Association between Optical Coherence Tomography and Fluorescein Angiography based retinal features in the diagnosis of Macular Edema

iSnoDi-MDRF: Identifying snoRNA-Disease Associations Based on Multiple Biological Data by Ranking Framework

Accumulating evidence indicates that the dysregulation of small nucleolar RNAs (snoRNAs) is relevant with diseases. Identifying snoRNA-disease associations by computational methods is desired for biologists, which can save considerable costs and time compared biological experiments. However, it still faces some challenges as followings: (i) Many snoRNAs are detected in recent years, but only a few snoRNAs have been proved to be associated with diseases; (ii) Computational predictors trained with only a few known snoRNA-disease associations fail to accurately identify the snoRNA-disease associations. In this study, we propose a ranking framework, called iSnoDi-MDRF, to identify potential snoRNA-disease associations based on multiple biological data, which has the following highlights: (i) iSnoDi-MDRF integrates ranking framework, which is not only able to identify potential associations between known snoRNAs and diseases, but also can identify diseases associated with new snoRNAs. (ii) Known gene-disease associations are employed to help train a mature model for predicting snoRNA-disease association. Experimental results illustrate that iSnoDi-MDRF is very suitable for identifying potential snoRNA-disease associations. The web server of iSnoDi-MDRF predictor is freely available at http://bliulab.net/iSnoDi-MDRF/.

Spatially adaptive blind deconvolution methods for optical coherence tomography

Optical coherence tomography (OCT) is a powerful noninvasive imaging technique for detecting microvascular abnormalities. Following optical imaging principles, an OCT image will be blurred in the out-of-focus domain. Digital deconvolution is a commonly used method for image deblurring. However, the accuracy of traditional digital deconvolution methods, e.g., the Richardson-Lucy method, depends on the prior knowledge of the point spread function (PSF), which varies with the imaging depth and is difficult to determine. In this paper, a spatially adaptive blind deconvolution framework is proposed for recovering clear OCT images from blurred images without a known PSF. First, a depth-dependent PSF is derived from the Gaussian beam model. Second, the blind deconvolution problem is formalized as a regularized energy minimization problem using the least squares method. Third, the clear image and imaging depth are simultaneously recovered from blurry images using an alternating optimization method. To improve the computational efficiency of the proposed method, an accelerated alternating optimization method is proposed based on the convolution theorem and Fourier transform. The proposed method is numerically implemented with various regularization terms, including total variation, Tikhonov, and l₁ norm terms. The proposed method is used to deblur synthetic and experimental OCT images. The influence of the regularization term on the deblurring performance is discussed. The results show that the proposed method can accurately deblur OCT images. The proposed acceleration method can significantly improve the computational efficiency of blind demodulation methods.

Region of interest-based predictive algorithm for subretinal hemorrhage detection using faster R-CNN

Macular edema (ME) is an essential sort of macular issue caused due to the storing of fluid underneath the macula. Age-related Macular Degeneration (AMD) and diabetic macular edema (DME) are the two customary visual contaminations that can lead to fragmentary or complete vision loss. This paper proposes a deep learning-based predictive algorithm that can be used to detect the presence of a Subretinal hemorrhage. Region Convolutional Neural Network (R-CNN) and faster R-CNN are used to develop the predictive algorithm that can improve the classification accuracy. This method initially detects the presence of Subretinal hemorrhage, and it then segments the Region of Interest (ROI) by a semantic segmentation process. The segmented ROI is applied to a predictive algorithm which is derived from the Fast Region Convolutional Neural Network algorithm, that can categorize the Subretinal hemorrhage as responsive or non-responsive. The dataset, provided by a medical institution, comprised of optical coherence tomography (OCT) images of both pre- and post-treatment images, was used for training the proposed Faster Region Convolutional Neural Network (Faster R-CNN). We also used the Kaggle dataset for performance comparison with the traditional methods that are derived from the convolutional neural network (CNN) algorithm. The evaluation results using the Kaggle dataset and the hospital images provide an average sensitivity, selectivity, and accuracy of 85.3%, 89.64%, and 93.48% respectively. Further, the proposed method provides a time complexity in testing as 2.64s, which is less than the traditional schemes like CNN, R-CNN, and Fast R-CNN.

Deep learning based joint segmentation and characterization of multi-class retinal fluid lesions on OCT scans for clinical use in anti-VEGF therapy

BACKGROUND

In anti-vascular endothelial growth factor (anti-VEGF) therapy, an accurate estimation of multi-class retinal fluid (MRF) is required for the activity prescription and intravitreal dose. This study proposes an end-to-end deep learning-based retinal fluids segmentation network (RFS-Net) to segment and recognize three MRF lesion manifestations, namely, intraretinal fluid (IRF), subretinal fluid (SRF), and pigment epithelial detachment (PED), from multi-vendor optical coherence tomography (OCT) imagery. The proposed image analysis tool will optimize anti-VEGF therapy and contribute to reducing the inter- and intra-observer variability.

METHOD

The proposed RFS-Net architecture integrates the atrous spatial pyramid pooling (ASPP), residual, and inception modules in the encoder path to learn better features and conserve more global information for precise segmentation and characterization of MRF lesions. The RFS-Net model is trained and validated using OCT scans from multiple vendors (Topcon, Cirrus, Spectralis), collected from three publicly available datasets. The first dataset consisted of OCT volumes obtained from 112 subjects (a total of 11,334 B-scans) is used for both training and evaluation purposes. Moreover, the remaining two datasets are only used for evaluation purposes to check the trained RFS-Net's generalizability on unseen OCT scans. The two evaluation datasets contain a total of 1572 OCT B-scans from 1255 subjects. The performance of the proposed RFS-Net model is assessed through various evaluation metrics.

RESULTS

The proposed RFS-Net model achieved the mean F₁ scores of 0.762, 0.796, and 0.805 for segmenting IRF, SRF, and PED. Moreover, with the automated segmentation of the three retinal manifestations, the RFS-Net brings a considerable gain in efficiency compared to the tedious and demanding manual segmentation procedure of the MRF.

CONCLUSIONS

Our proposed RFS-Net is a potential diagnostic tool for the automatic segmentation of MRF (IRF, SRF, and PED) lesions. It is expected to strengthen the inter-observer agreement, and standardization of dosimetry is envisaged as a result.

Weakly supervised detection of central serous chorioretinopathy based on local binary patterns and discrete wavelet transform

Central serous chorioretinopathy (CSCR) is a common fundus disease. Early detection of CSCR is of great importance to prevent visual loss. Therefore, a novel automatic detection method is presented in this paper which integrates technologies including discrete wavelet transform (DWT) image decomposition, local binary patterns (LBP) based texture feature extraction, and multi-instance learning (MIL). LBP is selected due to its robustness to low contrast and low quality images, which can reduce the interference of image itself on the detection method. DWT image decomposition provides high-frequency components with rich details for extracting LBP texture features, which can remove redundant information that is not necessary for diagnosis of CSCR in the raw image. The tedious task of accurately locating and segmenting CSCR lesions is avoided by using MIL. Experiments on 358 optical coherence tomography (OCT) B-scan images demonstrate the effectiveness of our method. Even under the condition of single threshold, the accuracy of 99.58% is obtained at K = 35 by only using a high-frequency feature fusion scheme, which is competitive with the existing methods. Additionally, through further detail innovation, such as multi-threshold optimization (MTO) and integrated decision-making (IDM), the performance of our method is further improved and the detection accuracy is 100% at K = 40.