Article
Computer Science, Interdisciplinary Applications
Carlos Hernandez-Matas, Xenophon Zabulis, Antonis A. Argyros
Summary: This study utilizes the REMPE framework for retinal image registration to achieve super resolution and eye shape estimation. Through quantitative assessment, the study demonstrates the applicability of the REMPE framework in these applications, as well as its effectiveness in longitudinal studies, image mosaicing, and multiple image registration.
COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE
(2021)
Article
Optics
Ming Liu, Xinjian Chen, Bo Wang
Summary: A method is proposed to suppress speckle noise in retinal optical coherence tomography by using image registration, which efficiently corrects motion-induced blurring in retinal images and improves image quality.
OPTICS COMMUNICATIONS
(2021)
Article
Computer Science, Artificial Intelligence
Cheolhong An, Yiqian Wang, Junkang Zhang, Truong Q. Nguyen
Summary: This paper proposes a self-supervised multimodal retina registration method to alleviate the burden of preparing training data, achieving comparable accuracy to the state-of-the-art supervised learning method in terms of registration accuracy and Dice coefficient.
IEEE TRANSACTIONS ON IMAGE PROCESSING
(2022)
Article
Biochemical Research Methods
David Rivas-Villar, Alice R. Motschi, Michael Pircher, Christoph K. Hitzenberger, Markus Schranz, Philipp K. Roberts, Ursula Schmidt-Erfurth, Hrvoje Bogunovic
Summary: In this study, a novel automated pipeline for registering OCT images from different devices is proposed. The pipeline utilizes deep learning for multi-modal 2D en-face registration and retinal layer segmentation for Z-axis registration. The experimental results show high-quality registrations, with mean errors of approximately 46 μm for 2D registration and 9.59 μm for Z-axis registration. This registration method can be valuable for various clinical applications such as layer segmentation validation.
BIOMEDICAL OPTICS EXPRESS
(2023)
Article
Engineering, Biomedical
Lingjiao Pan, Xinjian Chen
Summary: This paper presents retinal OCT image registration methods and their clinical applications. The paper systematically reviews registration methods based on volumetric transformation and image features. Furthermore, the applications of these methods in correcting scanning artifacts, reducing speckle noise, fusing and splicing images, and evaluating disease progression are studied. The paper also discusses the registration of retina with serious pathology and registration with deep learning technique.
IEEE REVIEWS IN BIOMEDICAL ENGINEERING
(2023)
Article
Multidisciplinary Sciences
Yan Hu, Jianfeng Ren, Jianlong Yang, Ruibing Bai, Jiang Liu
Summary: An adaptive denoising algorithm for OCT images is proposed in this paper, which has been proven effective through quantitative and subjective evaluation. The algorithm better removes noise and preserves image details. Furthermore, the proposed algorithm effectively transforms Poisson noise to Gaussian noise so that subsequent Shearlet transform can optimally remove noise.
SCIENTIFIC REPORTS
(2021)
Article
Mathematics, Applied
C. Cagini, D. Costarelli, R. Gujar, M. Lupidi, G. A. Lutty, M. Seracini, G. Vinti
Summary: This article focuses on providing an improved method for reconstructing and visualizing retinal superficial capillary plexus and choriocapillaris images from healthy subjects. The method uses multiple OCT scanned sequences, performs registration, averaging, and filtering, and evaluates the improvement achieved by the technique through quantitative analysis of the resulting images. Fluoroangiography and histological images are introduced as references to support the reliability and quality of the results.
APPLIED MATHEMATICS AND COMPUTATION
(2022)
Article
Biochemical Research Methods
Shulian Wu, Ryuhei Okada, Yi Liu, Yuhong Fang, Feng Yan, Chen Wang, Hui Li, Hisataka Kobayashi, Yu Chen, Qinggong Tang
Summary: NIR-PIT treatment can lead to a decrease in vascular density and lumen diameter inside blood vessels, as well as an increase in vascular permeability, resulting in an increase in blood pool volume and a decrease in free-moving red blood cells inside the blood vessels.
BIOMEDICAL OPTICS EXPRESS
(2021)
Article
Endocrinology & Metabolism
Kai Yang, Chunmei Li, Keai Shi, Xiaoxuan Zhu, Yunfan Xiao, Binbin Su, Ying Ju, Fan Lu, Jia Qu, Lele Cui, Ming Li
Summary: This study investigated the association between serum uric acid (SUA) levels and retinal capillary plexus (RCP) using optical coherence tomography angiography (OCTA). The results showed that higher SUA levels were significantly associated with lower RCP vessel density in men. These findings provide evidence for the importance of modulating SUA levels to prevent microvascular changes in the retina, especially in men.
FRONTIERS IN ENDOCRINOLOGY
(2022)
Article
Ophthalmology
Martin Hein, Andrew Mehnert, K. Bailey Freund, Dao-Yi Yu, Chandrakumar Balaratnasingam
Summary: This study investigates the variability of macular perfusion in patients with branch retinal vein occlusion (BRVO) using a novel approach based on optical coherence tomography angiography (OCTA) coefficient of variation (CoV) analysis. It was found that there is an increased variability in microvasculature perfusion in the ischemic regions of the macula affected by BRVO. This new technique has potential applications in studying the pathophysiology of other retinal vascular diseases.
INVESTIGATIVE OPHTHALMOLOGY & VISUAL SCIENCE
(2023)
Article
Biochemical Research Methods
Kazuhiro Kurokawa, James A. Crowell, Nhan Do, John J. Lee, Donald T. Miller
Summary: The study focuses on removing eye-movement artifacts from AO-OCT data efficiently, improving image quality, and enhancing visualization of retinal cellular features. The developed registration method allows for correcting eye motion at the level of individual A-lines, significantly improving the accuracy and robustness of image registration.
JOURNAL OF BIOMEDICAL OPTICS
(2021)
Article
Neurosciences
Ane Murueta-Goyena, Maitane Barrenechea, Asier Erramuzpe, Sara Teijeira-Portas, Marta Pengo, Unai Ayala, David Romero-Bascones, Marian Acera, Rocio Del Pino, Juan Carlos Gomez-Esteban, Inigo Gabilondo
Summary: Retinal microvascular alterations were observed in Parkinson's disease patients, affecting both the foveal and parafoveal regions. These alterations were associated with cognitive impairment and could potentially serve as diagnostic biomarkers for PD.
FRONTIERS IN NEUROSCIENCE
(2021)
Article
Multidisciplinary Sciences
Leo Puyo, Michel Paques, Michael Atlan
Summary: The study introduces a digital method based on Doppler spectrum asymmetry to reveal the local direction of blood flow in out-of-plane vessels, overlaying this directional information on standard blood flow images. By studying the strong contribution of backscattering to the Doppler spectrum in out-of-plane vessels, the local axial direction of blood flow can be revealed with high temporal resolution.
SCIENTIFIC REPORTS
(2021)
Article
Computer Science, Interdisciplinary Applications
Meng Wang, Weifang Zhu, Kai Yu, Zhongyue Chen, Fei Shi, Yi Zhou, Yuhui Ma, Yuanyuan Peng, Dengsen Bao, Shuanglang Feng, Lei Ye, Dehui Xiang, Xinjian Chen
Summary: A novel semi-supervised learning method for speckle noise denoising in retinal OCT images is proposed, utilizing Caps-cGAN network and a joint semi-supervised loss function to achieve better performance and parameter control.
IEEE TRANSACTIONS ON MEDICAL IMAGING
(2021)
Article
Engineering, Electrical & Electronic
Mahnoosh Tajmirriahi, Rahele Kafieh, Zahra Amini, Hossein Rabbani
Summary: The study implemented a lightweight convolutional AE network for mimicking the latest OCT image denoising method. The performance of the network was evaluated on various test data sets using visual inspection and quantitative metrics, confirming its good performance in removing speckle noise in OCT scans. The proposed network demonstrated generality, computational efficiency, and device independence, making it suitable for real-time, mobile applications.
IEEE TRANSACTIONS ON INSTRUMENTATION AND MEASUREMENT
(2021)
Article
Ophthalmology
Jessica Loo, Cindy X. Cai, John Choong, Emily Y. Chew, Martin Friedlander, Glenn J. Jaffe, Sina Farsiu
Summary: The aim of this study was to develop an automatic algorithm for segmenting retinal cavitations on OCT images of patients with MacTel2. The proposed method demonstrated high accuracy and efficiency, and could be a useful tool for clinicians to measure and assess changes in retinal cavitations over time.
BRITISH JOURNAL OF OPHTHALMOLOGY
(2022)
Article
Computer Science, Information Systems
Jessica Loo, Matthias F. Kriegel, Megan M. Tuohy, Kyeong Hwan Kim, Venkatesh Prajna, Maria A. Woodward, Sina Farsiu
Summary: The study presents a fully-automatic algorithm for segmenting ocular structures and MK biomarkers on SLP images. The algorithm performed well on all 133 eyes, showing good performance compared to manual annotations by a second physician on 75 eyes, especially in segmenting hypopyons, WBCs, and edema.
IEEE JOURNAL OF BIOMEDICAL AND HEALTH INFORMATICS
(2021)
Article
Biochemical Research Methods
Ziyun Yang, Somayyeh Soltanian-Zadeh, Kengyeh K. Chu, Haoran Zhang, Lama Moussa, Ariel E. Watts, Nicholas J. Shaheen, Adam Wax, Sina Farsiu
Summary: A novel neural network model, Bicon-CE, was proposed for in vivo human esophageal OCT layer segmentation, outperforming other neural networks by combining pixel connectivity modeling and pixel-wise tissue classification. The model can reduce common topological prediction issues in tissues from healthy patients and from patients with Barrett's esophagus.
BIOMEDICAL OPTICS EXPRESS
(2021)
Review
Optics
Kevin C. Zhou, Ruobing Qian, Al-Hafeez Dhalla, Sina Farsiu, Joseph A. Izatt
Summary: The paper presents a general theory of optical coherence tomography (OCT) that synthesizes the fundamental concepts and implementations of OCT under a common 3D k-space framework. By embracing a fully 3D k-space formalism, the theory explains nearly every fundamental physical phenomenon or property of OCT and unifies various related techniques.
ADVANCES IN OPTICS AND PHOTONICS
(2021)
Article
Engineering, Electrical & Electronic
Ali Hasan, Joao M. Pereira, Sina Farsiu, Vahid Tarokh
Summary: The method proposed in this study learns latent stochastic differential equations (SDEs) from high dimensional time series data using self-supervised learning, recovering both the underlying SDE coefficients and original latent variables. Validation was conducted through simulated video processing tasks and real world datasets.
IEEE TRANSACTIONS ON SIGNAL PROCESSING
(2022)
Article
Optics
Kevin C. Zhou, Al-Hafeez Dhalla, Ryan P. McNabb, Ruobing Qian, Sina Fars, Joseph A. Izatt
Summary: Researchers propose new strategies for multiangle imaging approaching 4pi steradians using concave parabolic or ellipsoidal mirrors and fast scanners. They demonstrate relationships between system parameters and achievable fields of view, showing that intrinsic tilt aberrations do not restrict field of view for many multiview imaging applications. Strategies are presented for avoiding spherical aberrations at obliquely illuminated flat boundaries.
JOURNAL OF THE OPTICAL SOCIETY OF AMERICA A-OPTICS IMAGE SCIENCE AND VISION
(2021)
Editorial Material
Biochemical Research Methods
Ruikang K. Wang, Sina Farsiu
Summary: The new Editor-in-Chief Ruikang (Ricky) Wang and Deputy Editor Sina Farsiu of Biomedical Optics Express share their introductory message as they start their editorial terms on 1 January 2022.
BIOMEDICAL OPTICS EXPRESS
(2022)
Article
Multidisciplinary Sciences
Ruobing Qian, Kevin C. Zhou, Jingkai Zhang, Christian Viehland, Al-Hafeez Dhalla, Joseph A. Izatt
Summary: This paper presents a high-speed FMCW-based 3D imaging system that combines grating beam steering with compressed time-frequency analysis for depth retrieval. The system achieves real-time densely sampled 3D imaging of moving objects with submillimeter localization accuracy.
NATURE COMMUNICATIONS
(2022)
Article
Optics
Kevin C. Zhou, Ryan P. McNabb, Ruobing Qian, Simone Degan, Al-Hafeez Dhalla, Sina Farsiu, Joseph A. Izatt
Summary: Optical coherence tomography (OCT) is a clinical diagnostic 3D imaging modality that has been successful in various fields. However, OCT has limitations that restrict its use as a 3D microscopy tool. In this paper, a computational extension of OCT called 3D optical coherence refraction tomography (OCRT) is introduced, which provides resolution-enhanced and noise-reduced 3D reconstructions.
Article
Robotics
William Edwards, Gao Tang, Yuan Tian, Mark Draelos, Joseph Izatt, Anthony Kuo, Kris Hauser
Summary: Deep anterior lamellar keratoplasty (DALK) is a technique for cornea transplantation that reduces patient morbidity. Robot microsurgery has been explored as a potential application for DALK due to its challenging nature for human surgeons. In this study, we have developed a data-driven autoregressive dynamic model and a model predictive controller to improve the accuracy of needle insertion during the surgery. Our experiments show that our controller significantly improves needle positioning accuracy compared to previous methods.
IEEE ROBOTICS AND AUTOMATION LETTERS
(2022)
Editorial Material
Biochemical Research Methods
Ruikang K. Wang, Sina Farsiu
Summary: The Editor-in-Chief and Deputy Editor of Biomedical Optics Express have introduced a new prize to honor the best paper published in the Journal between 2019 and 2021.
BIOMEDICAL OPTICS EXPRESS
(2023)
Article
Biochemical Research Methods
Somayyeh Soltanian-Zadeh, Zhuolin Liu, Yan Liu, Ayoub Lassoued, Catherine A. Cukras, Donald T. Miller, Daniel X. Hammer, Sina Farsiu
Summary: Objective quantification of photoreceptor cell morphology using AO-OCT is crucial for early and accurate diagnosis of retinal neurodegenerative diseases. We propose a comprehensive deep learning framework to automate the process of segmenting individual cone cells in AO-OCT scans, achieving human-level performance in assessing cone photoreceptors.
BIOMEDICAL OPTICS EXPRESS
(2023)
Article
Computer Science, Interdisciplinary Applications
Reza Rasti, Armin Biglari, Mohammad Rezapourian, Ziyun Yang, Sina Farsiu
Summary: In this study, a new convolutional neural network architecture called RetiFluidNet is proposed for multi-class retinal fluid segmentation. The model incorporates a self-adaptive dual-attention module, multiple self-adaptive attention-based skip connections, and a novel multi-scale deep self-supervision learning scheme for hierarchical representation learning. The model is optimized using a joint loss function comprising a weighted version of dice overlap and edge-preserved connectivity-based losses. Experimental results on three publicly available datasets demonstrate the effectiveness of the proposed model in retinal OCT fluid segmentation, outperforming existing state-of-the-art algorithms.
IEEE TRANSACTIONS ON MEDICAL IMAGING
(2023)
Article
Ophthalmology
Shwetha Mangalesh, Brendan McGeehan, Vincent Tai, Xi Chen, Du Tran-Viet, Lejla Vajzovic, Christian Viehland, Joseph A. Izatt, C. Michael Cotten, Sharon F. Freedman, Maureen G. Maguire, Cynthia A. Toth
Summary: The study reported the reliability of capturing, grading, and analyzing bedside macular OCT images from preterm infants at 36 +/- 1 weeks' postmenstrual age, and the OCT findings were related to biological factors and retinopathy of prematurity status. Macular edema was present in 60% of eyes, and thicker inner nuclear layer was associated with more severe edema. Variations in layer thicknesses at 36 +/- 1 weeks' PMA in preterm infants may reflect abnormalities resulting from delay in foveal development impacted by macular edema, ROP, or both.
OPHTHALMOLOGY RETINA
(2021)
Article
Computer Science, Artificial Intelligence
Yijun Bao, Somayyeh Soltanian-Zadeh, Sina Farsiu, Yiyang Gong
Summary: The Shallow U-Net Neuron Segmentation (SUNS) method can accurately and quickly segment active neurons from two-photon fluorescence imaging videos. This method is faster and more accurate than existing techniques, and can be used online for real-time neuroscience experiments.
NATURE MACHINE INTELLIGENCE
(2021)