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Register a new userLIFE: A Generalizable Autodidactic Pipeline for 3D OCT-A Vessel Segmentation
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Optical coherence tomography (OCT) is a non-invasive imaging technique widely used for ophthalmology. It can be extended to OCT angiography (OCT-A), which reveals the retinal vasculature with improved contrast. Recent deep learning algorithms produced promising vascular segmentation results; however, 3D retinal vessel segmentation remains difficult due to the lack of manually annotated training data. We propose a learning-based method that is only supervised by a self-synthesized modality named local intensity fusion (LIF). LIF is a capillary-enhanced volume computed directly from the input OCT-A. We then construct the local intensity fusion encoder (LIFE) to map a given OCT-A volume and its LIF counterpart to a shared latent space. The latent space of LIFE has the same dimensions as the input data and it contains features common to both modalities. By binarizing this latent space, we obtain a volumetric vessel segmentation. Our method is evaluated in a human fovea OCT-A and three zebrafish OCT-A volumes with manual labels. It yields a Dice score of 0.7736 on human data and 0.8594 +/- 0.0275 on zebrafish data, a dramatic improvement over existing unsupervised algorithms.
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Optical Coherence Tomography Angiography (OCT-A) is a non-invasive imaging technique, and has been increasingly used to image the retinal vasculature at capillary level resolution. However, automated segmentation of retinal vessels in OCT-A has been under-studied due to various challenges such as low capillary visibility and high vessel complexity, despite its significance in understanding many eye-related diseases. In addition, there is no publicly available OCT-A dataset with manually graded vessels for training and validation. To address these issues, for the first time in the field of retinal image analysis we construct a dedicated Retinal OCT-A SEgmentation dataset (ROSE), which consists of 229 OCT-A images with vessel annotations at either centerline-level or pixel level. This dataset has been released for public access to assist researchers in the community in undertaking research in related topics. Secondly, we propose a novel Split-based Coarse-to-Fine vessel segmentation network (SCF-Net), with the ability to detect thick and thin vessels separately. In the SCF-Net, a split-based coarse segmentation (SCS) module is first introduced to produce a preliminary confidence map of vessels, and a split-based refinement (SRN) module is then used to optimize the shape/contour of the retinal microvasculature. Thirdly, we perform a thorough evaluation of the state-of-the-art vessel segmentation models and our SCF-Net on the proposed ROSE dataset. The experimental results demonstrate that our SCF-Net yields better vessel segmentation performance in OCT-A than both traditional methods and other deep learning methods.
Optical Coherence Tomography Angiography (OCTA) has been increasingly used in the management of eye and systemic diseases in recent years. Manual or automatic analysis of blood vessel in 2D OCTA images (en face angiograms) is commonly used in clinical practice, however it may lose rich 3D spatial distribution information of blood vessels or capillaries that are useful for clinical decision-making. In this paper, we introduce a novel 3D vessel reconstruction framework based on the estimation of vessel depth maps from OCTA images. First, we design a network with structural constraints to predict the depth of blood vessels in OCTA images. In order to promote the accuracy of the predicted depth map at both the overall structure- and pixel- level, we combine MSE and SSIM loss as the training loss function. Finally, the 3D vessel reconstruction is achieved by utilizing the estimated depth map and 2D vessel segmentation results. Experimental results demonstrate that our method is effective in the depth prediction and 3D vessel reconstruction for OCTA images.% results may be used to guide subsequent vascular analysis
3D to 2D retinal vessel segmentation is a challenging problem in Optical Coherence Tomography Angiography (OCTA) images. Accurate retinal vessel segmentation is important for the diagnosis and prevention of ophthalmic diseases. However, making full use of the 3D data of OCTA volumes is a vital factor for obtaining satisfactory segmentation results. In this paper, we propose a Progressive Attention-Enhanced Network (PAENet) based on attention mechanisms to extract rich feature representation. Specifically, the framework consists of two main parts, the three-dimensional feature learning path and the two-dimensional segmentation path. In the three-dimensional feature learning path, we design a novel Adaptive Pooling Module (APM) and propose a new Quadruple Attention Module (QAM). The APM captures dependencies along the projection direction of volumes and learns a series of pooling coefficients for feature fusion, which efficiently reduces feature dimension. In addition, the QAM reweights the features by capturing four-group cross-dimension dependencies, which makes maximum use of 4D feature tensors. In the two-dimensional segmentation path, to acquire more detailed information, we propose a Feature Fusion Module (FFM) to inject 3D information into the 2D path. Meanwhile, we adopt the Polarized Self-Attention (PSA) block to model the semantic interdependencies in spatial and channel dimensions respectively. Experimentally, our extensive experiments on the OCTA-500 dataset show that our proposed algorithm achieves state-of-the-art performance compared with previous methods.
Automatic quantification of perifoveal vessel densities in optical coherence tomography angiography (OCT-A) images face challenges such as variable intra- and inter-image signal to noise ratios, projection artefacts from outer vasculature layers, and motion artefacts. This study demonstrates the utility of deep neural networks for automatic quantification of foveal avascular zone (FAZ) parameters and perifoveal vessel density of OCT-A images in healthy and diabetic eyes. OCT-A images of the foveal region were acquired using three OCT-A systems: a 1060nm Swept Source (SS)-OCT prototype, RTVue XR Avanti (Optovue Inc., Fremont, CA), and the ZEISS Angioplex (Carl Zeiss Meditec, Dublin, CA). Automated segmentation was then performed using a deep neural network. Four FAZ morphometric parameters (area, min/max diameter, and eccentricity) and perifoveal vessel density were used as outcome measures. The accuracy, sensitivity and specificity of the DNN vessel segmentations were comparable across all three device platforms. No significant difference between the means of the measurements from automated and manual segmentations were found for any of the outcome measures on any system. The intraclass correlation coefficient (ICC) was also good (> 0.51) for all measurements. Automated deep learning vessel segmentation of OCT-A may be suitable for both commercial and research purposes for better quantification of the retinal circulation.
Retinal vessel segmentation is a fundamental step in screening, diagnosis, and treatment of various cardiovascular and ophthalmic diseases. Robustness is one of the most critical requirements for practical utilization, since the test images may be captured using different fundus cameras, or be affected by various pathological changes. We investigate this problem from a data augmentation perspective, with the merits of no additional training data or inference time. In this paper, we propose two new data augmentation modules, namely, channel-wise random Gamma correction and channel-wise random vessel augmentation. Given a training color fundus image, the former applies random gamma correction on each color channel of the entire image, while the latter intentionally enhances or decreases only the fine-grained blood vessel regions using morphological transformations. With the additional training samples generated by applying these two modules sequentially, a model could learn more invariant and discriminating features against both global and local disturbances. Experimental results on both real-world and synthetic datasets demonstrate that our method can improve the performance and robustness of a classic convolutional neural network architecture. Source codes are available https://github.com/PaddlePaddle/Research/tree/master/CV/robust_vessel_segmentation
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