COSTA: A Multi-center TOF-MRA Dataset and A Style Self-Consistency Network for Cerebrovascular Segmentation.

Time-of-flight magnetic resonance angiography (TOF-MRA) is the least invasive and ionizing radiation-free approach for cerebrovascular imaging, but variations in imaging artifacts across different clinical centers and imaging vendors result in inter-site and inter-vendor heterogeneity, making its accurate and robust cerebrovascular segmentation challenging. Moreover, the limited availability and quality of annotated data pose further challenges for segmentation methods to generalize well to unseen datasets. In this paper, we construct the largest and most diverse TOF-MRA dataset (COSTA) from 8 individual imaging centers, with all the volumes manually annotated. Then we propose a novel network for cerebrovascular segmentation, namely CESAR, with the ability to tackle feature granularity and image style heterogeneity issues. Specifically, a coarse-to-fine architecture is implemented to refine cerebrovascular segmentation in an iterative manner. An automatic feature selection module is proposed to selectively fuse global long-range dependencies and local contextual information of cerebrovascular structures. A style self-consistency loss is then introduced to explicitly align diverse styles of TOF-MRA images to a standardized one. Extensive experimental results on the COSTA dataset demonstrate the effectiveness of our CESAR network against state-of-the-art methods. We have made 6 subsets of COSTA with the source code online available, in order to promote relevant research in the community.

Base-Promoted Synthesis of Isoquinolines through a Tandem Reaction of 2-Methyl-arylaldehydes and Nitriles.

A convenient method for preparing 3-aryl isoquinolines via a base-promoted tandem reaction is presented. Simply combining commercially available 2-methyl-arylaldehydes, benzonitriles, NaN(SiMe3)2, and Cs2CO3 enabled the synthesis of a variety of isoquinolines (23 examples, ≤90% yield). Among the syntheses of isoquinolines, the transition metal-free method described here is straightforward, practical, and operationally simple.

Choroidal Layer Analysis in OCT images via Ambiguous Boundary-aware Attention.

Optical Coherence Tomography (OCT) is a commonly used retina imaging technique, and it is capable of revealing the morphology of the choroid. However, the segmentation and quantitative analysis of the sublayers and vessels in choroid are rarely explored, primarily due to the indistinct boundaries of choroidal sublayers, and imbalanced distribution of vessels observed in OCT imagery. In this paper, we propose a novel two-stage architecture called Choroidal Layer Analysis network (CLA), that may be considered the first attempt in this research community for joint segmentation of choroidal sublayers and choroidal vessels in OCT images. CLA employs the encoder-decoder network with the residual U-shape module as the backbone. In order to empower the ability of the segmentation model to identify the inconspicuous boundaries of choroidal sublayers, we introduce an Ambiguous Boundary Attention block (ABA) into the bottleneck of the encoder-decoder network in the first stage. For more accurate segmentation of large choroidal vessels with ambiguous contours and imbalanced spatial distribution, the second stage introduces an active contour-based loss to refine the contours of choroidal vessels simultaneously with precise identification of each vessel via contextual modeling. To train, test and validate the proposed model, we conducted a choroidal segmentation dataset containing 800 OCT images, with their sublayers and large choroidal vessels manually annotated. Experimental results demonstrate the superiority of the proposed approach compared with other state-of-the-art segmentation networks in large margins. It is worth noting that we also reconstructed the large choroidal vessels in three-dimensional (3D) based on the segmentation results, and multiple 3D morphological parameters were calculated. The statistical analysis of these parameters demonstrates significant differences between the healthy control and high myopia group, and this further confirms the proposed work may facilitate subsequent disease understanding and clinical decision-making.

Automated evaluation of retinal hyperreflective foci changes in diabetic macular edema patients before and after intravitreal injection.

Purpose: Fast and automated reconstruction of retinal hyperreflective foci (HRF) is of great importance for many eye-related disease understanding. In this paper, we introduced a new automated framework, driven by recent advances in deep learning to automatically extract 12 three-dimensional parameters from the segmented hyperreflective foci in optical coherence tomography (OCT). Methods: Unlike traditional convolutional neural networks, which struggle with long-range feature correlations, we introduce a spatial and channel attention module within the bottleneck layer, integrated into the nnU-Net architecture. Spatial Attention Block aggregates features across spatial locations to capture related features, while Channel Attention Block heightens channel feature contrasts. The proposed model was trained and tested on 162 retinal OCT volumes of patients with diabetic macular edema (DME), yielding robust segmentation outcomes. We further investigate HRF's potential as a biomarker of DME. Results: Results unveil notable discrepancies in the amount and volume of HRF subtypes. In the whole retinal layer (WR), the mean distance from HRF to the retinal pigmented epithelium was significantly reduced after treatment. In WR, the improvement in central macular thickness resulting from intravitreal injection treatment was positively correlated with the mean distance from HRF subtypes to the fovea. Conclusion: Our study demonstrates the applicability of OCT for automated quantification of retinal HRF in DME patients, offering an objective, quantitative approach for clinical and research applications.

StruNet: Perceptual and low-rank regularized transformer for medical image denoising.

BACKGROUND: Various types of noise artifacts inevitably exist in some medical imaging modalities due to limitations of imaging techniques, which impair either clinical diagnosis or subsequent analysis. Recently, deep learning approaches have been rapidly developed and applied on medical images for noise removal or image quality enhancement. Nevertheless, due to complexity and diversity of noise distribution representations in different medical imaging modalities, most of the existing deep learning frameworks are incapable to flexibly remove noise artifacts while retaining detailed information. As a result, it remains challenging to design an effective and unified medical image denoising method that will work across a variety of noise artifacts for different imaging modalities without requiring specialized knowledge in performing the task. PURPOSE: In this paper, we propose a novel encoder-decoder architecture called Swin transformer-based residual u-shape Network (StruNet), for medical image denoising. METHODS: Our StruNet adopts a well-designed block as the backbone of the encoder-decoder architecture, which integrates Swin Transformer modules with residual block in parallel connection. Swin Transformer modules could effectively learn hierarchical representations of noise artifacts via self-attention mechanism in non-overlapping shifted windows and cross-window connection, while residual block is advantageous to compensate loss of detailed information via shortcut connection. Furthermore, perceptual loss and low-rank regularization are incorporated into loss function respectively in order to constrain the denoising results on feature-level consistency and low-rank characteristics. RESULTS: To evaluate the performance of the proposed method, we have conducted experiments on three medical imaging modalities including computed tomography (CT), optical coherence tomography (OCT) and optical coherence tomography angiography (OCTA). CONCLUSIONS: The results demonstrate that the proposed architecture yields a promising performance of suppressing multiform noise artifacts existing in different imaging modalities.

Choroidal layer segmentation in OCT images by a boundary enhancement network.

Morphological changes of the choroid have been proved to be associated with the occurrence and pathological mechanism of many ophthalmic diseases. Optical Coherence Tomography (OCT) is a non-invasive technique for imaging of ocular biological tissues, that can reveal the structure of the retinal and choroidal layers in micron-scale resolution. However, unlike the retinal layer, the interface between the choroidal layer and the sclera is ambiguous in OCT, which makes it difficult for ophthalmologists to identify with certainty. In this paper, we propose a novel boundary-enhanced encoder-decoder architecture for choroid segmentation in retinal OCT images, in which a Boundary Enhancement Module (BEM) forms the backbone of each encoder-decoder layer. The BEM consists of three parallel branches: 1) a Feature Extraction Branch (FEB) to obtain feature maps with different receptive fields; 2) a Channel Enhancement Branch (CEB) to extract the boundary information of different channels; and 3) a Boundary Activation Branch (BAB) to enhance the boundary information via a novel activation function. In addition, in order to incorporate expert knowledge into the segmentation network, soft key point maps are generated on the choroidal boundary, and are combined with the predicted images to facilitate precise choroidal boundary segmentation. In order to validate the effectiveness and superiority of the proposed method, both qualitative and quantitative evaluations are employed on three retinal OCT datasets for choroid segmentation. The experimental results demonstrate that the proposed method yields better choroid segmentation performance than other deep learning approaches. Moreover, both 2D and 3D features are extracted for statistical analysis from normal and highly myopic subjects based on the choroid segmentation results, which is helpful in revealing the pathology of high myopia. Code is available at https://github.com/iMED-Lab/Choroid-segmentation.

Sparse-Based Domain Adaptation Network for OCTA Image Super-Resolution Reconstruction.

Retinal Optical Coherence Tomography Angiography (OCTA) with high-resolution is important for the quantification and analysis of retinal vasculature. However, the resolution of OCTA images is inversely proportional to the field of view at the same sampling frequency, which is not conducive to clinicians for analyzing larger vascular areas. In this paper, we propose a novel Sparse-based domain Adaptation Super-Resolution network (SASR) for the reconstruction of realistic [Formula: see text]/low-resolution (LR) OCTA images to high-resolution (HR) representations. To be more specific, we first perform a simple degradation of the [Formula: see text]/high-resolution (HR) image to obtain the synthetic LR image. An efficient registration method is then employed to register the synthetic LR with its corresponding [Formula: see text] image region within the [Formula: see text] image to obtain the cropped realistic LR image. We then propose a multi-level super-resolution model for the fully-supervised reconstruction of the synthetic data, guiding the reconstruction of the realistic LR images through a generative-adversarial strategy that allows the synthetic and realistic LR images to be unified in the feature domain. Finally, a novel sparse edge-aware loss is designed to dynamically optimize the vessel edge structure. Extensive experiments on two OCTA sets have shown that our method performs better than state-of-the-art super-resolution reconstruction methods. In addition, we have investigated the performance of the reconstruction results on retina structure segmentations, which further validate the effectiveness of our approach.

Nonlinearity-aware PS-PAM-16 transmission for C-band net-300-Gbit/s/λ short-reach optical interconnects with a single DAC.

A nonlinearity-aware signal transmission scheme based on a low-complexity 3rd-order diagonally pruned absolute-term nonlinear equalizer (NLE) with weight sharing (DP-AT-NLE-WS) and rate-adaptable probabilistically shaped 16-level pulse amplitude modulation (PS-PAM-16) signal is proposed and experimentally demonstrated for C-band net-300-Gbit/s/λ short-reach optical interconnects. By replacing the multiplication operation with the absolute operation and applying weight sharing to reduce the kernel redundancy, the computational complexity of the proposed 3rd-order DP-AT-NLE-WS is reduced by >40% compared with the 3rd-order DP-Volterra NLE (DP-VNLE), DP-AT-NLE, and DP-VNLE-WS, with the achieved normalized general mutual information (NGMI) above a threshold of 0.857. Employing a commercial 32-GHz Mach-Zehnder modulator (MZM) and a single digital-to-analog converter (DAC), we demonstrate the single-lane transmission of 100-GBaud PS-PAM-16 signal using DP-AT-NLE-WS in the C band at record 370-Gbit/s line rate and 300.4-Gbit/s net rate over 1-km standard single-mode fiber (SSMF), achieving 21.2% (15.5%) capacity improvement over 100 (105)-GBaud PAM-8 transmission. To the best of our knowledge, this is the first net-300-Gbit/s intensity modulation and direct detection (IM/DD) short-reach transmission in the C band using commercially available components.

Attentional Mechanisms and Improved Residual Networks for Diabetic Retinopathy Severity Classification.

Diabetic retinopathy is a main cause of blindness in diabetic patients; therefore, detection and treatment of diabetic retinopathy at an early stage has an important effect on delaying and avoiding vision loss. In this paper, we propose a feasible solution for diabetic retinopathy classification using ResNet as the backbone network. By modifying the structure of the residual blocks and improving the downsampling level, we can increase the feature information of the hidden layer feature maps. In addition, attention mechanism is utilized to enhance the feature extraction effect. The experimental results show that the proposed model can effectively detect and classify diabetic retinopathy and achieve better results than the original model.

Automated Segmentation of Trigeminal Nerve and Cerebrovasculature in MR-Angiography Images by Deep Learning.

Trigeminal neuralgia caused by paroxysmal and severe pain in the distribution of the trigeminal nerve is a rare chronic pain disorder. It is generally accepted that compression of the trigeminal root entry zone by vascular structures is the major cause of primary trigeminal neuralgia, and vascular decompression is the prior choice in neurosurgical treatment. Therefore, accurate preoperative modeling/segmentation/visualization of trigeminal nerve and its surrounding cerebrovascular is important to surgical planning. In this paper, we propose an automated method to segment trigeminal nerve and its surrounding cerebrovascular in the root entry zone, and to further reconstruct and visual these anatomical structures in three-dimensional (3D) Magnetic Resonance Angiography (MRA). The proposed method contains a two-stage neural network. Firstly, a preliminary confidence map of different anatomical structures is produced by a coarse segmentation stage. Secondly, a refinement segmentation stage is proposed to refine and optimize the coarse segmentation map. To model the spatial and morphological relationship between trigeminal nerve and cerebrovascular structures, the proposed network detects the trigeminal nerve, cerebrovasculature, and brainstem simultaneously. The method has been evaluated on a dataset including 50 MRA volumes, and the experimental results show the state-of-the-art performance of the proposed method with an average Dice similarity coefficient, Hausdorff distance, and average surface distance error of 0.8645, 0.2414, and 0.4296 on multi-tissue segmentation, respectively.

Outer Retinal Layer Thickness Changes in White Matter Hyperintensity and Parkinson's Disease.

Purpose: To investigate the thickness changes of outer retinal layers in subjects with white matter hyperintensities (WMH) and Parkinson's Disease (PD). Methods: 56 eyes from 31 patients with WMH, 11 eyes from 6 PD patients, and 58 eyes from 32 healthy controls (HC) were enrolled in this study. A macular-centered scan was conducted on each participant using a spectral-domain optical coherence tomography (SD-OCT) device. After speckle noise reduction, a state-of-the-art deep learning method (i.e., a context encoder network) was employed to segment the outer retinal layers from OCT B-scans. Thickness quantification of the outer retinal layers was conducted on the basis of the segmentation results. Results: WMH patients had significantly thinner Henle fiber layers, outer nuclear layers (HFL+ONL) and photoreceptor outer segments (OS) than HC (p = 0.031, and p = 0.005), while PD patients showed a significant increase of mean thickness in the interdigitation zone and the retinal pigment epithelium/Bruch complex (IZ+RPE) (19.619 ± 4.626) compared to HC (17.434 ± 1.664). There were no significant differences in the thickness of the outer plexiform layer (OPL), the myoid and ellipsoid zone (MEZ), and the IZ+RPE layer between WMH and HC subjects. Similarly, there were also no obvious differences in the thickness of the OPL, HFL+ONL, MEZ and the OS layer between PD and HC subjects. Conclusion: Thickness changes in HFL+ONL, OS, and IZ+RPE layers may correlate with brain-related diseases such as WMH and PD. Further longitudinal study is needed to confirm HFL+ONL/OS/IZ+RPE layer thickness as potential biomarkers for detecting certain brain-related diseases.

Angle-closure assessment in anterior segment OCT images via deep learning.

Precise characterization and analysis of anterior chamber angle (ACA) are of great importance in facilitating clinical examination and diagnosis of angle-closure disease. Currently, the gold standard for diagnostic angle assessment is observation of ACA by gonioscopy. However, gonioscopy requires direct contact between the gonioscope and patients' eye, which is uncomfortable for patients and may deform the ACA, leading to false results. To this end, in this paper, we explore a potential way for grading ACAs into open-, appositional- and synechial angles by Anterior Segment Optical Coherence Tomography (AS-OCT), rather than the conventional gonioscopic examination. The proposed classification schema can be beneficial to clinicians who seek to better understand the progression of the spectrum of angle-closure disease types, so as to further assist the assessment and required treatment at different stages of angle-closure disease. To be more specific, we first use an image alignment method to generate sequences of AS-OCT images. The ACA region is then localized automatically by segmenting an important biomarker - the iris - as this is a primary structural cue in identifying angle-closure disease. Finally, the AS-OCT images acquired in both dark and bright illumination conditions are fed into our Multi-Sequence Deep Network (MSDN) architecture, in which a convolutional neural network (CNN) module is applied to extract feature representations, and a novel ConvLSTM-TC module is employed to study the spatial state of these representations. In addition, a novel time-weighted cross-entropy loss (TC) is proposed to optimize the output of the ConvLSTM, and the extracted features are further aggregated for the purposes of classification. The proposed method is evaluated across 66 eyes, which include 1584 AS-OCT sequences, and a total of 16,896 images. The experimental results show that the proposed method outperforms existing state-of-the-art methods in applicability, effectiveness, and accuracy.

Speckle reduction of OCT via super resolution reconstruction and its application on retinal layer segmentation.

Optical coherence tomography (OCT) is a rapidly developing non-invasive three dimensional imaging approach, and it has been widely used in examination and diagnosis of eye diseases. However, speckle noise are often inherited from image acquisition process, and may obscure the anatomical structure, such as the retinal layers. In this paper, we propose a novel method to reduce the speckle noise in 3D OCT scans, by introducing a new super-resolution approach. It uses a multi-frame fusion mechanism that merges multiple scans for the same scene, and utilizes the movements of sub-pixels to recover missing signals in one pixel, which significantly improves the image quality. To evaluate the effectiveness of the proposed speckle noise reduction method, we have applied it for the application of retinal layer segmentation. Results show that the proposed method has produced promising enhancement performance, and enable deep learning-based methods to obtain more accurate retinal layer segmentation results.

Automated retinal lesion detection via image saliency analysis.

BACKGROUND AND OBJECTIVE: The detection of abnormalities such as lesions or leakage from retinal images is an important health informatics task for automated early diagnosis of diabetic and malarial retinopathy or other eye diseases, in order to prevent blindness and common systematic conditions. In this work, we propose a novel retinal lesion detection method by adapting the concepts of saliency. METHODS: Retinal images are first segmented as superpixels, two new saliency feature representations: uniqueness and compactness, are then derived to represent the superpixels. The pixel level saliency is then estimated from these superpixel saliency values via a bilateral filter. These extracted saliency features form a matrix for low-rank analysis to achieve saliency detection. The precise contour of a lesion is finally extracted from the generated saliency map after removing confounding structures such as blood vessels, the optic disk, and the fovea. The main novelty of this method is that it is an effective tool for detecting different abnormalities at the pixel level from different modalities of retinal images, without the need to tune parameters. RESULTS: To evaluate its effectiveness, we have applied our method to seven public datasets of diabetic and malarial retinopathy with four different types of lesions: exudate, hemorrhage, microaneurysms, and leakage. The evaluation was undertaken at the pixel level, lesion level, or image level according to ground truth availability in these datasets. CONCLUSIONS: The experimental results show that the proposed method outperforms existing state-of-the-art ones in applicability, effectiveness, and accuracy.

Preparation of methacrylic acid-modified rice husk improved by an experimental design and application for paraquat adsorption.

Methacrylic acid (MAA) grafted rice husk was synthesized using graft copolymerization with Fenton's reagent as the redox initiator and applied to the adsorption of paraquat. The highest grafting percentage of 44.3% was obtained using the traditional kinetic method. However, a maximum grafting percentage of 65.3% was calculated using the central composite design. Experimental results based on the recipes predicted from the statistical analysis are consistent with theoretical calculations. A representative polymethacrylic acid-g-rice husk (PMAA-g-rice husk) copolymer was hydrolyzed to a salt type and applied to the adsorption of paraquat. The adsorption equilibrium data correlate more closely with the Langmuir isotherm than with the Freundlich equation. The maximum adsorption capacity of modified rice husk is 292.5mg/g-adsorbent. This value exceeds those for Fuller's earth and activated carbon, which are the most common binding agents used for paraquat. The samples at various stages were characterized by solid-state (13)C NMR spectroscopy.