerebrovascular structure and revealing the pathogenesis of brain diseases. Existing deep learning methods use a single type of annotated labels with the same pixel weight to train the neural network and segment vessels. Due to the variation in the shape, density and brightness of vessels in whole-brain fluorescence images, it is difficult for a neural network trained with a single type of label to segment all vessels accurately. To address this problem, we proposed a deep learning cerebral vasculature segmentation framework based on multi-perspective labels. First, the pixels in the central region of thick vessels and the skeleton region of vessels were extracted separately using morphological operations based on the binary annotated labels to generate two different labels. Then, we designed a three-stage 3D convolutional neural network containing three sub-networks, namely thick-vessel enhancement network, vessel skeleton enhancement network and multi-channel fusion segmentation network. The first two sub-networks were trained by the two labels generated in the previous step, respectively, and pre-segmented the vessels. The third sub-network was responsible for fusing the pre-segmented results to precisely segment the vessels. We validated our method on two mouse cerebral vascular datasets generated by different fluorescence imaging modalities. The results showed that our method outperforms the state-of-the-art methods, and the proposed method can be applied to segment the vasculature on large-scale volumes.

A 3D Tubular Flux Model for Centerline Extraction in Neuron Volumetric Images

Digital morphology reconstruction from neuron volumetric images is essential for computational neuroscience. The centerline of the axonal and dendritic tree provides an effective shape representation and serves as a basis for further neuron reconstruction. However, it is still a challenge to directly extract the accurate centerline from the complex neuron structure with poor image quality. In this paper, we propose a neuron centerline extraction method based on a 3D tubular flux model via a two-stage CNN framework. In the first stage, a 3D CNN is used to learn the latent neuron structure features, namely flux features, from neuron images. In the second stage, a light-weight U-Net takes the learned flux features as input to extract the centerline with a spatial weighted average strategy to constrain the multi-voxel width response. Specifically, the labels of flux features in the first stage are generated by the 3D tubular model which calculates the geometric representations of the flux between each voxel in the tubular region and the nearest point on the centerline ground truth. Compared with self-learned features by networks, flux features, as a kind of prior knowledge, explicitly take advantage of the contextual distance and direction distribution information around the centerline, which is beneficial for the precise centerline extraction. Experiments on two challenging datasets demonstrate that the proposed method outperforms other state-of-the-art methods by 18% and 35.1% in F1-measurement and average distance scores at the most, and the extracted centerline is helpful to improve the neuron reconstruction performance.

Multi-scale Interactive Network with Artery/Vein Discriminator for Retinal Vessel Classification

Automatic classification of retinal arteries and veins plays an important role in assisting clinicians to diagnosis cardiovascular and eye-related diseases. However, due to the high degree of anatomical variation across the population, and the presence of inconsistent labels by the subjective judgment of annotators in available training data, most of existing methods generally suffer from blood vessel discontinuity and arteriovenous confusion, the artery/vein (A/V) classification task still faces great challenges. In this work, we propose a multi-scale interactive network with A/V discriminator for retinal artery and vein recognition, which can reduce the arteriovenous confusion and alleviate the disturbance of noisy label. A multi-scale interaction (MI) module is designed in encoder for realizing the cross-space multi-scale features interaction of fundus images, effectively integrate high-level and low-level context information. In particular, we design an ingenious A/V discriminator (AVD) that utilizes the independent and shared information between arteries and veins, and combine with topology loss, to further strengthen the learning ability of model to resolve the arteriovenous confusion. In addition, we adopt a sample re-weighting (SW) strategy to effectively alleviate the disturbance from data labeling errors. The proposed model is verified on three publicly available fundus image datasets (AV-DRIVE, HRF, LES-AV) and a private dataset. We achieve the accuracy of 97.47%, 96.91%, 97.79%, and 98.18% respectively on these four datasets. Extensive experimental results demonstrate that our method achieves competitive performance compared with state-of-the-art methods for A/V classification. To address the problem of training data scarcity, we publicly release 100 fundus images with A/V annotations to promote relevant research in the community.

Artery vein classification in fundus images using serially connected U-Nets

BACKGROUND AND OBJECTIVE

Retinal vessels provide valuable information when diagnosing or monitoring various diseases affecting the retina and disorders affecting the cardiovascular or central nervous systems. Automated retinal vessel segmentation can assist clinicians and researchers when interpreting retinal images. As there are differences in both the structure and function of retinal arteries and veins, separating these two vessel types is essential. As manual segmentation of retinal images is impractical, an accurate automated method is required.

METHODS

In this paper, we propose a convolutional neural network based on serially connected U-nets that simultaneously segment the retinal vessels and classify them as arteries or veins. Detailed ablation experiments are performed to understand how the major components contribute to the overall system's performance. The proposed method is trained and tested on the public DRIVE and HRF datasets and a proprietary dataset.

RESULTS

The proposed convolutional neural network achieves an F₁ score of 0.829 for vessel segmentation on the DRIVE dataset and an F₁ score of 0.814 on the HRF dataset, consistent with the state-of-the-art methods on the former and outperforming the state-of-the-art on the latter. On the task of classifying the vessels into arteries and veins, the method achieves an F₁ score of 0.952 for the DRIVE dataset exceeding the state-of-the-art performance. On the HRF dataset, the method achieves an F₁ score of 0.966, which is consistent with the state-of-the-art.

CONCLUSIONS

The proposed method demonstrates competitive performance on both vessel segmentation and artery vein classification compared with state-of-the-art methods. The method outperforms human experts on the DRIVE dataset when classifying retinal images into arteries, veins, and background simultaneously. The method segments the vasculature on the proprietary dataset and classifies the retinal vessels accurately, even on challenging pathological images. The ablation experiments which utilize repeated runs for each configuration provide statistical evidence for the appropriateness of the proposed solution. Connecting several simple U-nets significantly improved artery vein classification performance. The proposed way of serially connecting base networks is not limited to the proposed base network or segmenting the retinal vessels and could be applied to other tasks.

CXR-RefineDet: Single-Shot Refinement Neural Network for Chest X-Ray Radiograph Based on Multiple Lesions Detection

The workload of radiologists has dramatically increased in the context of the COVID-19 pandemic, causing misdiagnosis and missed diagnosis of diseases. The use of artificial intelligence technology can assist doctors in locating and identifying lesions in medical images. In order to improve the accuracy of disease diagnosis in medical imaging, we propose a lung disease detection neural network that is superior to the current mainstream object detection model in this paper. By combining the advantages of RepVGG block and Resblock in information fusion and information extraction, we design a backbone RRNet with few parameters and strong feature extraction capabilities. After that, we propose a structure called Information Reuse, which can solve the problem of low utilization of the original network output features by connecting the normalized features back to the network. Combining the network of RRNet and the improved RefineDet, we propose the overall network which was called CXR-RefineDet. Through a large number of experiments on the largest public lung chest radiograph detection dataset VinDr-CXR, it is found that the detection accuracy and inference speed of CXR-RefineDet have reached 0.1686 mAP and 6.8 fps, respectively, which is better than the two-stage object detection algorithm using a strong backbone like ResNet-50 and ResNet-101. In addition, the fast reasoning speed of CXR-RefineDet also provides the possibility for the actual implementation of the computer-aided diagnosis system.

Automatic multi-plaque tracking and segmentation in ultrasonic videos

Carotid plaque tracking and segmentation in ultrasound videos is the premise for subsequent plaque property evaluation and treatment plan development. However, the task is quite challenging, as it needs to address the problems of poor image quality, plaque shape variations among frames, the existence of multiple plaques, etc. To overcome these challenges, we propose a new automatic multi-plaque tracking and segmentation (AMPTS) framework. AMPTS consists of three modules. The first module is a multi-object detector, in which a Dual Attention U-Net is proposed to detect multiple plaques and vessels simultaneously. The second module is a set of single-object trackers that can utilize the previous tracking results efficiently and achieve stable tracking of the current target by using channel attention and a ranking strategy. To make the first module and the second module work together, a parallel tracking module based on a simplified 'tracking-by-detection' mechanism is proposed to solve the challenge of tracking object variation. Extensive experiments are conducted to compare the proposed method with several state-of-the-art deep learning based methods. The experimental results demonstrate that the proposed method has high accuracy and generalizability with a Dice similarity coefficient of 0.83 which is 0.16, 0.06 and 0.27 greater than MAST (Lai et al., 2020), Track R-CNN (Voigtlaender et al., 2019) and VSD (Yang et al., 2019) respectively and has made significant improvements on seven other indicators. In the additional Testing set 2, our method achieved a Dice similarity coefficient of 0.80, an accuracy of 0.79, a precision of 0.91, a Recall 0.70, a F1 score of 0.79, an AP@0.5 of 0.92, an AP@0.7 of 0.74, and an expected average overlap of 0.79. Numerous ablation studies suggest the effectiveness of each proposed component and the great potential for multiple carotid plaques tracking and segmentation in clinical practice.

CMM-Net: Contextual multi-scale multi-level network for efficient biomedical image segmentation

Medical image segmentation of tissue abnormalities, key organs, or blood vascular system is of great significance for any computerized diagnostic system. However, automatic segmentation in medical image analysis is a challenging task since it requires sophisticated knowledge of the target organ anatomy. This paper develops an end-to-end deep learning segmentation method called Contextual Multi-Scale Multi-Level Network (CMM-Net). The main idea is to fuse the global contextual features of multiple spatial scales at every contracting convolutional network level in the U-Net. Also, we re-exploit the dilated convolution module that enables an expansion of the receptive field with different rates depending on the size of feature maps throughout the networks. In addition, an augmented testing scheme referred to as Inversion Recovery (IR) which uses logical "OR" and "AND" operators is developed. The proposed segmentation network is evaluated on three medical imaging datasets, namely ISIC 2017 for skin lesions segmentation from dermoscopy images, DRIVE for retinal blood vessels segmentation from fundus images, and BraTS 2018 for brain gliomas segmentation from MR scans. The experimental results showed superior state-of-the-art performance with overall dice similarity coefficients of 85.78%, 80.27%, and 88.96% on the segmentation of skin lesions, retinal blood vessels, and brain tumors, respectively. The proposed CMM-Net is inherently general and could be efficiently applied as a robust tool for various medical image segmentations.