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Ni G, Wu R, Zheng F, Li M, Huang S, Ge X, Liu L, Liu Y. Toward Ground-Truth Optical Coherence Tomography via Three-Dimensional Unsupervised Deep Learning Processing and Data. IEEE TRANSACTIONS ON MEDICAL IMAGING 2024; 43:2395-2407. [PMID: 38324426 DOI: 10.1109/tmi.2024.3363416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Optical coherence tomography (OCT) can perform non-invasive high-resolution three-dimensional (3D) imaging and has been widely used in biomedical fields, while it is inevitably affected by coherence speckle noise which degrades OCT imaging performance and restricts its applications. Here we present a novel speckle-free OCT imaging strategy, named toward-ground-truth OCT ( t GT-OCT), that utilizes unsupervised 3D deep-learning processing and leverages OCT 3D imaging features to achieve speckle-free OCT imaging. Specifically, our proposed t GT-OCT utilizes an unsupervised 3D-convolution deep-learning network trained using random 3D volumetric data to distinguish and separate speckle from real structures in 3D imaging volumetric space; moreover, t GT-OCT effectively further reduces speckle noise and reveals structures that would otherwise be obscured by speckle noise while preserving spatial resolution. Results derived from different samples demonstrated the high-quality speckle-free 3D imaging performance of t GT-OCT and its advancement beyond the previous state-of-the-art. The code is available online: https://github.com/Voluntino/tGT-OCT.
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Yuan Z, Yang D, Zhao J, Liang Y. Enhancement of OCT en faceimages by unsupervised deep learning. Phys Med Biol 2024; 69:115042. [PMID: 38749469 DOI: 10.1088/1361-6560/ad4c52] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 05/15/2024] [Indexed: 05/31/2024]
Abstract
Objective. The quality of optical coherence tomography (OCT)en faceimages is crucial for clinical visualization of early disease. As a three dimensional and coherent imaging, defocus and speckle noise are inevitable, which seriously affect evaluation of microstructure of bio-samples in OCT images. The deep learning has demonstrated great potential in OCT refocusing and denoising, but it is limited by the difficulty of sufficient paired training data. This work aims to develop an unsupervised method to enhance the quality of OCTen faceimages.Approach. We proposed an unsupervised deep learning-based pipeline. The unregistered defocused conventional OCT images and focused speckle-free OCT images were collected by a home-made speckle modulating OCT system to construct the dataset. The image enhancement model was trained with the cycle training strategy. Finally, the speckle noise and defocus were both effectively improved.Main results. The experimental results on complex bio-samples indicated that the proposed method is effective and generalized in enhancing the quality of OCTen faceimages.Significance. The proposed unsupervised deep learning method helps to reduce the complexity of data construction, which is conducive to practical applications in OCT bio-sample imaging.
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Affiliation(s)
- Zhuoqun Yuan
- Institute of Modern Optics, Nankai University, Tianjin Key Laboratory of Micro-scale Optical Information Science and Technology, Tianjin 300350, People's Republic of China
| | - Di Yang
- Institute of Modern Optics, Nankai University, Tianjin Key Laboratory of Micro-scale Optical Information Science and Technology, Tianjin 300350, People's Republic of China
| | - Jingzhu Zhao
- Department of Thyroid and Neck Tumor, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin 300060, People's Republic of China
| | - Yanmei Liang
- Institute of Modern Optics, Nankai University, Tianjin Key Laboratory of Micro-scale Optical Information Science and Technology, Tianjin 300350, People's Republic of China
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3
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Zhou Y, Zhou L, Yan J, Yan X, Chen Z. Using optical coherence tomography to assess luster of pearls: technique suitability and insights. Sci Rep 2024; 14:11126. [PMID: 38750292 PMCID: PMC11096156 DOI: 10.1038/s41598-024-62125-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 05/14/2024] [Indexed: 05/18/2024] Open
Abstract
Luster is one of the vital indexes in pearl grading. To find a fast, nondestructive, and low-cost grading method, optical coherence tomography (OCT) is introduced to predict the luster grade through the texture features. After background removal, flattening, and segmentation, the speckle pattern of the region of interest is described by seven kinds of feature textures, including center-symmetric auto-correlation (CSAC), fractal dimension (FD), Gabor, gray level co-occurrence matrix (GLCM), histogram of oriented gradients (HOG), laws texture energy (LAWS), and local binary patterns (LBP). To find the relations between speckle-derived texture features and luster grades, four Four groups of pearl samples were used in the experiment to detect texture differences based on support vector machines (SVMs) and random forest classifier (RFC)) for investigating the relations between speckle-derived texture features and luster grades. The precision, recall, F1-score, and accuracy are more significant than 0.9 in several simulations, even after dimension reduction. This demonstrates that the texture feature from OCT images can be applied to class the pearl luster based on speckle changes.
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Affiliation(s)
- Yang Zhou
- School of Information and Electronic Engineering, Zhejiang University of Science and Technology, Hangzhou, 310023, Zhejiang, China.
- School of Innovation and Entrepreneurship, Zhejiang University of Science and Technology, Hangzhou, 310023, Zhejiang, China.
| | - Lifeng Zhou
- School of Information and Electronic Engineering, Zhejiang University of Science and Technology, Hangzhou, 310023, Zhejiang, China
| | - Jun Yan
- Zhejiang Fangyuan Test Group Co., Ltd, Hangzhou, 310013, Zhejiang, China
| | - Xuejun Yan
- Zhejiang Fangyuan Test Group Co., Ltd, Hangzhou, 310013, Zhejiang, China
| | - Zhengwei Chen
- School of Innovation and Entrepreneurship, Zhejiang University of Science and Technology, Hangzhou, 310023, Zhejiang, China
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4
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Ghaderi Daneshmand P, Rabbani H. Total variation regularized tensor ring decomposition for OCT image denoising and super-resolution. Comput Biol Med 2024; 177:108591. [PMID: 38788372 DOI: 10.1016/j.compbiomed.2024.108591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Revised: 04/15/2024] [Accepted: 05/09/2024] [Indexed: 05/26/2024]
Abstract
This paper suggests a novel hybrid tensor-ring (TR) decomposition and first-order tensor-based total variation (FOTTV) model, known as the TRFOTTV model, for super-resolution and noise suppression of optical coherence tomography (OCT) images. OCT imaging faces two fundamental problems undermining correct OCT-based diagnosis: significant noise levels and low sampling rates to speed up the capturing process. Inspired by the effectiveness of TR decomposition in analyzing complicated data structures, we suggest the TRFOTTV model for noise suppression and super-resolution of OCT images. Initially, we extract the nonlocal 3D patches from OCT data and group them to create a third-order low-rank tensor. Subsequently, using TR decomposition, we extract the correlations among all modes of the grouped OCT tensor. Finally, FOTTV is integrated into the TR model to enhance spatial smoothness in OCT images and conserve layer structures more effectively. The proximal alternating minimization and alternative direction method of multipliers are applied to solve the obtained optimization problem. The effectiveness of the suggested method is verified by four OCT datasets, demonstrating superior visual and numerical outcomes compared to state-of-the-art procedures.
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Affiliation(s)
- Parisa Ghaderi Daneshmand
- Medical Image & Signal Processing Research Center, School of Advanced Technologies in Medicine, Isfahan University of Medical Sciences, Isfahan, 8174673461, Iran
| | - Hossein Rabbani
- Medical Image & Signal Processing Research Center, School of Advanced Technologies in Medicine, Isfahan University of Medical Sciences, Isfahan, 8174673461, Iran.
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Aleksandrova PV, Zaytsev KI, Nikitin PV, Alekseeva AI, Zaitsev VY, Dolganov KB, Reshetov IV, Karalkin PA, Kurlov VN, Tuchin VV, Dolganova IN. Quantification of attenuation and speckle features from endoscopic OCT images for the diagnosis of human brain glioma. Sci Rep 2024; 14:10722. [PMID: 38729956 PMCID: PMC11087587 DOI: 10.1038/s41598-024-61292-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 05/03/2024] [Indexed: 05/12/2024] Open
Abstract
Application of optical coherence tomography (OCT) in neurosurgery mostly includes the discrimination between intact and malignant tissues aimed at the detection of brain tumor margins. For particular tissue types, the existing approaches demonstrate low performance, which stimulates the further research for their improvement. The analysis of speckle patterns of brain OCT images is proposed to be taken into account for the discrimination between human brain glioma tissue and intact cortex and white matter. The speckle properties provide additional information of tissue structure, which could help to increase the efficiency of tissue differentiation. The wavelet analysis of OCT speckle patterns was applied to extract the power of local brightness fluctuations in speckle and its standard deviation. The speckle properties are analysed together with attenuation ones using a set of ex vivo brain tissue samples, including glioma of different grades. Various combinations of these features are considered to perform linear discriminant analysis for tissue differentiation. The results reveal that it is reasonable to include the local brightness fluctuations at first two wavelet decomposition levels in the analysis of OCT brain images aimed at neurosurgical diagnosis.
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Affiliation(s)
- P V Aleksandrova
- Prokhorov General Physics Institute of the Russian Academy of Sciences, Moscow, Russia, 119991.
| | - K I Zaytsev
- Prokhorov General Physics Institute of the Russian Academy of Sciences, Moscow, Russia, 119991
| | - P V Nikitin
- Department of Biomedical Engineering, University of Houston, Houston, TX, USA
- N.N. Burdenko National Medical Research Center for Neurosurgery, Moscow, Russia, 125047
| | - A I Alekseeva
- Avtsyn Research Institute of Human Morphology, FSBSI "Petrovsky National Research Centre of Surgery", Moscow, Russia, 117418
| | - V Y Zaitsev
- A.V. Gaponov-Grekhov Institute of Applied Physics of the Russian Academy of Sciences, Nizhny Novgorod, Russia, 603950
| | - K B Dolganov
- Prokhorov General Physics Institute of the Russian Academy of Sciences, Moscow, Russia, 119991
| | - I V Reshetov
- Institute for Cluster Oncology, Sechenov First Moscow State Medical University, Moscow, Russia, 119991
| | - P A Karalkin
- Institute for Cluster Oncology, Sechenov First Moscow State Medical University, Moscow, Russia, 119991
| | - V N Kurlov
- Osipyan Institute of Solid State Physics of the Russian Academy of Sciences, Chernogolovka, Russia, 142432
| | - V V Tuchin
- Science Medical Center, Saratov State University, Saratov, Russia, 410000
- Institute of Precision Mechanics and Control, FRC "Saratov Scientific Centre of the Russian Academy of Sciences", Saratov, Russia, 410028
- Tomsk State University, Tomsk, Russia, 634050
| | - I N Dolganova
- Osipyan Institute of Solid State Physics of the Russian Academy of Sciences, Chernogolovka, Russia, 142432.
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Wijesinghe RE, Kahatapitiya NS, Lee C, Han S, Kim S, Saleah SA, Seong D, Silva BN, Wijenayake U, Ravichandran NK, Jeon M, Kim J. Growing Trend to Adopt Speckle Variance Optical Coherence Tomography for Biological Tissue Assessments in Pre-Clinical Applications. MICROMACHINES 2024; 15:564. [PMID: 38793137 PMCID: PMC11122893 DOI: 10.3390/mi15050564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 04/19/2024] [Accepted: 04/22/2024] [Indexed: 05/26/2024]
Abstract
Speckle patterns are a generic feature in coherent imaging techniques like optical coherence tomography (OCT). Although speckles are granular like noise texture, which degrades the image, they carry information that can be benefited by processing and thereby furnishing crucial information of sample structures, which can serve to provide significant important structural details of samples in in vivo longitudinal pre-clinical monitoring and assessments. Since the motions of tissue molecules are indicated through speckle patterns, speckle variance OCT (SV-OCT) can be well-utilized for quantitative assessments of speckle variance (SV) in biological tissues. SV-OCT has been acknowledged as a promising method for mapping microvasculature in transverse-directional blood vessels with high resolution in micrometers in both the transverse and depth directions. The fundamental scope of this article reviews the state-of-the-art and clinical benefits of SV-OCT to assess biological tissues for pre-clinical applications. In particular, focus on precise quantifications of in vivo vascular response, therapy assessments, and real-time temporal vascular effects of SV-OCT are primarily emphasized. Finally, SV-OCT-incorporating pre-clinical techniques with high potential are presented for future biomedical applications.
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Affiliation(s)
- Ruchire Eranga Wijesinghe
- Department of Electrical and Electronic Engineering, Faculty of Engineering, Sri Lanka Institute of Information Technology, Malabe 10115, Sri Lanka;
- Center for Excellence in Intelligent Informatics, Electronics & Transmission (CIET), Sri Lanka Institute of Information Technology, Malabe 10115, Sri Lanka
| | - Nipun Shantha Kahatapitiya
- Department of Computer Engineering, Faculty of Engineering, University of Sri Jayewardenepura, Nugegoda 10250, Sri Lanka; (N.S.K.); (U.W.)
| | - Changho Lee
- Department of Artificial Intelligence Convergence, Chonnam National University, Gwangju 61186, Republic of Korea
- Department of Nuclear Medicine, Chonnam National University Medical School & Hwasun Hospital, 264, Seoyang-ro, Hwasun 58128, Republic of Korea
| | - Sangyeob Han
- ICT Convergence Research Center, Kyungpook National University, 80, Daehak-ro, Buk-gu, Daegu 41566, Republic of Korea
| | - Shinheon Kim
- ICT Convergence Research Center, Kyungpook National University, 80, Daehak-ro, Buk-gu, Daegu 41566, Republic of Korea
| | - Sm Abu Saleah
- ICT Convergence Research Center, Kyungpook National University, 80, Daehak-ro, Buk-gu, Daegu 41566, Republic of Korea
| | - Daewoon Seong
- School of Electronic and Electrical Engineering, College of IT Engineering, Kyungpook National University, 80, Daehak-ro, Buk-gu, Daegu 41566, Republic of Korea
| | - Bhagya Nathali Silva
- Center for Excellence in Intelligent Informatics, Electronics & Transmission (CIET), Sri Lanka Institute of Information Technology, Malabe 10115, Sri Lanka
- Faculty of Computing, Sri Lanka Institute of Information Technology, Malabe 10115, Sri Lanka
| | - Udaya Wijenayake
- Department of Computer Engineering, Faculty of Engineering, University of Sri Jayewardenepura, Nugegoda 10250, Sri Lanka; (N.S.K.); (U.W.)
| | - Naresh Kumar Ravichandran
- Center for Scientific Instrumentation, Korea Basic Science Institute, 169-148, Gwahak-ro, Yuseong-gu, Daejeon 34133, Republic of Korea
| | - Mansik Jeon
- School of Electronic and Electrical Engineering, College of IT Engineering, Kyungpook National University, 80, Daehak-ro, Buk-gu, Daegu 41566, Republic of Korea
| | - Jeehyun Kim
- School of Electronic and Electrical Engineering, College of IT Engineering, Kyungpook National University, 80, Daehak-ro, Buk-gu, Daegu 41566, Republic of Korea
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Winetraub Y, Van Vleck A, Yuan E, Terem I, Zhao J, Yu C, Chan W, Do H, Shevidi S, Mao M, Yu J, Hong M, Blankenberg E, Rieger KE, Chu S, Aasi S, Sarin KY, de la Zerda A. Noninvasive virtual biopsy using micro-registered optical coherence tomography (OCT) in human subjects. SCIENCE ADVANCES 2024; 10:eadi5794. [PMID: 38598626 PMCID: PMC11006228 DOI: 10.1126/sciadv.adi5794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 03/07/2024] [Indexed: 04/12/2024]
Abstract
Histological hematoxylin and eosin-stained (H&E) tissue sections are used as the gold standard for pathologic detection of cancer, tumor margin detection, and disease diagnosis. Producing H&E sections, however, is invasive and time-consuming. While deep learning has shown promise in virtual staining of unstained tissue slides, true virtual biopsy requires staining of images taken from intact tissue. In this work, we developed a micron-accuracy coregistration method [micro-registered optical coherence tomography (OCT)] that can take a two-dimensional (2D) H&E slide and find the exact corresponding section in a 3D OCT image taken from the original fresh tissue. We trained a conditional generative adversarial network using the paired dataset and showed high-fidelity conversion of noninvasive OCT images to virtually stained H&E slices in both 2D and 3D. Applying these trained neural networks to in vivo OCT images should enable physicians to readily incorporate OCT imaging into their clinical practice, reducing the number of unnecessary biopsy procedures.
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Affiliation(s)
- Yonatan Winetraub
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA
- Molecular Imaging Program at Stanford, Stanford, CA 94305, USA
- The Bio-X Program, Stanford, CA 94305, USA
- Biophysics Program at Stanford, Stanford, CA 94305, USA
| | - Aidan Van Vleck
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA
| | - Edwin Yuan
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA
- Molecular Imaging Program at Stanford, Stanford, CA 94305, USA
- Department of Applied Physics, Stanford University, Stanford, CA 94305, USA
| | - Itamar Terem
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA
- Molecular Imaging Program at Stanford, Stanford, CA 94305, USA
- Department of Electrical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Jinjing Zhao
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA
| | - Caroline Yu
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA
- Molecular Imaging Program at Stanford, Stanford, CA 94305, USA
| | - Warren Chan
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Hanh Do
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Saba Shevidi
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA
- Molecular Imaging Program at Stanford, Stanford, CA 94305, USA
| | - Maiya Mao
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA
- Molecular Imaging Program at Stanford, Stanford, CA 94305, USA
| | - Jacqueline Yu
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA
- Molecular Imaging Program at Stanford, Stanford, CA 94305, USA
| | - Megan Hong
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA
- Molecular Imaging Program at Stanford, Stanford, CA 94305, USA
| | - Erick Blankenberg
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA
- Molecular Imaging Program at Stanford, Stanford, CA 94305, USA
| | - Kerri E. Rieger
- Department of Pathology, Stanford University School of Medicine and Stanford Cancer Institute, Stanford, CA 94305, USA
| | - Steven Chu
- The Bio-X Program, Stanford, CA 94305, USA
- Biophysics Program at Stanford, Stanford, CA 94305, USA
- Departments of Physics and Molecular and Cellular Physiology, Energy, Science and Engineering Stanford University, Stanford, CA 94305, USA
| | - Sumaira Aasi
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kavita Y. Sarin
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Adam de la Zerda
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA
- Molecular Imaging Program at Stanford, Stanford, CA 94305, USA
- The Bio-X Program, Stanford, CA 94305, USA
- Biophysics Program at Stanford, Stanford, CA 94305, USA
- Department of Electrical Engineering, Stanford University, Stanford, CA 94305, USA
- The Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
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8
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Das V, Zhang F, Bower AJ, Li J, Liu T, Aguilera N, Alvisio B, Liu Z, Hammer DX, Tam J. Revealing speckle obscured living human retinal cells with artificial intelligence assisted adaptive optics optical coherence tomography. COMMUNICATIONS MEDICINE 2024; 4:68. [PMID: 38600290 PMCID: PMC11006674 DOI: 10.1038/s43856-024-00483-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 03/13/2024] [Indexed: 04/12/2024] Open
Abstract
BACKGROUND In vivo imaging of the human retina using adaptive optics optical coherence tomography (AO-OCT) has transformed medical imaging by enabling visualization of 3D retinal structures at cellular-scale resolution, including the retinal pigment epithelial (RPE) cells, which are essential for maintaining visual function. However, because noise inherent to the imaging process (e.g., speckle) makes it difficult to visualize RPE cells from a single volume acquisition, a large number of 3D volumes are typically averaged to improve contrast, substantially increasing the acquisition duration and reducing the overall imaging throughput. METHODS Here, we introduce parallel discriminator generative adversarial network (P-GAN), an artificial intelligence (AI) method designed to recover speckle-obscured cellular features from a single AO-OCT volume, circumventing the need for acquiring a large number of volumes for averaging. The combination of two parallel discriminators in P-GAN provides additional feedback to the generator to more faithfully recover both local and global cellular structures. Imaging data from 8 eyes of 7 participants were used in this study. RESULTS We show that P-GAN not only improves RPE cell contrast by 3.5-fold, but also improves the end-to-end time required to visualize RPE cells by 99-fold, thereby enabling large-scale imaging of cells in the living human eye. RPE cell spacing measured across a large set of AI recovered images from 3 participants were in agreement with expected normative ranges. CONCLUSIONS The results demonstrate the potential of AI assisted imaging in overcoming a key limitation of RPE imaging and making it more accessible in a routine clinical setting.
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Affiliation(s)
- Vineeta Das
- National Eye Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Furu Zhang
- National Eye Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Andrew J Bower
- National Eye Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Joanne Li
- National Eye Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Tao Liu
- National Eye Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Nancy Aguilera
- National Eye Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Bruno Alvisio
- National Eye Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Zhuolin Liu
- Center for Devices and Radiological Health, U.S. Food and Drug Administration, Silver Spring, MD, 20993, USA
| | - Daniel X Hammer
- Center for Devices and Radiological Health, U.S. Food and Drug Administration, Silver Spring, MD, 20993, USA
| | - Johnny Tam
- National Eye Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
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9
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Cornelio A, Collazo Martinez A, Lu H, Jones C, Kashani AH. Rigid alignment method for secondary analyses of optical coherence tomography volumes. BIOMEDICAL OPTICS EXPRESS 2024; 15:938-952. [PMID: 38404338 PMCID: PMC10890897 DOI: 10.1364/boe.508123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 01/08/2024] [Accepted: 01/09/2024] [Indexed: 02/27/2024]
Abstract
Optical coherence tomography (OCT) provides micron level resolution of retinal tissue and is widely used in ophthalmology. Millions of pre-existing OCT images are available from research and clinical databases. Analysis of this data often requires or can benefit significantly from image registration and reduction of speckle noise. One method of reducing noise is to align and average multiple OCT scans together. We propose to use surface feature information and whole volume information to create a novel and simple pipeline that can rigidly align, and average multiple previously acquired 3D OCT volumes from a commercially available OCT device. This pipeline significantly improves both image quality and visualization of clinically relevant image features over single, unaligned volumes from the commercial scanner.
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Affiliation(s)
- Andrew Cornelio
- Wilmer Eye Institute, Johns Hopkins Hospital, Baltimore, MD 21287, USA
| | | | - Hanzhang Lu
- Department of Radiology and Radiological Science, Johns Hopkins University Hospital, Baltimore, MD 21287, USA
| | - Craig Jones
- Wilmer Eye Institute, Johns Hopkins Hospital, Baltimore, MD 21287, USA
- Department of Radiology and Radiological Science, Johns Hopkins University Hospital, Baltimore, MD 21287, USA
- Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Amir H Kashani
- Wilmer Eye Institute, Johns Hopkins Hospital, Baltimore, MD 21287, USA
- Department of Biomedical Engineering, Johns Hopkins Hospital, Baltimore, MD 21287, USA
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10
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Allegrini D, Raimondi R, Sorrentino T, Tripepi D, Stradiotto E, Caruso M, De Rosa FP, Romano MR. The effect of optical degradation from cataract using a new Deep Learning optical coherence tomography segmentation algorithm. Graefes Arch Clin Exp Ophthalmol 2024; 262:431-440. [PMID: 37843567 DOI: 10.1007/s00417-023-06261-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 09/25/2023] [Accepted: 09/28/2023] [Indexed: 10/17/2023] Open
Abstract
PURPOSE To assess the validity of the results of a freely available online Deep Learning segmentation tool and its sensitivity to noise introduced by cataract. METHODS The OCT images were collected with a Spectralis SD-OCT (Heidelberg Engineering, Heidelberg, Germany) as part of normal clinical practice. Data were segmented using a freely available online tool called Relayer ( https://www.relayer.online/ ), based on a cross-platform Deep Learning segmentation architecture specifically adapted for retinal OCT images. The segmentations were read into MATLAB (The MathWorks, Natick, MA, USA) and analyzed. RESULTS There was an excellent agreement between the ETDRS measurements obtained from the two algorithms. Upon visual inspection, the segmentation based on Deep Learning obtained with Relayer appeared more accurate except in one case of apparent good quality image showing interrupted segmentations in some of the B-scans. CONCLUSION A freely available online Deep Learning segmentation tool showed good and promising performance in healthy retinas before and after cataract surgery, proving robust to optical degradation of the image from media opacities.
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Affiliation(s)
| | - Raffaele Raimondi
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4Pieve Emanuele, 20072, Milan, Italy.
| | - Tania Sorrentino
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4Pieve Emanuele, 20072, Milan, Italy
| | - Domenico Tripepi
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4Pieve Emanuele, 20072, Milan, Italy
| | - Elisa Stradiotto
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4Pieve Emanuele, 20072, Milan, Italy
| | - Marco Caruso
- PolitoBIOMed Lab-Biomedical Engineering Lab and Department of Electronics and Telecommunications, Politecnico Di Torino, 10129, Turin, Italy
| | - Francesco Paolo De Rosa
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4Pieve Emanuele, 20072, Milan, Italy
| | - Mario R Romano
- Eye Center, Humanitas Gavazzeni-Castelli, Bergamo, Italy
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4Pieve Emanuele, 20072, Milan, Italy
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11
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Maltais-Tariant R, Itzamna Becerra-Deana R, Brais-Brunet S, Dehaes M, Boudoux C. Speckle contrast reduction through the use of a modally-specific photonic lantern for optical coherence tomography. BIOMEDICAL OPTICS EXPRESS 2023; 14:6250-6259. [PMID: 38420311 PMCID: PMC10898554 DOI: 10.1364/boe.504861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 10/31/2023] [Accepted: 11/02/2023] [Indexed: 03/02/2024]
Abstract
A few-mode optical coherence tomography (FM-OCT) system was developed around a 2 × 1 modally-specific photonic lantern (MSPL) centered at 1310 nm. The MSPL allowed FM-OCT to acquire two coregistered images with uncorrelated speckle patterns generated by their specific coherent spread function. Here, we showed that averaging such images in vitro and in vivo reduced the speckle contrast by up to 28% and increased signal-to-noise ratio (SNR) by up to 48% with negligible impact on image spatial resolution. This method is compatible with other speckle reduction techniques to further improve OCT image quality.
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Affiliation(s)
| | | | - Simon Brais-Brunet
- Research Centre, CHU Sainte-Justine, Montréal, Canada
- Université de Montréal, Institute of Biomedical Engineering, Montréal, Canada
| | - Mathieu Dehaes
- Research Centre, CHU Sainte-Justine, Montréal, Canada
- Université de Montréal, Institute of Biomedical Engineering, Montréal, Canada
- Université de Montréal, Department of Radiology, Radio-oncology and Nuclear Medicine, Montréal, Canada
| | - Caroline Boudoux
- Polytechnique Montréal, Department of Engineering Physics, Montréal, Canada
- Castor Optics, Saint-Laurent, Canada
- Research Centre, CHU Sainte-Justine, Montréal, Canada
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12
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Namekata N, Kobayashi N, Nomura K, Sako T, Takata N, Inoue S. Quantum optical tomography based on time-resolved and mode-selective single-photon detection by femtosecond up-conversion. Sci Rep 2023; 13:21080. [PMID: 38030670 PMCID: PMC10687223 DOI: 10.1038/s41598-023-48270-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 11/24/2023] [Indexed: 12/01/2023] Open
Abstract
We developed an optical time-of-flight measurement system using a time-resolved and mode-selective up-conversion single-photon detector for acquiring tomographic images of a mouse brain. The probe and pump pulses were spectrally carved from a 100-femtosecond mode-locked fiber laser at 1556 nm using 4f systems, so that their center wavelengths were situated at either side of the phase matching band separated by 30 nm. We demonstrated a sensitivity of 111 dB which is comparable to that of shot-noise-limited optical coherence tomography and an axial resolution of 57 μm (a refractive index of 1.37) with 380 femtosecond probe and pump pulses whose average powers were 1.5 mW and 30 μW, respectively. The proposed technique will open a new way of non-contact and non-invasive three-dimensional structural imaging of biological specimens with ultraweak optical irradiation.
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Affiliation(s)
- Naoto Namekata
- Institute of Quantum Science, Nihon University, 1-8-14 Kanda-Surugadai, Chiyoda-Ku, Tokyo, 101-8308, Japan.
| | - Nobuaki Kobayashi
- Department of Precision Machinery Engineering, College of Science and Technology, Nihon University, 7-24-1 Narashinodai, Funabashi, Chiba, 274-8501, Japan
| | - Kenya Nomura
- Laboratory of Physics, College of Science and Technology, Nihon University, 7-24-1 Narashinodai, Funabashi, Chiba, 274-8501, Japan
| | - Tokuei Sako
- Laboratory of Physics, College of Science and Technology, Nihon University, 7-24-1 Narashinodai, Funabashi, Chiba, 274-8501, Japan
| | - Norio Takata
- Division of Brain Science, Institute for Advanced Medical Research, Keio University School of Medicine, 35 Shinanomachi, Shinjyuku, Tokyo, 160-8582, Japan
| | - Shuichiro Inoue
- Institute of Quantum Science, Nihon University, 1-8-14 Kanda-Surugadai, Chiyoda-Ku, Tokyo, 101-8308, Japan
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13
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Pereg D. Domain-Aware Few-Shot Learning for Optical Coherence Tomography Noise Reduction. J Imaging 2023; 9:237. [PMID: 37998084 PMCID: PMC10672362 DOI: 10.3390/jimaging9110237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 10/08/2023] [Accepted: 10/10/2023] [Indexed: 11/25/2023] Open
Abstract
Speckle noise has long been an extensively studied problem in medical imaging. In recent years, there have been significant advances in leveraging deep learning methods for noise reduction. Nevertheless, adaptation of supervised learning models to unseen domains remains a challenging problem. Specifically, deep neural networks (DNNs) trained for computational imaging tasks are vulnerable to changes in the acquisition system's physical parameters, such as: sampling space, resolution, and contrast. Even within the same acquisition system, performance degrades across datasets of different biological tissues. In this work, we propose a few-shot supervised learning framework for optical coherence tomography (OCT) noise reduction, that offers high-speed training (of the order of seconds) and requires only a single image, or part of an image, and a corresponding speckle-suppressed ground truth, for training. Furthermore, we formulate the domain shift problem for OCT diverse imaging systems and prove that the output resolution of a despeckling trained model is determined by the source domain resolution. We also provide possible remedies. We propose different practical implementations of our approach, verify and compare their applicability, robustness, and computational efficiency. Our results demonstrate the potential to improve sample complexity, generalization, and time efficiency, for coherent and non-coherent noise reduction via supervised learning models, that can also be leveraged for other real-time computer vision applications.
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Affiliation(s)
- Deborah Pereg
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA;
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
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14
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Che H, Tang Y. A Simplified Convex Optimization Model for Image Restoration with Multiplicative Noise. J Imaging 2023; 9:229. [PMID: 37888336 PMCID: PMC10607615 DOI: 10.3390/jimaging9100229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/11/2023] [Accepted: 10/16/2023] [Indexed: 10/28/2023] Open
Abstract
In this paper, we propose a novel convex variational model for image restoration with multiplicative noise. To preserve the edges in the restored image, our model incorporates a total variation regularizer. Additionally, we impose an equality constraint on the data fidelity term, which simplifies the model selection process and promotes sparsity in the solution. We adopt the alternating direction method of multipliers (ADMM) method to solve the model efficiently. To validate the effectiveness of our model, we conduct numerical experiments on both real and synthetic noise images, and compare its performance with existing methods. The experimental results demonstrate the superiority of our model in terms of PSNR and visual quality.
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Affiliation(s)
- Haoxiang Che
- Department of Mathematics, Nanchang University, Nanchang 330031, China;
| | - Yuchao Tang
- School of Mathematics and Information Science, Guangzhou University, Guangzhou 510006, China
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15
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Puyo L, Pfäffle C, Spahr H, Franke J, Bublitz D, Hillmann D, Hüttmann G. Diffuse-illumination holographic optical coherence tomography. OPTICS EXPRESS 2023; 31:33500-33517. [PMID: 37859131 DOI: 10.1364/oe.498654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 09/11/2023] [Indexed: 10/21/2023]
Abstract
Holographic optical coherence tomography (OCT) is a powerful imaging technique, but its ability to reveal low-reflectivity features is limited. In this study, we performed holographic OCT by incoherently averaging volumes with changing diffuse illumination of numerical aperture (NA) equal to the detection NA. While the reduction of speckle from singly scattered light is only modest, we discovered that speckle from multiply scattered light can be arbitrarily reduced, resulting in substantial improvements in image quality. This technique also offers the advantage of suppressing noises arising from spatial coherence, and can be implemented with a partially spatially incoherent light source for further mitigation of multiple scattering. Finally, we show that although holographic reconstruction capabilities are increasingly lost with decreasing spatial coherence, they can be retained over an axial range sufficient to standard OCT applications.
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16
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Liao J, Yang S, Zhang T, Li C, Huang Z. A hand-held optical coherence tomography angiography scanner based on angiography reconstruction transformer networks. JOURNAL OF BIOPHOTONICS 2023; 16:e202300100. [PMID: 37264544 DOI: 10.1002/jbio.202300100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 05/18/2023] [Accepted: 05/24/2023] [Indexed: 06/03/2023]
Abstract
Optical coherence tomography angiography (OCTA) has successfully demonstrated its viability for clinical applications in dermatology. Due to the high optical scattering property of skin, extracting high-quality OCTA images from skin tissues requires at least six-repeated scans. While the motion artifacts from the patient and the free hand-held probe can lead to a low-quality OCTA image. Our deep-learning-based scan pipeline enables fast and high-quality OCTA imaging with 0.3-s data acquisition. We utilize a fast scanning protocol with a 60 μm/pixel spatial interval rate and introduce angiography-reconstruction-transformer (ART) for 4× super-resolution of low transverse resolution OCTA images. The ART outperforms state-of-the-art networks in OCTA image super-resolution and provides a lighter network size. ART can restore microvessels while reducing the processing time by 85%, and maintaining improvements in structural similarity and peak-signal-to-noise ratio. This study represents that ART can achieve fast and flexible skin OCTA imaging while maintaining image quality.
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Affiliation(s)
- Jinpeng Liao
- School of Science and Engineering, University of Dundee, Scotland, UK
| | - Shufan Yang
- School of Computing, Engineering and Built Environment, Edinburgh Napier University, Edinburgh, UK
- Research Department of Orthopaedics and Musculoskeletal Science, University College London, UK
| | - Tianyu Zhang
- School of Science and Engineering, University of Dundee, Scotland, UK
| | - Chunhui Li
- School of Science and Engineering, University of Dundee, Scotland, UK
| | - Zhihong Huang
- School of Science and Engineering, University of Dundee, Scotland, UK
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17
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Kasireddy HR, Kallam UR, Mantrala SKS, Kongara H, Shivhare A, Saita J, Vijay S, Prasad R, Raman R, Seelamantula CS. Deep-Learning-Based Visualization and Volumetric Analysis of Fluid Regions in Optical Coherence Tomography Scans. Diagnostics (Basel) 2023; 13:2659. [PMID: 37627918 PMCID: PMC10453848 DOI: 10.3390/diagnostics13162659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/27/2023] [Accepted: 07/28/2023] [Indexed: 08/27/2023] Open
Abstract
Retinal volume computation is one of the critical steps in grading pathologies and evaluating the response to a treatment. We propose a deep-learning-based visualization tool to calculate the fluid volume in retinal optical coherence tomography (OCT) images. The pathologies under consideration are Intraretinal Fluid (IRF), Subretinal Fluid (SRF), and Pigmented Epithelial Detachment (PED). We develop a binary classification model for each of these pathologies using the Inception-ResNet-v2 and the small Inception-ResNet-v2 models. For visualization, we use several standard Class Activation Mapping (CAM) techniques, namely Grad-CAM, Grad-CAM++, Score-CAM, Ablation-CAM, and Self-Matching CAM, to visualize the pathology-specific regions in the image and develop a novel Ensemble-CAM visualization technique for robust visualization of OCT images. In addition, we demonstrate a Graphical User Interface that takes the visualization heat maps as the input and calculates the fluid volume in the OCT C-scans. The volume is computed using both the region-growing algorithm and selective thresholding technique and compared with the ground-truth volume based on expert annotation. We compare the results obtained using the standard Inception-ResNet-v2 model with a small Inception-ResNet-v2 model, which has half the number of trainable parameters compared with the original model. This study shows the relevance and usefulness of deep-learning-based visualization techniques for reliable volumetric analysis.
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Affiliation(s)
- Harishwar Reddy Kasireddy
- Department of Electrical Engineering, Indian Institute of Science, Bengaluru 560012, India; (H.R.K.); (U.R.K.); (S.K.S.M.); (H.K.); (A.S.)
| | - Udaykanth Reddy Kallam
- Department of Electrical Engineering, Indian Institute of Science, Bengaluru 560012, India; (H.R.K.); (U.R.K.); (S.K.S.M.); (H.K.); (A.S.)
| | | | - Hemanth Kongara
- Department of Electrical Engineering, Indian Institute of Science, Bengaluru 560012, India; (H.R.K.); (U.R.K.); (S.K.S.M.); (H.K.); (A.S.)
| | - Anshul Shivhare
- Department of Electrical Engineering, Indian Institute of Science, Bengaluru 560012, India; (H.R.K.); (U.R.K.); (S.K.S.M.); (H.K.); (A.S.)
| | - Jayesh Saita
- Carl Zeiss India Pvt. Ltd., Bengaluru 560099, India; (J.S.); (S.V.); (R.P.)
| | - Sharanya Vijay
- Carl Zeiss India Pvt. Ltd., Bengaluru 560099, India; (J.S.); (S.V.); (R.P.)
| | - Raghu Prasad
- Carl Zeiss India Pvt. Ltd., Bengaluru 560099, India; (J.S.); (S.V.); (R.P.)
| | - Rajiv Raman
- Shri Bhagwan Mahavir Vitreoretinal Services, Sankara Nethralaya, Chennai 600006, India;
| | - Chandra Sekhar Seelamantula
- Department of Electrical Engineering, Indian Institute of Science, Bengaluru 560012, India; (H.R.K.); (U.R.K.); (S.K.S.M.); (H.K.); (A.S.)
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18
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Hao S, Amaral MM, Zhou C. High dynamic range 3D motion tracking using circular scans with optical coherence tomography. BIOMEDICAL OPTICS EXPRESS 2023; 14:3881-3898. [PMID: 37799687 PMCID: PMC10549755 DOI: 10.1364/boe.493725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 06/21/2023] [Accepted: 06/21/2023] [Indexed: 10/07/2023]
Abstract
Motion artifacts, from such sources as heartbeats, respiration, or peristalsis, often degrade microscopic images or videos of live subjects. We have developed a method using circular optical coherence tomography (OCT) scans to track the transverse and axial motion of biological samples at speeds ranging from several micrometers per second to several centimeters per second. We achieve fast and high-precision measurements of the magnitude and direction of the sample's motion by adaptively controlling the circular scan pattern settings and applying interframe and intraframe analyses. These measurements are the basis of active motion compensation via feedback control for future in vivo microscopic and macroscopic imaging applications.
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Affiliation(s)
- Senyue Hao
- Department of Electrical & Systems Engineering,
Washington University in Saint Louis, USA
| | - Marcello Magri Amaral
- Department of Biomedical Engineering, Washington University in Saint Louis, USA
- Biomedical Engineering, Universidade Brasil, Brazil
| | - Chao Zhou
- Department of Electrical & Systems Engineering,
Washington University in Saint Louis, USA
- Department of Biomedical Engineering, Washington University in Saint Louis, USA
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19
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Miażdżyk M, Consejo A, Iskander DR. OCT based corneal densitometry: the confounding effect of epithelial speckle. BIOMEDICAL OPTICS EXPRESS 2023; 14:3871-3880. [PMID: 37799674 PMCID: PMC10549732 DOI: 10.1364/boe.489054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 06/06/2023] [Accepted: 06/12/2023] [Indexed: 10/07/2023]
Abstract
Corneal densitometry is a clinically validated method for objectively assessing the transparency of stroma. The technique is currently dominated by Scheimpflug technology. Still, optical coherence tomography (OCT), in which examination of the statistical properties of corneal speckle is undertaken, has also been considered to assess corneal densitometry. In-vivo, the stroma is observed via the epithelium. However, the effect of this external layer on stromal densitometry has not been considered as yet. This study aims to quantify the influence of epithelium integrity on corneal OCT densitometry. OCT images from eleven freshly enucleated porcine eyes before and after epithelial debridement were used. OCT densitometry was investigated at different stromal depths using four metrics of speckle statistics. Results indicate that there exist statistically significant differences in speckle statistics for a given stromal depth depending on the presence or absence of the epithelium. The estimation error in speckle statistics can reach over 20% depending on the stromal depth. The anterior stroma densitometry values are the ones most affected by epithelial integrity. In conclusion, if OCT densitometry stromal parameters are to be considered in absolute terms, it is essential to consider the confounding effect of the epithelial layer in the analysis.
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Affiliation(s)
- Maria Miażdżyk
- Department of Biomedical Engineering,
Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Alejandra Consejo
- Department of Applied Physics, University of Zaragoza, Zaragoza, Spain
- Aragon Institute for Engineering Research (I3A), University of Zaragoza, Zaragoza, Spain
| | - D. Robert Iskander
- Department of Biomedical Engineering,
Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
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20
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Plekhanov AA, Gubarkova EV, Sirotkina MA, Sovetsky AA, Vorontsov DA, Matveev LA, Kuznetsov SS, Bogomolova AY, Vorontsov AY, Matveyev AL, Gamayunov SV, Zagaynova EV, Zaitsev VY, Gladkova ND. Compression OCT-elastography combined with speckle-contrast analysis as an approach to the morphological assessment of breast cancer tissue. BIOMEDICAL OPTICS EXPRESS 2023; 14:3037-3056. [PMID: 37342703 PMCID: PMC10278614 DOI: 10.1364/boe.489021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 05/15/2023] [Accepted: 05/18/2023] [Indexed: 06/23/2023]
Abstract
Currently, optical biopsy technologies are being developed for rapid and label-free visualization of biological tissue with micrometer-level resolution. They can play an important role in breast-conserving surgery guidance, detection of residual cancer cells, and targeted histological analysis. For solving these problems, compression optical coherence elastography (C-OCE) demonstrated impressive results based on differences in the elasticity of different tissue constituents. However, sometimes straightforward C-OCE-based differentiation is insufficient because of the similar stiffness of certain tissue components. We present a new automated approach to the rapid morphological assessment of human breast cancer based on the combined usage of C-OCE and speckle-contrast (SC) analysis. Using the SC analysis of structural OCT images, the threshold value of the SC coefficient was established to enable the separation of areas of adipose cells from necrotic cancer cells, even if they are highly similar in elastic properties. Consequently, the boundaries of the tumor bed can be reliably identified. The joint analysis of structural and elastographic images enables automated morphological segmentation based on the characteristic ranges of stiffness (Young's modulus) and SC coefficient established for four morphological structures of breast-cancer samples from patients post neoadjuvant chemotherapy (residual cancer cells, cancer stroma, necrotic cancer cells, and mammary adipose cells). This enabled precise automated detection of residual cancer-cell zones within the tumor bed for grading cancer response to chemotherapy. The results of C-OCE/SC morphometry highly correlated with the histology-based results (r =0.96-0.98). The combined C-OCE/SC approach has the potential to be used intraoperatively for achieving clean resection margins in breast cancer surgery and for performing targeted histological analysis of samples, including the evaluation of the efficacy of cancer chemotherapy.
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Affiliation(s)
- Anton A. Plekhanov
- Institute of Experimental Oncology and Biomedical Technologies, Privolzhsky Research Medical University, Minin and Pozharsky sq. 10/1, 603950 Nizhny Novgorod, Russia
| | - Ekaterina V. Gubarkova
- Institute of Experimental Oncology and Biomedical Technologies, Privolzhsky Research Medical University, Minin and Pozharsky sq. 10/1, 603950 Nizhny Novgorod, Russia
| | - Marina A. Sirotkina
- Institute of Experimental Oncology and Biomedical Technologies, Privolzhsky Research Medical University, Minin and Pozharsky sq. 10/1, 603950 Nizhny Novgorod, Russia
| | - Alexander A. Sovetsky
- Institute of Applied Physics of the Russian Academy of Sciences, Ulyanova st. 46, 603950 Nizhny Novgorod, Russia
| | - Dmitry A. Vorontsov
- Nizhny Novgorod Regional Oncologic Hospital, Delovaya st. 11/1, 603093 Nizhny Novgorod, Russia
| | - Lev A. Matveev
- Institute of Applied Physics of the Russian Academy of Sciences, Ulyanova st. 46, 603950 Nizhny Novgorod, Russia
| | - Sergey S. Kuznetsov
- Nizhny Novgorod Regional Oncologic Hospital, Delovaya st. 11/1, 603093 Nizhny Novgorod, Russia
| | - Alexandra Y. Bogomolova
- Institute of Experimental Oncology and Biomedical Technologies, Privolzhsky Research Medical University, Minin and Pozharsky sq. 10/1, 603950 Nizhny Novgorod, Russia
- Lobachevsky State University, Gagarin Avenue 23, 603950 Nizhny Novgorod, Russia
| | - Alexey Y. Vorontsov
- Nizhny Novgorod Regional Oncologic Hospital, Delovaya st. 11/1, 603093 Nizhny Novgorod, Russia
| | - Alexander L. Matveyev
- Institute of Applied Physics of the Russian Academy of Sciences, Ulyanova st. 46, 603950 Nizhny Novgorod, Russia
| | - Sergey V. Gamayunov
- Nizhny Novgorod Regional Oncologic Hospital, Delovaya st. 11/1, 603093 Nizhny Novgorod, Russia
| | - Elena V. Zagaynova
- Institute of Experimental Oncology and Biomedical Technologies, Privolzhsky Research Medical University, Minin and Pozharsky sq. 10/1, 603950 Nizhny Novgorod, Russia
- Lobachevsky State University, Gagarin Avenue 23, 603950 Nizhny Novgorod, Russia
| | - Vladimir Y. Zaitsev
- Institute of Applied Physics of the Russian Academy of Sciences, Ulyanova st. 46, 603950 Nizhny Novgorod, Russia
| | - Natalia D. Gladkova
- Institute of Experimental Oncology and Biomedical Technologies, Privolzhsky Research Medical University, Minin and Pozharsky sq. 10/1, 603950 Nizhny Novgorod, Russia
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21
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Xie G, Wang S, Zhang Y, Hu B, Fu Y, Yu Q, Li Y. An Efficient Method for Laser Welding Depth Determination Using Optical Coherence Tomography. SENSORS (BASEL, SWITZERLAND) 2023; 23:s23115223. [PMID: 37299951 DOI: 10.3390/s23115223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 05/28/2023] [Accepted: 05/29/2023] [Indexed: 06/12/2023]
Abstract
Online monitoring of laser welding depth is increasingly important, with the growing demand for the precise welding depth in the field of power battery manufacturing for new energy vehicles. The indirect methods of welding depth measurement based on optical radiation, visual image and acoustic signals in the process zone have low accuracy in the continuous monitoring. Optical coherence tomography (OCT) provides a direct welding depth measurement during laser welding and shows high achievable accuracy in continuous monitoring. Statistical evaluation approach accurately extracts the welding depth from OCT data but suffers from complexity in noise removal. In this paper, an efficient method coupled DBSCAN (Density-Based Spatial Clustering of Application with Noise) and percentile filter for laser welding depth determination was proposed. The noise of the OCT data were viewed as outliers and detected by DBSCAN. After eliminating the noise, the percentile filter was used to extract the welding depth. By comparing the welding depth determined by this approach and the actual weld depth of longitudinal cross section, an average error of less than 5% was obtained. The precise laser welding depth can be efficiently achieved by the method.
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Affiliation(s)
- Guanming Xie
- Institute of Intelligent Optical Measurement and Detection, Shenzhen University, Shenzhen 518060, China
- College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Sanhong Wang
- Shenzhen Sincevision Technology Co., Ltd., Shenzhen 518055, China
| | - Yueqiang Zhang
- Institute of Intelligent Optical Measurement and Detection, Shenzhen University, Shenzhen 518060, China
- College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Biao Hu
- Institute of Intelligent Optical Measurement and Detection, Shenzhen University, Shenzhen 518060, China
- College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Yu Fu
- Institute of Intelligent Optical Measurement and Detection, Shenzhen University, Shenzhen 518060, China
- College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Qifeng Yu
- Institute of Intelligent Optical Measurement and Detection, Shenzhen University, Shenzhen 518060, China
- College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - You Li
- National Key Laboratory of Human Factors Engineering, China Astronaut Research and Training Center, Beijing 100094, China
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22
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Miller DA, Grannonico M, Liu M, Savier E, McHaney K, Erisir A, Netland PA, Cang J, Liu X, Zhang HF. Visible-Light Optical Coherence Tomography Fibergraphy of the Tree Shrew Retinal Ganglion Cell Axon Bundles. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.16.541062. [PMID: 37293064 PMCID: PMC10245691 DOI: 10.1101/2023.05.16.541062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
We seek to develop techniques for high-resolution imaging of the tree shrew retina for visualizing and parameterizing retinal ganglion cell (RGC) axon bundles in vivo. We applied visible-light optical coherence tomography fibergraphy (vis-OCTF) and temporal speckle averaging (TSA) to visualize individual RGC axon bundles in the tree shrew retina. For the first time, we quantified individual RGC bundle width, height, and cross-sectional area and applied vis-OCT angiography (vis-OCTA) to visualize the retinal microvasculature in tree shrews. Throughout the retina, as the distance from the optic nerve head (ONH) increased from 0.5 mm to 2.5 mm, bundle width increased by 30%, height decreased by 67%, and cross-sectional area decreased by 36%. We also showed that axon bundles become vertically elongated as they converge toward the ONH. Ex vivo confocal microscopy of retinal flat-mounts immunostained with Tuj1 confirmed our in vivo vis-OCTF findings.
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23
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Lee W, Nam HS, Seok JY, Oh WY, Kim JW, Yoo H. Deep learning-based image enhancement in optical coherence tomography by exploiting interference fringe. Commun Biol 2023; 6:464. [PMID: 37117279 PMCID: PMC10147647 DOI: 10.1038/s42003-023-04846-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 04/17/2023] [Indexed: 04/30/2023] Open
Abstract
Optical coherence tomography (OCT), an interferometric imaging technique, provides non-invasive, high-speed, high-sensitive volumetric biological imaging in vivo. However, systemic features inherent in the basic operating principle of OCT limit its imaging performance such as spatial resolution and signal-to-noise ratio. Here, we propose a deep learning-based OCT image enhancement framework that exploits raw interference fringes to achieve further enhancement from currently obtainable optimized images. The proposed framework for enhancing spatial resolution and reducing speckle noise in OCT images consists of two separate models: an A-scan-based network (NetA) and a B-scan-based network (NetB). NetA utilizes spectrograms obtained via short-time Fourier transform of raw interference fringes to enhance axial resolution of A-scans. NetB was introduced to enhance lateral resolution and reduce speckle noise in B-scan images. The individually trained networks were applied sequentially. We demonstrate the versatility and capability of the proposed framework by visually and quantitatively validating its robust performance. Comparative studies suggest that deep learning utilizing interference fringes can outperform the existing methods. Furthermore, we demonstrate the advantages of the proposed method by comparing our outcomes with multi-B-scan averaged images and contrast-adjusted images. We expect that the proposed framework will be a versatile technology that can improve functionality of OCT.
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Affiliation(s)
- Woojin Lee
- Department of Mechanical Engineering, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Hyeong Soo Nam
- Department of Mechanical Engineering, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Jae Yeon Seok
- Department of Pathology, Yongin Severance Hospital, Yonsei University College of Medicine, 363 Dongbaekjukjeon-daero, Giheung-gu, Yongin-si, Gyeonggi-do, 16995, Republic of Korea
| | - Wang-Yuhl Oh
- Department of Mechanical Engineering, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Jin Won Kim
- Multimodal Imaging and Theranostic Lab, Cardiovascular Center, Korea University Guro Hospital, 148 Gurodong-ro, Guro-gu, Seoul, 08308, Republic of Korea
| | - Hongki Yoo
- Department of Mechanical Engineering, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea.
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24
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Lan G, Twa MD, Song C, Feng J, Huang Y, Xu J, Qin J, An L, Wei X. In vivo corneal elastography: A topical review of challenges and opportunities. Comput Struct Biotechnol J 2023; 21:2664-2687. [PMID: 37181662 PMCID: PMC10173410 DOI: 10.1016/j.csbj.2023.04.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 04/07/2023] [Accepted: 04/12/2023] [Indexed: 05/16/2023] Open
Abstract
Clinical measurement of corneal biomechanics can aid in the early diagnosis, progression tracking, and treatment evaluation of ocular diseases. Over the past two decades, interdisciplinary collaborations between investigators in optical engineering, analytical biomechanical modeling, and clinical research has expanded our knowledge of corneal biomechanics. These advances have led to innovations in testing methods (ex vivo, and recently, in vivo) across multiple spatial and strain scales. However, in vivo measurement of corneal biomechanics remains a long-standing challenge and is currently an active area of research. Here, we review the existing and emerging approaches for in vivo corneal biomechanics evaluation, which include corneal applanation methods, such as ocular response analyzer (ORA) and corneal visualization Scheimpflug technology (Corvis ST), Brillouin microscopy, and elastography methods, and the emerging field of optical coherence elastography (OCE). We describe the fundamental concepts, analytical methods, and current clinical status for each of these methods. Finally, we discuss open questions for the current state of in vivo biomechanics assessment techniques and requirements for wider use that will further broaden our understanding of corneal biomechanics for the detection and management of ocular diseases, and improve the safety and efficacy of future clinical practice.
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Affiliation(s)
- Gongpu Lan
- Guangdong-Hong Kong-Macao Intelligent Micro-Nano Optoelectronic Technology Joint Laboratory, School of Physics and Optoelectronic Engineering, Foshan University, Foshan, Guangdong 528000, China
- Weiren Meditech Co., Ltd., Foshan, Guangdong 528000, China
| | - Michael D Twa
- College of Optometry, University of Houston, Houston, TX 77204, United States
| | - Chengjin Song
- Guangdong-Hong Kong-Macao Intelligent Micro-Nano Optoelectronic Technology Joint Laboratory, School of Physics and Optoelectronic Engineering, Foshan University, Foshan, Guangdong 528000, China
| | - JinPing Feng
- Institute of Engineering and Technology, Hubei University of Science and Technology, Xianning, Hubei 437100, China
| | - Yanping Huang
- Guangdong-Hong Kong-Macao Intelligent Micro-Nano Optoelectronic Technology Joint Laboratory, School of Physics and Optoelectronic Engineering, Foshan University, Foshan, Guangdong 528000, China
- Weiren Meditech Co., Ltd., Foshan, Guangdong 528000, China
| | - Jingjiang Xu
- Guangdong-Hong Kong-Macao Intelligent Micro-Nano Optoelectronic Technology Joint Laboratory, School of Physics and Optoelectronic Engineering, Foshan University, Foshan, Guangdong 528000, China
- Weiren Meditech Co., Ltd., Foshan, Guangdong 528000, China
| | - Jia Qin
- Weiren Meditech Co., Ltd., Foshan, Guangdong 528000, China
| | - Lin An
- Weiren Meditech Co., Ltd., Foshan, Guangdong 528000, China
| | - Xunbin Wei
- Biomedical Engineering Department, Peking University, Beijing 100081, China
- International Cancer Institute, Peking University, Beijing 100191, China
- Institute of Medical Technology, Peking University Health Science Center, Beijing 100191, China
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25
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Nienhaus J, Matten P, Britten A, Scherer J, Höck E, Freytag A, Drexler W, Leitgeb RA, Schlegl T, Schmoll T. Live 4D-OCT denoising with self-supervised deep learning. Sci Rep 2023; 13:5760. [PMID: 37031338 PMCID: PMC10082772 DOI: 10.1038/s41598-023-32695-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 03/31/2023] [Indexed: 04/10/2023] Open
Abstract
By providing three-dimensional visualization of tissues and instruments at high resolution, live volumetric optical coherence tomography (4D-OCT) has the potential to revolutionize ophthalmic surgery. However, the necessary imaging speed is accompanied by increased noise levels. A high data rate and the requirement for minimal latency impose major limitations for real-time noise reduction. In this work, we propose a low complexity neural network for denoising, directly incorporated into the image reconstruction pipeline of a microscope-integrated 4D-OCT prototype with an A-scan rate of 1.2 MHz. For this purpose, we trained a blind-spot network on unpaired OCT images using a self-supervised learning approach. With an optimized U-Net, only a few milliseconds of additional latency were introduced. Simultaneously, these architectural adaptations improved the numerical denoising performance compared to the basic setup, outperforming non-local filtering algorithms. Layers and edges of anatomical structures in B-scans were better preserved than with Gaussian filtering despite comparable processing time. By comparing scenes with and without denoising employed, we show that neural networks can be used to improve visual appearance of volumetric renderings in real time. Enhancing the rendering quality is an important step for the clinical acceptance and translation of 4D-OCT as an intra-surgical guidance tool.
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Affiliation(s)
- Jonas Nienhaus
- Center for Medical Physics and Biomedical Engineering, Medical University of Vienna, Vienna, Austria.
| | - Philipp Matten
- Center for Medical Physics and Biomedical Engineering, Medical University of Vienna, Vienna, Austria
| | - Anja Britten
- Center for Medical Physics and Biomedical Engineering, Medical University of Vienna, Vienna, Austria
| | - Julius Scherer
- Center for Medical Physics and Biomedical Engineering, Medical University of Vienna, Vienna, Austria
| | | | | | - Wolfgang Drexler
- Center for Medical Physics and Biomedical Engineering, Medical University of Vienna, Vienna, Austria
| | - Rainer A Leitgeb
- Center for Medical Physics and Biomedical Engineering, Medical University of Vienna, Vienna, Austria
| | - Thomas Schlegl
- Center for Medical Physics and Biomedical Engineering, Medical University of Vienna, Vienna, Austria
| | - Tilman Schmoll
- Center for Medical Physics and Biomedical Engineering, Medical University of Vienna, Vienna, Austria
- Carl Zeiss Meditec, Inc., Dublin, USA
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26
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Kayadibi İ, Güraksın GE. An Explainable Fully Dense Fusion Neural Network with Deep Support Vector Machine for Retinal Disease Determination. INT J COMPUT INT SYS 2023. [DOI: 10.1007/s44196-023-00210-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023] Open
Abstract
AbstractRetinal issues are crucial because they result in visual loss. Early diagnosis can aid physicians in initiating treatment and preventing visual loss. Optical coherence tomography (OCT), which portrays retinal morphology cross-sectionally and noninvasively, is used to identify retinal abnormalities. The process of analyzing OCT images, on the other hand, takes time. This study has proposed a hybrid approach based on a fully dense fusion neural network (FD-CNN) and dual preprocessing to identify retinal diseases, such as choroidal neovascularization, diabetic macular edema, drusen from OCT images. A dual preprocessing methodology, in other words, a hybrid speckle reduction filter was initially used to diminish speckle noise present in OCT images. Secondly, the FD-CNN architecture was trained, and the features obtained from this architecture were extracted. Then Deep Support Vector Machine (D-SVM) and Deep K-Nearest Neighbor (D-KNN) classifiers were proposed to reclassify those features and tested on University of California San Diego (UCSD) and Duke OCT datasets. D-SVM demonstrated the best performance in both datasets. D-SVM achieved 99.60% accuracy, 99.60% sensitivity, 99.87% specificity, 99.60% precision and 99.60% F1 score in the UCSD dataset. It achieved 97.50% accuracy, 97.64% sensitivity, 98.91% specificity, 96.61% precision, and 97.03% F1 score in Duke dataset. Additionally, the results were compared to state-of-the-art works on the both datasets. The D-SVM was demonstrated to be an efficient and productive strategy for improving the robustness of automatic retinal disease classification. Also, in this study, it is shown that the unboxing of how AI systems' black-box choices is made by generating heat maps using the local interpretable model-agnostic explanation method, which is an explainable artificial intelligence (XAI) technique. Heat maps, in particular, may contribute to the development of more stable deep learning-based systems, as well as enhancing the confidence in the diagnosis of retinal disease in the analysis of OCT image for ophthalmologists.
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27
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Fitzgerald S, Akhtar J, Schartner E, Ebendorff-Heidepriem H, Mahadevan-Jansen A, Li J. Multimodal Raman spectroscopy and optical coherence tomography for biomedical analysis. JOURNAL OF BIOPHOTONICS 2023; 16:e202200231. [PMID: 36308009 PMCID: PMC10082563 DOI: 10.1002/jbio.202200231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 10/19/2022] [Accepted: 10/26/2022] [Indexed: 06/16/2023]
Abstract
Optical techniques hold great potential to detect and monitor disease states as they are a fast, non-invasive toolkit. Raman spectroscopy (RS) in particular is a powerful label-free method capable of quantifying the biomolecular content of tissues. Still, spontaneous Raman scattering lacks information about tissue morphology due to its inability to rapidly assess a large field of view. Optical Coherence Tomography (OCT) is an interferometric optical method capable of fast, depth-resolved imaging of tissue morphology, but lacks detailed molecular contrast. In many cases, pairing label-free techniques into multimodal systems allows for a more diverse field of applications. Integrating RS and OCT into a single instrument allows for both structural imaging and biochemical interrogation of tissues and therefore offers a more comprehensive means for clinical diagnosis. This review summarizes the efforts made to date toward combining spontaneous RS-OCT instrumentation for biomedical analysis, including insights into primary design considerations and data interpretation.
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Affiliation(s)
- Sean Fitzgerald
- Vanderbilt Biophotonics Center, Nashville, Tennessee, USA
- Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee, USA
| | - Jobaida Akhtar
- School of Physical Sciences, The University of Adelaide, Adelaide, South Australia, Australia
- Institute for Photonics and Advanced Sensing, The University of Adelaide, Adelaide, South Australia, Australia
- Australian Research Council Centre of Excellence for Nanoscale BioPhotonics, Adelaide, South Australia, Australia
| | - Erik Schartner
- School of Physical Sciences, The University of Adelaide, Adelaide, South Australia, Australia
- Institute for Photonics and Advanced Sensing, The University of Adelaide, Adelaide, South Australia, Australia
- Australian Research Council Centre of Excellence for Nanoscale BioPhotonics, Adelaide, South Australia, Australia
| | - Heike Ebendorff-Heidepriem
- School of Physical Sciences, The University of Adelaide, Adelaide, South Australia, Australia
- Institute for Photonics and Advanced Sensing, The University of Adelaide, Adelaide, South Australia, Australia
- Australian Research Council Centre of Excellence for Nanoscale BioPhotonics, Adelaide, South Australia, Australia
| | - Anita Mahadevan-Jansen
- Vanderbilt Biophotonics Center, Nashville, Tennessee, USA
- Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee, USA
| | - Jiawen Li
- Institute for Photonics and Advanced Sensing, The University of Adelaide, Adelaide, South Australia, Australia
- Australian Research Council Centre of Excellence for Nanoscale BioPhotonics, Adelaide, South Australia, Australia
- School of Electrical and Electronic Engineering, The University of Adelaide, Adelaide, South Australia, Australia
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28
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Xie Q, Ma Z, Zhu L, Fan F, Meng X, Gao X, Zhu J. Multi-task generative adversarial network for retinal optical coherence tomography image denoising. Phys Med Biol 2023; 68. [PMID: 36137542 DOI: 10.1088/1361-6560/ac944a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 09/22/2022] [Indexed: 02/07/2023]
Abstract
Objective. Optical coherence tomography (OCT) has become an essential imaging modality for the assessment of ophthalmic diseases. However, speckle noise in OCT images obscures subtle but important morphological details and hampers its clinical applications. In this work, a novel multi-task generative adversarial network (MGAN) is proposed for retinal OCT image denoising.Approach. To strengthen the preservation of retinal structural information in the OCT denoising procedure, the proposed MGAN integrates adversarial learning and multi-task learning. Specifically, the generator of MGAN simultaneously undertakes two tasks, including the denoising task and the segmentation task. The segmentation task aims at the generation of the retinal segmentation map, which can guide the denoising task to focus on the retina-related region based on the retina-attention module. In doing so, the denoising task can enhance the attention to the retinal region and subsequently protect the structural detail based on the supervision of the structural similarity index measure loss.Main results. The proposed MGAN was evaluated and analyzed on three public OCT datasets. The qualitative and quantitative comparisons show that the MGAN method can achieve higher image quality, and is more effective in both speckle noise reduction and structural information preservation than previous denoising methods.Significance. We have presented a MGAN for retinal OCT image denoising. The proposed method provides an effective way to strengthen the preservation of structural information while suppressing speckle noise, and can promote the OCT applications in the clinical observation and diagnosis of retinopathy.
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Affiliation(s)
- Qiaoxue Xie
- Key Laboratory of the Ministry of Education for Optoelectronic Measurement Technology and Instrument, Beijing Information Science and Technology University, Beijing 100192, People's Republic of China.,Beijing Laboratory of Biomedical Testing Technology and Instruments, Beijing Information Science and Technology University, Beijing 100192, People's Republic of China
| | - Zongqing Ma
- Key Laboratory of the Ministry of Education for Optoelectronic Measurement Technology and Instrument, Beijing Information Science and Technology University, Beijing 100192, People's Republic of China.,Beijing Laboratory of Biomedical Testing Technology and Instruments, Beijing Information Science and Technology University, Beijing 100192, People's Republic of China
| | - Lianqing Zhu
- Key Laboratory of the Ministry of Education for Optoelectronic Measurement Technology and Instrument, Beijing Information Science and Technology University, Beijing 100192, People's Republic of China.,Beijing Laboratory of Biomedical Testing Technology and Instruments, Beijing Information Science and Technology University, Beijing 100192, People's Republic of China
| | - Fan Fan
- Key Laboratory of the Ministry of Education for Optoelectronic Measurement Technology and Instrument, Beijing Information Science and Technology University, Beijing 100192, People's Republic of China.,Beijing Laboratory of Biomedical Testing Technology and Instruments, Beijing Information Science and Technology University, Beijing 100192, People's Republic of China
| | - Xiaochen Meng
- Key Laboratory of the Ministry of Education for Optoelectronic Measurement Technology and Instrument, Beijing Information Science and Technology University, Beijing 100192, People's Republic of China.,Beijing Laboratory of Biomedical Testing Technology and Instruments, Beijing Information Science and Technology University, Beijing 100192, People's Republic of China
| | - Xinxiao Gao
- Beijing Anzhen Hospital, Capital Medical University, Beijing 100029, People's Republic of China
| | - Jiang Zhu
- Key Laboratory of the Ministry of Education for Optoelectronic Measurement Technology and Instrument, Beijing Information Science and Technology University, Beijing 100192, People's Republic of China.,Beijing Laboratory of Biomedical Testing Technology and Instruments, Beijing Information Science and Technology University, Beijing 100192, People's Republic of China
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29
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Gende M, de Moura J, Novo J, Penedo MG, Ortega M. A new generative approach for optical coherence tomography data scarcity: unpaired mutual conversion between scanning presets. Med Biol Eng Comput 2023; 61:1093-1112. [PMID: 36680707 PMCID: PMC10083164 DOI: 10.1007/s11517-022-02742-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 12/09/2022] [Indexed: 01/22/2023]
Abstract
In optical coherence tomography (OCT), there is a trade-off between the scanning time and image quality, leading to a scarcity of high quality data. OCT platforms provide different scanning presets, producing visually distinct images, limiting their compatibility. In this work, a fully automatic methodology for the unpaired visual conversion of the two most prevalent scanning presets is proposed. Using contrastive unpaired translation generative adversarial architectures, low quality images acquired with the faster Macular Cube preset can be converted to the visual style of high visibility Seven Lines scans and vice-versa. This modifies the visual appearance of the OCT images generated by each preset while preserving natural tissue structure. The quality of original and synthetic generated images was compared using BRISQUE. The synthetic generated images achieved very similar scores to original images of their target preset. The generative models were validated in automatic and expert separability tests. These models demonstrated they were able to replicate the genuine look of the original images. This methodology has the potential to create multi-preset datasets with which to train robust computer-aided diagnosis systems by exposing them to the visual features of different presets they may encounter in real clinical scenarios without having to obtain additional data. Graphical Abstract Unpaired mutual conversion between scanning presets. Two generative adversarial models are trained for the conversion of OCT images into images of another scanning preset, replicating the visual features that characterise said preset.
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Affiliation(s)
- Mateo Gende
- Grupo, VARPA, Instituto de Investigación Biomédica de A Coruña (INIBIC), Universidade da Coruña, Xubias de Arriba, 84, A Coruña, 15006, A Coruña, Spain.,Centro de investigación, CITIC, Universidade da Coruña, Campus de Elviña s/n, A Coruña, 15071, A Coruña, Spain
| | - Joaquim de Moura
- Grupo, VARPA, Instituto de Investigación Biomédica de A Coruña (INIBIC), Universidade da Coruña, Xubias de Arriba, 84, A Coruña, 15006, A Coruña, Spain. .,Centro de investigación, CITIC, Universidade da Coruña, Campus de Elviña s/n, A Coruña, 15071, A Coruña, Spain.
| | - Jorge Novo
- Grupo, VARPA, Instituto de Investigación Biomédica de A Coruña (INIBIC), Universidade da Coruña, Xubias de Arriba, 84, A Coruña, 15006, A Coruña, Spain.,Centro de investigación, CITIC, Universidade da Coruña, Campus de Elviña s/n, A Coruña, 15071, A Coruña, Spain
| | - Manuel G Penedo
- Grupo, VARPA, Instituto de Investigación Biomédica de A Coruña (INIBIC), Universidade da Coruña, Xubias de Arriba, 84, A Coruña, 15006, A Coruña, Spain.,Centro de investigación, CITIC, Universidade da Coruña, Campus de Elviña s/n, A Coruña, 15071, A Coruña, Spain
| | - Marcos Ortega
- Grupo, VARPA, Instituto de Investigación Biomédica de A Coruña (INIBIC), Universidade da Coruña, Xubias de Arriba, 84, A Coruña, 15006, A Coruña, Spain.,Centro de investigación, CITIC, Universidade da Coruña, Campus de Elviña s/n, A Coruña, 15071, A Coruña, Spain
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30
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Philippi D, Rothaus K, Castelli M. A vision transformer architecture for the automated segmentation of retinal lesions in spectral domain optical coherence tomography images. Sci Rep 2023; 13:517. [PMID: 36627357 PMCID: PMC9832034 DOI: 10.1038/s41598-023-27616-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 01/04/2023] [Indexed: 01/12/2023] Open
Abstract
Neovascular age-related macular degeneration (nAMD) is one of the major causes of irreversible blindness and is characterized by accumulations of different lesions inside the retina. AMD biomarkers enable experts to grade the AMD and could be used for therapy prognosis and individualized treatment decisions. In particular, intra-retinal fluid (IRF), sub-retinal fluid (SRF), and pigment epithelium detachment (PED) are prominent biomarkers for grading neovascular AMD. Spectral-domain optical coherence tomography (SD-OCT) revolutionized nAMD early diagnosis by providing cross-sectional images of the retina. Automatic segmentation and quantification of IRF, SRF, and PED in SD-OCT images can be extremely useful for clinical decision-making. Despite the excellent performance of convolutional neural network (CNN)-based methods, the task still presents some challenges due to relevant variations in the location, size, shape, and texture of the lesions. This work adopts a transformer-based method to automatically segment retinal lesion from SD-OCT images and qualitatively and quantitatively evaluate its performance against CNN-based methods. The method combines the efficient long-range feature extraction and aggregation capabilities of Vision Transformers with data-efficient training of CNNs. The proposed method was tested on a private dataset containing 3842 2-dimensional SD-OCT retina images, manually labeled by experts of the Franziskus Eye-Center, Muenster. While one of the competitors presents a better performance in terms of Dice score, the proposed method is significantly less computationally expensive. Thus, future research will focus on the proposed network's architecture to increase its segmentation performance while maintaining its computational efficiency.
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Affiliation(s)
- Daniel Philippi
- grid.10772.330000000121511713NOVA Information Management School (NOVA IMS), Universidade Nova de Lisboa, 1070-312 Lisbon, Portugal
| | - Kai Rothaus
- grid.416655.5Department of Ophthalmology, St. Franziskus Hospital, 48145 Muenster, Germany
| | - Mauro Castelli
- NOVA Information Management School (NOVA IMS), Universidade Nova de Lisboa, 1070-312, Lisbon, Portugal. .,School of Economics and Business, University of Ljubljana, Ljubljana, Slovenia.
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31
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Bian H, Wang J, Hong C, Liu L, Ji R, Cao S, Abdalla AN, Chen X. GPU-accelerated image registration algorithm in ophthalmic optical coherence tomography. BIOMEDICAL OPTICS EXPRESS 2023; 14:194-207. [PMID: 36698653 PMCID: PMC9841998 DOI: 10.1364/boe.479343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/28/2022] [Accepted: 11/28/2022] [Indexed: 06/17/2023]
Abstract
Limited to the power of the light source in ophthalmic optical coherence tomography (OCT), the signal-to-noise ratio (SNR) of the reconstructed images is usually lower than OCT used in other fields. As a result, improvement of the SNR is required. The traditional method is averaging several images at the same lateral position. However, the image registration average costs too much time, which limits its real-time imaging application. In response to this problem, graphics processing unit (GPU)-side kernel functions are applied to accelerate the reconstruction of the OCT signals in this paper. The SNR of the images reconstructed from different numbers of A-scans and B-scans were compared. The results demonstrated that: 1) There is no need to realize the axial registration with every A-scan. The number of the A-scans used to realize axial registration is suitable to set as ∼25, when the A-line speed was set as ∼12.5kHz. 2) On the basis of ensuring the quality of the reconstructed images, the GPU can achieve 43× speedup compared with CPU.
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Affiliation(s)
- Haiyi Bian
- Faculty of Electronic Information Engineering, Huaiyin Institute of Technology, Huai’an, Jiangsu, 223003, China
| | - Jingtao Wang
- School of Electronic and Information Engineering, Soochow University, 215006, Suzhou, China
| | - Chengjian Hong
- School of Electronic and Information Engineering, Soochow University, 215006, Suzhou, China
| | - Lei Liu
- Faculty of Electronic Information Engineering, Huaiyin Institute of Technology, Huai’an, Jiangsu, 223003, China
| | - Rendong Ji
- Faculty of Electronic Information Engineering, Huaiyin Institute of Technology, Huai’an, Jiangsu, 223003, China
| | - Suqun Cao
- Faculty of Electronic Information Engineering, Huaiyin Institute of Technology, Huai’an, Jiangsu, 223003, China
| | - Ahmed N. Abdalla
- Faculty of Electronic Information Engineering, Huaiyin Institute of Technology, Huai’an, Jiangsu, 223003, China
| | - Xinjian Chen
- Faculty of Electronic Information Engineering, Huaiyin Institute of Technology, Huai’an, Jiangsu, 223003, China
- School of Electronic and Information Engineering, Soochow University, 215006, Suzhou, China
- State Key Laboratory of Radiation Medicine and Protection, Soochow University, 215123, Suzhou, China
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32
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Li HY, Wang DX, Dong L, Wei WB. Deep learning algorithms for detection of diabetic macular edema in OCT images: A systematic review and meta-analysis. Eur J Ophthalmol 2023; 33:278-290. [PMID: 35473414 DOI: 10.1177/11206721221094786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
PURPOSE Artificial intelligence (AI) can detect diabetic macular edema (DME) from optical coherence tomography (OCT) images. We aimed to evaluate the performance of deep learning neural networks in DME detection. METHODS Embase, Pubmed, the Cochrane Library, and IEEE Xplore were searched up to August 14, 2021. We included studies using deep learning algorithms to detect DME from OCT images. Two reviewers extracted the data independently, and the Quality Assessment of Diagnostic Accuracy Studies-2 (QUADAS-2) tool was applied to assess the risk of bias. The study is reported according to Preferred Reporting Items for a Systematic Review and Meta-analysis of Diagnostic Test Accuracy Studies (PRISMA-DTA). RESULTS Ninteen studies involving 41005 subjects were included. The pooled sensitivity and specificity were 96.0% (95% confidence interval (CI): 93.9% to 97.3%) and 99.3% (95% CI: 98.2% to 99.7%), respectively. Subgroup analyses found that data set selection, sample size of training set and the choice of OCT devices contributed to the heterogeneity (all P < 0.05). While there was no association between the diagnostic accuracy and transfer learning adoption or image management (all P > 0.05). CONCLUSIONS Deep learning methods, particularly the convolutional neural networks (CNNs) could effectively detect clinically significant DME, which can provide referral suggestions to the patients.
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Affiliation(s)
- He-Yan Li
- Beijing Tongren Eye Center, Beijing Key Laboratory of Intraocular Tumor Diagnosis and Treatment, Beijing Ophthalmology & Visual Sciences Key Lab, Medical Artificial Intelligence Research and Verification Key Laboratory of the Ministry of Industry and Information Technology, 117902Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Dai-Xi Wang
- 12517Capital Medical University, Beijing, China
| | - Li Dong
- Beijing Tongren Eye Center, Beijing Key Laboratory of Intraocular Tumor Diagnosis and Treatment, Beijing Ophthalmology & Visual Sciences Key Lab, Medical Artificial Intelligence Research and Verification Key Laboratory of the Ministry of Industry and Information Technology, 117902Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Wen-Bin Wei
- Beijing Tongren Eye Center, Beijing Key Laboratory of Intraocular Tumor Diagnosis and Treatment, Beijing Ophthalmology & Visual Sciences Key Lab, Medical Artificial Intelligence Research and Verification Key Laboratory of the Ministry of Industry and Information Technology, 117902Beijing Tongren Hospital, Capital Medical University, Beijing, China
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33
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Chen H, Gao J. Non-Local Mean Denoising Algorithm Based on Fractional Compact Finite Difference Scheme Effectively Reduces Speckle Noise in Optical Coherence Tomography Images. MICROMACHINES 2022; 13:2039. [PMID: 36557339 PMCID: PMC9781262 DOI: 10.3390/mi13122039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/18/2022] [Accepted: 11/19/2022] [Indexed: 06/17/2023]
Abstract
Optical coherence tomography (OCT) is used in various fields such, as medical diagnosis and material inspection, as a non-invasive and high-resolution optical imaging modality. However, an OCT image is damaged by speckle noise during its generation, thus reducing the image quality. To address this problem, a non-local means (NLM) algorithm based on the fractional compact finite difference scheme (FCFDS) is proposed to remove the speckle noise in OCT images. FCFDS uses more local pixel information when compared to integer-order difference operators. The FCFDS operator is introduced into the NLM algorithm to construct a high-precision weight calculation so that the proposed algorithm can effectively reduce the speckle noise in the OCT images. Experiments on simulations and real OCT images show that the proposed method is comparable to other state-of-the-art despeckling methods and can substantially reduce noise and preserve image details such as edges and structures. Speckle noise removal can further promote the application of the proposed algorithm in medical diagnosis and industrial detection, as it has key research value.
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Affiliation(s)
- Huaiguang Chen
- School of Science, Shandong Jianzhu University, Jinan 250101, China
- Center for Engineering Computation and Software Development, Shandong Jianzhu University, Jinan 250101, China
| | - Jing Gao
- School of Science, Shandong Jianzhu University, Jinan 250101, China
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Wu H, Wang J, Amaya Catano JA, Sun C, Li Z. Optical coherence elastography based on inverse compositional Gauss-Newton digital volume correlation with second-order shape function. OPTICS EXPRESS 2022; 30:41954-41968. [PMID: 36366659 DOI: 10.1364/oe.473898] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
A digital volume correlation (DVC)-based optical coherence elastography (OCE) method with inverse compositional Gauss-Newton (IC-GN) algorithm and second-order shape function is presented in this study. The systematic measurement errors of displacement and strain from our OCE method were less than 0.2 voxel and 4 × 10-4, respectively. Second-order shape function could better match complex deformation and decrease speckle rigidity-induced error. Compared to conventional methods, our OCE method could track a larger strain range up to 0.095 and reduce relative error by 30-50%. This OCE method has the potential to become an effective tool in characterising mechanical properties of biological tissue.
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35
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Chiu KS, Tanifuji M, Sun CW, Rajagopalan UM, Nakamichi Y. Temporal mirror-symmetry in functional signals recorded from rat barrel cortex with optical coherence tomography. Cereb Cortex 2022; 33:4904-4914. [PMID: 36227198 DOI: 10.1093/cercor/bhac388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 08/31/2022] [Accepted: 09/01/2022] [Indexed: 11/14/2022] Open
Abstract
Functional optical coherence tomography (fOCT) detects activity-dependent light scattering changes in micro-structures of neural tissue, drawing attention as in vivo volumetric functional imaging technique at a sub-columnar level. There are 2 plausible origins for the light scattering changes: (i) hemodynamic responses such as changes in blood volume and in density of blood cells and (ii) reorientation of dipoles in cellular membrane. However, it has not been clarified which is the major contributor to fOCT signals. Furthermore, previous studies showed both increase and decrease of reflectivity as fOCT signals, making interpretation more difficult. We proposed combination of fOCT with Fourier imaging and adaptive statistics to the rat barrel cortex. Active voxels revealed barrels elongating throughout layers with mini-columns in superficial layers consistent with physiological studies, suggesting that active voxels revealed by fOCT reflect spatial patterns of activated neurons. These voxels included voxels with negative changes in reflectivity and those with positive changes in reflectivity. However, they were temporally mirror-symmetric, suggesting that they share common sources. It is hard to explain that hemodynamic responses elicit positive signals in some voxels and negative signals in the other. On the other hand, considering membrane dipoles, polarities of OCT signals can be positive and negative depending on orientations of scattering particles relative to the incident light. Therefore, the present study suggests that fOCT signals are induced by the reorientation of membrane dipoles.
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Affiliation(s)
- Kai-Shih Chiu
- Biomedical Optical Imaging Lab., Department of Photonics, College of Electrical and Computer Engineering, National Yang Ming Chiao Tung University, No. 1001, Daxue Rd., 30010, East Dist., Hsinchu, Taiwan, ROC
| | - Manabu Tanifuji
- Department of Life Science and Medical Bioscience, School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, 162-8480, Shinjuku, Tokyo, Japan
| | - Chia-Wei Sun
- Biomedical Optical Imaging Lab., Department of Photonics, College of Electrical and Computer Engineering, National Yang Ming Chiao Tung University, No. 1001, Daxue Rd., 30010, East Dist., Hsinchu, Taiwan, ROC.,Institute of Biomedical Engineering, College of Electrical and Computer Engineering, National Yang Ming Chiao Tung University, No. 1001, Daxue Rd., 30010, East Dist., Hsinchu, Taiwan, ROC.,Medical Device Innovation and Translation Center, National Yang Ming Chiao Tung University, No. 155, Sec. 2, Linong St., 112304, Beitou Dist., Taipei, Taiwan, ROC
| | - Uma Maheswari Rajagopalan
- Department of Mechanical Engineering, Shibaura Institute of Technology, 3-7-5 Toyosu, 135-8548, Koto City, Tokyo, Japan
| | - Yu Nakamichi
- Department of Mechanical Engineering, Faculty of Engineering, Sanyo-Onoda City University, 1-1-1 Daigaku-dori, 756-0884, Sanyo-Onoda, Yamaguchi, Japan
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36
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Bayhaqi YA, Hamidi A, Canbaz F, Navarini AA, Cattin PC, Zam A. Deep-Learning-Based Fast Optical Coherence Tomography (OCT) Image Denoising for Smart Laser Osteotomy. IEEE TRANSACTIONS ON MEDICAL IMAGING 2022; 41:2615-2628. [PMID: 35442883 DOI: 10.1109/tmi.2022.3168793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Laser osteotomy promises precise cutting and minor bone tissue damage. We proposed Optical Coherence Tomography (OCT) to monitor the ablation process toward our smart laser osteotomy approach. The OCT image is helpful to identify tissue type and provide feedback for the ablation laser to avoid critical tissues such as bone marrow and nerve. Furthermore, in the implementation, the tissue classifier's accuracy is dependent on the quality of the OCT image. Therefore, image denoising plays an important role in having an accurate feedback system. A common OCT image denoising technique is the frame-averaging method. Inherent to this method is the need for multiple images, i.e., the more images used, the better the resulting image quality. However, this approach comes at the price of increased acquisition time and sensitivity to motion artifacts. To overcome these limitations, we applied a deep-learning denoising method capable of imitating the frame-averaging method. The resulting image had a similar image quality to the frame-averaging and was better than the classical digital filtering methods. We also evaluated if this method affects the tissue classifier model's accuracy that will provide feedback to the ablation laser. We found that image denoising significantly increased the accuracy of the tissue classifier. Furthermore, we observed that the classifier trained using the deep learning denoised images achieved similar accuracy to the classifier trained using frame-averaged images. The results suggest the possibility of using the deep learning method as a pre-processing step for real-time tissue classification in smart laser osteotomy.
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37
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Demonstration of speckle resistance using space-time light sheets. Sci Rep 2022; 12:14064. [PMID: 35982074 PMCID: PMC9388688 DOI: 10.1038/s41598-022-18153-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 08/05/2022] [Indexed: 11/08/2022] Open
Abstract
The capacity of self-healing fields to reconstruct after passing through scattering media may prove useful in reducing speckle formation. Here, we study the speckle response of the space-time (ST) light sheet compared to a Gaussian wave packet, Airy beam, and Bessel Gauss beam. We find that the Pearson's correlation coefficient for the ST light sheet is 50%, 48% and 40% larger than that of the Gaussian, Airy beam and Bessel Gauss beams, respectively, demonstrating a strong correlation to an input beam that has not been speckled. These results suggest that the ST light sheet exhibits considerable resistance to speckle generation. We also investigate the speckle response of the ST light sheet at its second-harmonic frequency and observe a mean Pearson's correlation coefficient close to 0.6, comparable to the second-harmonic Bessel Gauss beam, and 2.8 × the value obtained for the second-harmonic Gaussian beam. Our results lend themselves to a variety of applications including bioimaging, communications, and optical tweezers.
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38
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Varadarajan D, Magnain C, Fogarty M, Boas DA, Fischl B, Wang H. A novel algorithm for multiplicative speckle noise reduction in ex vivo human brain OCT images. Neuroimage 2022; 257:119304. [PMID: 35568350 PMCID: PMC10018743 DOI: 10.1016/j.neuroimage.2022.119304] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 05/06/2022] [Accepted: 05/10/2022] [Indexed: 10/18/2022] Open
Abstract
Optical coherence tomography (OCT) images of ex vivo human brain tissue are corrupted by multiplicative speckle noise that degrades the contrast to noise ratio (CNR) of microstructural compartments. This work proposes a novel algorithm to reduce noise corruption in OCT images that minimizes the penalized negative log likelihood of gamma distributed speckle noise. The proposed method is formulated as a majorize-minimize problem that reduces to solving an iterative regularized least squares optimization. We demonstrate the usefulness of the proposed method by removing speckle in simulated data, phantom data and real OCT images of human brain tissue. We compare the proposed method with state of the art filtering and non-local means based denoising methods. We demonstrate that our approach removes speckle accurately, improves CNR between different tissue types and better preserves small features and edges in human brain tissue.
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Affiliation(s)
- Divya Varadarajan
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA 02129, USA; Radiology, Harvard Medical School, Boston, MA 02115, USA.
| | - Caroline Magnain
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA 02129, USA; Radiology, Harvard Medical School, Boston, MA 02115, USA
| | - Morgan Fogarty
- Imaging Science Program, Washington University McKelvey School of Engineering, St. Louis, MO 63130, USA; Radiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - David A Boas
- Biomedical Engineering and Electrical and Computer Engineering, Boston University, Boston, MA 02215, USA
| | - Bruce Fischl
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA 02129, USA; Radiology, Harvard Medical School, Boston, MA 02115, USA; Harvard-MIT Health Science and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Hui Wang
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA 02129, USA; Radiology, Harvard Medical School, Boston, MA 02115, USA
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39
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Noise Reduction of OCT Images Based on the External Patch Prior Guided Internal Clustering and Morphological Analysis. PHOTONICS 2022. [DOI: 10.3390/photonics9080543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Optical coherence tomography (OCT) is widely used in biomedical imaging. However, noise severely affects diagnosing and identifying diseased tissues on OCT images. Here, a noise reduction method based on the external patch prior guided internal clustering and morphological analysis (E2PGICMA) is developed to remove the noise of OCT images. The external patch prior guided internal clustering algorithm is used to reduce speckle noise. The morphological analysis algorithm is employed to the background for contrast enhancement. OCT images of in vivo normal skin tissues were analyzed to remove noise using the proposed method. The estimated standard deviations of the noise were chosen as different values for evaluating the quantitative metrics. The visual quality improvement includes more textures and fine detail preservation. The denoising effects of different methods were compared. Then, quantitative and qualitative evaluations of this proposed method were conducted. The results demonstrated that the SNR, PSNR, and XCOR were higher than those of the other noise-reduction methods, reaching 15.05 dB, 27.48 dB, and 0.9959, respectively. Furthermore, the presented method’s noise reduction ratio (NRR) reached 0.8999. This proposed method can efficiently remove the background and speckle noise. Improving the proposed noise reduction method would outperform existing state-of-the-art OCT despeckling methods.
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40
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Ibrahim MN, Bashar SB, Rasheed MA, Selvam A, Sant V, Sahel JA, Chhablani J, Vupparaboina KK, Jana S. Volumetric quantification of choroid and Haller's sublayer using OCT scans: An accurate and unified approach based on stratified smoothing. Comput Med Imaging Graph 2022; 99:102086. [PMID: 35717830 DOI: 10.1016/j.compmedimag.2022.102086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 05/10/2022] [Accepted: 05/31/2022] [Indexed: 11/23/2022]
Abstract
BACKGROUND AND OBJECTIVE The choroid, a dense vascular structure in the posterior segment of the eye, maintains the health of the retina by supplying oxygen and nutrients, and assumes clinical significance in screening ocular diseases including age-related macular degeneration (AMD) and central serous chorioretinopathy (CSCR). As a technological assist, algorithmic estimation of choroidal biomarkers has been suggested based on sectional (B-scan) optical coherence tomography (OCT) images. However, most such 2D estimation techniques are compute-intensive, yet enjoy limited accuracy and have only been validated on OCT image datasets of healthy eyes. Not surprisingly, fine-scale analyses, including those involving Haller's sublayer, remain relatively rare and unsophisticated. Against this backdrop, we propose an efficient algorithm to quantify desired biomarkers with improved accuracy based on volume OCT scans. Specifically, we attempted an accurate, computationally light volumetric segmentation method involving stratified smoothing to detect choroid and Haller's sublayer. METHODS For detecting the various boundaries of the choroid and the Haller's sublayer, we propose a common volumetric method that performs suitable exponential enhancement and maintains smooth spatial continuity across 2D B-scans. Further, we achieve suitable volumetric smoothing by primarily deploying light-duty linear regression, and sparingly using compute-intensive tensor voting, and hence significantly reduce overall complexity. The proposed methodology is tested on five health and five diseased OCT volumes considering various metrics including volumetric Dice coefficient and corresponding quotient measures to facilitate comparison vis-à-vis intra-observer repeatability. RESULTS On five healthy and five diseased OCT volumes, respectively, the proposed method for choroid segmentation recorded volumetric Dice coefficients of 93.53 % and 93.30 %, which closely approximate the respective reference observer repeatability values of 95.60 % and 95.49 %. In terms of related quotient measures, our method achieved more than 50 % improvement over a recently reported method. In detecting Haller's sublayer as well, our algorithm records statistical performance closely matching that of reference manual method. CONCLUSION Advancing the state-of-the-art, the proposed volumetric segmentation, tested on both healthy and diseased datasets, demonstrated close match with the manual reference. Our method assumes significance in accurate screening of chorioretinal diseases including AMD, CSCR and pachychoroid. Further, it enables generating accurate training data for developing deep learning models for improved detection of choroid and Haller's sublayer.
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Affiliation(s)
- M N Ibrahim
- Dept. of Electrical Engg, Indian Institute of Technology Hyderabad, Telangana, India; Dept. of Ophthalmology, University of Pittsburgh, Pittsburgh, PA, USA
| | - S Bin Bashar
- L. V. Prasad Eye Institute, Hyderabad, Telangana, India
| | - M A Rasheed
- School of Optometry and Vision Science, University of Waterloo, Ontario, Canada
| | - A Selvam
- School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - V Sant
- Fox Chapel Area High School, Pittsburgh, PA, USA
| | - J A Sahel
- Dept. of Ophthalmology, University of Pittsburgh, Pittsburgh, PA, USA
| | - J Chhablani
- Dept. of Ophthalmology, University of Pittsburgh, Pittsburgh, PA, USA
| | - K K Vupparaboina
- Dept. of Ophthalmology, University of Pittsburgh, Pittsburgh, PA, USA.
| | - S Jana
- Dept. of Electrical Engg, Indian Institute of Technology Hyderabad, Telangana, India
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41
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Automatic choroid layer segmentation in OCT images via context efficient adaptive network. APPL INTELL 2022. [DOI: 10.1007/s10489-022-03723-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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42
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Wen H, Zhao J, Xiang S, Lin L, Liu C, Wang T, An L, Liang L, Huang B. Towards more efficient ophthalmic disease classification and lesion location via convolution transformer. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2022; 220:106832. [PMID: 35525213 DOI: 10.1016/j.cmpb.2022.106832] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 04/01/2022] [Accepted: 04/21/2022] [Indexed: 06/14/2023]
Abstract
OBJECTIVE A retina optical coherence tomography (OCT) image differs from a traditional image due to its significant speckle noise, irregularity, and inconspicuous features. A conventional deep learning architecture cannot effectively improve the classification accuracy, sensitivity, and specificity of OCT images, and noisy images are not conducive to further diagnosis. This paper proposes a novel lesion-localization convolution transformer (LLCT) method, which combines both convolution and self-attention to classify ophthalmic diseases more accurately and localize the lesions in retina OCT images. METHODS A novel architecture design is accomplished through applying customized feature maps generated by convolutional neutral network (CNN) as the input sequence of self-attention network. This design takes advantages of CNN's extracting image features and transformer's consideration of global context and dynamic attention. Part of the model is backward propagated to calculate the gradient as a weight parameter, which is multiplied and summed with the global features generated by the forward propagation process to locate the lesion. RESULTS Extensive experiments show that our proposed design achieves improvement of about 7.6% in overall accuracy, 10.9% in overall sensitivity, and 9.2% in overall specificity compared with previous methods. And the lesions can be localized without the labeling data of lesion location in OCT images. CONCLUSION The results prove that our method significantly improves the performance and reduces the computation complexity in artificial intelligence assisted analysis of ophthalmic disease through OCT images. SIGNIFICANCE Our method has a significance boost in ophthalmic disease classification and location via convolution transformer. This is applicable to assist ophthalmologists greatly.1.
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Affiliation(s)
- Huajie Wen
- College of Big Data and Internet, Shenzhen Technology University, Shenzhen 518118, China; College of Applied Science, Shenzhen University, Shenzhen 518060, China
| | - Jian Zhao
- College of Big Data and Internet, Shenzhen Technology University, Shenzhen 518118, China
| | - Shaohua Xiang
- College of Big Data and Internet, Shenzhen Technology University, Shenzhen 518118, China
| | - Lin Lin
- College of Big Data and Internet, Shenzhen Technology University, Shenzhen 518118, China
| | - Chengjian Liu
- College of Big Data and Internet, Shenzhen Technology University, Shenzhen 518118, China
| | - Tao Wang
- College of Big Data and Internet, Shenzhen Technology University, Shenzhen 518118, China
| | - Lin An
- Guangdong Vision Medical Science & Technology Co., Ltd. Foshan 528000, China
| | - Lixin Liang
- College of Big Data and Internet, Shenzhen Technology University, Shenzhen 518118, China.
| | - Bingding Huang
- College of Big Data and Internet, Shenzhen Technology University, Shenzhen 518118, China.
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43
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Zhou Q, Wen M, Ding M, Zhang X. Unsupervised despeckling of optical coherence tomography images by combining cross-scale CNN with an intra-patch and inter-patch based transformer. OPTICS EXPRESS 2022; 30:18800-18820. [PMID: 36221673 DOI: 10.1364/oe.459477] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 05/03/2022] [Indexed: 06/16/2023]
Abstract
Optical coherence tomography (OCT) has found wide application to the diagnosis of ophthalmic diseases, but the quality of OCT images is degraded by speckle noise. The convolutional neural network (CNN) based methods have attracted much attention in OCT image despeckling. However, these methods generally need noisy-clean image pairs for training and they are difficult to capture the global context information effectively. To address these issues, we have proposed a novel unsupervised despeckling method. This method uses the cross-scale CNN to extract the local features and uses the intra-patch and inter-patch based transformer to extract and merge the local and global feature information. Based on these extracted features, a reconstruction network is used to produce the final denoised result. The proposed network is trained using a hybrid unsupervised loss function, which is defined by the loss produced from Nerighbor2Neighbor, the structural similarity between the despeckled results of the probabilistic non-local means method and our method as well as the mean squared error between their features extracted by the VGG network. Experiments on two clinical OCT image datasets show that our method performs better than several popular despeckling algorithms in terms of visual evaluation and quantitative indexes.
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44
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Ni G, Wu R, Zhong J, Chen Y, Wan L, Xie Y, Mei J, Liu Y. Hybrid-structure network and network comparative study for deep-learning-based speckle-modulating optical coherence tomography. OPTICS EXPRESS 2022; 30:18919-18938. [PMID: 36221682 DOI: 10.1364/oe.454504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 04/26/2022] [Indexed: 06/16/2023]
Abstract
Optical coherence tomography (OCT), a promising noninvasive bioimaging technique, can resolve sample three-dimensional microstructures. However, speckle noise imposes obvious limitations on OCT resolving capabilities. Here we proposed a deep-learning-based speckle-modulating OCT based on a hybrid-structure network, residual-dense-block U-Net generative adversarial network (RDBU-Net GAN), and further conducted a comprehensively comparative study to explore multi-type deep-learning architectures' abilities to extract speckle pattern characteristics and remove speckle, and resolve microstructures. This is the first time that network comparative study has been performed on a customized dataset containing mass more-general speckle patterns obtained from a custom-built speckle-modulating OCT, but not on retinal OCT datasets with limited speckle patterns. Results demonstrated that the proposed RDBU-Net GAN has a more excellent ability to extract speckle pattern characteristics and remove speckle, and resolve microstructures. This work will be useful for future studies on OCT speckle removing and deep-learning-based speckle-modulating OCT.
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45
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Ni G, Wu R, Zhong J, Liu Y. Depth-resolved transverse-plane motion tracking with configurable measurement features via optical coherence tomography. OPTICS EXPRESS 2022; 30:12215-12227. [PMID: 35472861 DOI: 10.1364/oe.450590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 02/21/2022] [Indexed: 06/14/2023]
Abstract
Optical coherence tomography (OCT), a promising noninvasive bioimaging technique, has become one of the most successful optical technologies implemented in medicine and clinical practice. Here we report a novel technique of depth-resolved transverse-plane motion tracking with configurable measurement features via optical coherence tomography, termed OCT-MT. Based on OCT circular scanning combined with speckle spatial oversampling, the OCT-MT technique can perform depth-resolved transverse-plane motion tracking. Benefitting from the optical interference and depth-resolved feature, the proposed OCT-MT can reduce the requirements on the input power of the irradiation signal and the surface reflectivity and roughness of the target, when performing motion tracking. Furthermore, OCT-MT can conduct such kind of motion tracking with configurable measurement ranges and resolutions by configuring A-line number per scanning circle, circular scanning radius, and A-line scanning time. The proposed OCT-MT technique may expand the ability of motion tracking for OCT in addition to imaging.
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Choi Y, Kim M, Park C, Park J, Park Y, Cho YH. Wide-Field Super-Resolution Optical Fluctuation Imaging through Dynamic Near-Field Speckle Illumination. NANO LETTERS 2022; 22:2194-2201. [PMID: 35240776 PMCID: PMC8949730 DOI: 10.1021/acs.nanolett.1c03691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 02/18/2022] [Indexed: 06/14/2023]
Abstract
Stochastic optical fluctuation imaging (SOFI) generates super-resolution fluorescence images by emphasizing the positions of fluorescent emitters via statistical analysis of their on-and-off blinking dynamics. In SOFI with speckle illumination (S-SOFI), the diffraction-limited grain size of the far-field speckles prevents independent blinking of closely located emitters, becoming a hurdle to realize the full super-resolution granted by SOFI processing. Here, we present a surface-sensitive super-resolution technique exploiting dynamic near-field speckle illumination to bring forth the full super-resolving power of SOFI without blinking fluorophores. With our near-field S-SOFI technique, up to 2.8- and 2.3-fold enhancements in lateral spatial resolution are demonstrated with computational and experimental fluorescent test targets labeled with conventional fluorophores, respectively. Fluorescent beads separated by 175 nm are also super-resolved by near-field speckles of 150 nm grain size, promising sub-100 nm resolution with speckle patterns of much smaller grain size.
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Affiliation(s)
- Young Choi
- Department
of Physics, Korea Advanced Institute of
Science and Technology (KAIST), Daejeon 34141, Republic
of Korea
| | - MinKwan Kim
- Department
of Physics, Korea Advanced Institute of
Science and Technology (KAIST), Daejeon 34141, Republic
of Korea
- Graduate
School of Nanoscience and Technology, KAIST, Daejeon 34141, Republic of Korea
| | - ChungHyun Park
- Department
of Physics, Korea Advanced Institute of
Science and Technology (KAIST), Daejeon 34141, Republic
of Korea
- KAIST
Institute for the NanoCentury, KAIST, Daejeon 34141, Republic of Korea
| | - Jongchan Park
- Department
of Physics, Korea Advanced Institute of
Science and Technology (KAIST), Daejeon 34141, Republic
of Korea
| | - YongKeun Park
- Department
of Physics, Korea Advanced Institute of
Science and Technology (KAIST), Daejeon 34141, Republic
of Korea
- KAIST, Institute for Health Science and Technology, Daejeon 34141, Republic of Korea
- Tomocube,
Inc., Daejeon 34051, Republic of Korea
| | - Yong-Hoon Cho
- Department
of Physics, Korea Advanced Institute of
Science and Technology (KAIST), Daejeon 34141, Republic
of Korea
- KAIST
Institute for the NanoCentury, KAIST, Daejeon 34141, Republic of Korea
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47
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Harper DJ, Vakoc BJ. Relationship between axial resolution and signal-to-noise ratio in optical coherence tomography. OPTICS LETTERS 2022; 47:1517-1520. [PMID: 35290353 PMCID: PMC8958905 DOI: 10.1364/ol.449421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 02/15/2022] [Indexed: 06/14/2023]
Abstract
In optical coherence tomography (OCT), axial resolution and signal-to-noise ratio (SNR) are typically viewed as uncoupled parameters. We show that this is true only for mirror-like surfaces and that in diffuse scattering samples such as biological tissues there is an inherent coupling between axial resolution and measurement SNR. We explain the origin of this coupling and demonstrate that it can be used to achieve increased imaging penetration depth at the expense of resolution. Finally, we argue that this coupling should be considered during OCT system design processes that seek to balance the competing needs of resolution, sensitivity, and system/source complexity.
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Affiliation(s)
- Danielle J. Harper
- Wellman Center for Photomedicine, Massachusetts General Hospital, 40 Blossom Street, Boston, MA 02114, USA
- Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA
| | - Benjamin J. Vakoc
- Wellman Center for Photomedicine, Massachusetts General Hospital, 40 Blossom Street, Boston, MA 02114, USA
- Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA
- Harvard-MIT Division of Health Sciences and Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
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48
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Rico-Jimenez JJ, Hu D, Tang EM, Oguz I, Tao YK. Real-time OCT image denoising using a self-fusion neural network. BIOMEDICAL OPTICS EXPRESS 2022; 13:1398-1409. [PMID: 35415003 PMCID: PMC8973187 DOI: 10.1364/boe.451029] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/20/2022] [Accepted: 02/06/2022] [Indexed: 06/07/2023]
Abstract
Optical coherence tomography (OCT) has become the gold standard for ophthalmic diagnostic imaging. However, clinical OCT image-quality is highly variable and limited visualization can introduce errors in the quantitative analysis of anatomic and pathologic features-of-interest. Frame-averaging is a standard method for improving image-quality, however, frame-averaging in the presence of bulk-motion can degrade lateral resolution and prolongs total acquisition time. We recently introduced a method called self-fusion, which reduces speckle noise and enhances OCT signal-to-noise ratio (SNR) by using similarity between from adjacent frames and is more robust to motion-artifacts than frame-averaging. However, since self-fusion is based on deformable registration, it is computationally expensive. In this study a convolutional neural network was implemented to offset the computational overhead of self-fusion and perform OCT denoising in real-time. The self-fusion network was pretrained to fuse 3 frames to achieve near video-rate frame-rates. Our results showed a clear gain in peak SNR in the self-fused images over both the raw and frame-averaged OCT B-scans. This approach delivers a fast and robust OCT denoising alternative to frame-averaging without the need for repeated image acquisition. Real-time self-fusion image enhancement will enable improved localization of OCT field-of-view relative to features-of-interest and improved sensitivity for anatomic features of disease.
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Affiliation(s)
- Jose J. Rico-Jimenez
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN 37232, USA
| | - Dewei Hu
- Department of Electrical Engineering and Computer Science, Vanderbilt University, Nashville, TN 37235 USA, USA
| | - Eric M. Tang
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN 37232, USA
| | - Ipek Oguz
- Department of Electrical Engineering and Computer Science, Vanderbilt University, Nashville, TN 37235 USA, USA
| | - Yuankai K. Tao
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN 37232, USA
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Silva VB, Andrade De Jesus D, Klein S, van Walsum T, Cardoso J, Brea LS, Vaz PG. Signal-carrying speckle in optical coherence tomography: a methodological review on biomedical applications. JOURNAL OF BIOMEDICAL OPTICS 2022; 27:030901. [PMID: 35289154 PMCID: PMC8919025 DOI: 10.1117/1.jbo.27.3.030901] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 02/22/2022] [Indexed: 06/14/2023]
Abstract
SIGNIFICANCE Speckle has historically been considered a source of noise in coherent light imaging. However, a number of works in optical coherence tomography (OCT) imaging have shown that speckle patterns may contain relevant information regarding subresolution and structural properties of the tissues from which it is originated. AIM The objective of this work is to provide a comprehensive overview of the methods developed for retrieving speckle information in biomedical OCT applications. APPROACH PubMed and Scopus databases were used to perform a systematic review on studies published until December 9, 2021. From 146 screened studies, 40 were eligible for this review. RESULTS The studies were clustered according to the nature of their analysis, namely static or dynamic, and all features were described and analyzed. The results show that features retrieved from speckle can be used successfully in different applications, such as classification and segmentation. However, the results also show that speckle analysis is highly application-dependant, and the best approach varies between applications. CONCLUSIONS Several of the reviewed analyses were only performed in a theoretical context or using phantoms, showing that signal-carrying speckle analysis in OCT imaging is still in its early stage, and further work is needed to validate its applicability and reproducibility in a clinical context.
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Affiliation(s)
- Vania B. Silva
- University of Coimbra, Laboratory for Instrumentation, Biomedical Engineering and Radiation Physics (LIBPhys-UC), Department of Physics, Coimbra, Portugal
- University Medical Center Rotterdam, Department of Radiology and Nuclear Medicine, Erasmus MC, Biomedical Imaging Group Rotterdam, Rotterdam, The Netherlands
| | - Danilo Andrade De Jesus
- University Medical Center Rotterdam, Department of Radiology and Nuclear Medicine, Erasmus MC, Biomedical Imaging Group Rotterdam, Rotterdam, The Netherlands
| | - Stefan Klein
- University Medical Center Rotterdam, Department of Radiology and Nuclear Medicine, Erasmus MC, Biomedical Imaging Group Rotterdam, Rotterdam, The Netherlands
| | - Theo van Walsum
- University Medical Center Rotterdam, Department of Radiology and Nuclear Medicine, Erasmus MC, Biomedical Imaging Group Rotterdam, Rotterdam, The Netherlands
| | - João Cardoso
- University of Coimbra, Laboratory for Instrumentation, Biomedical Engineering and Radiation Physics (LIBPhys-UC), Department of Physics, Coimbra, Portugal
| | - Luisa Sánchez Brea
- University Medical Center Rotterdam, Department of Radiology and Nuclear Medicine, Erasmus MC, Biomedical Imaging Group Rotterdam, Rotterdam, The Netherlands
| | - Pedro G. Vaz
- University of Coimbra, Laboratory for Instrumentation, Biomedical Engineering and Radiation Physics (LIBPhys-UC), Department of Physics, Coimbra, Portugal
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Pahlevaninezhad M, Huang YW, Pahlevani M, Bouma B, Suter MJ, Capasso F, Pahlevaninezhad H. Metasurface-based bijective illumination collection imaging provides high-resolution tomography in three dimensions. NATURE PHOTONICS 2022; 16:203-211. [PMID: 35937091 PMCID: PMC9355264 DOI: 10.1038/s41566-022-00956-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 01/10/2022] [Indexed: 06/08/2023]
Abstract
Microscopic imaging in three dimensions enables numerous biological and clinical applications. However, high-resolution optical imaging preserved in a relatively large depth range is hampered by the rapid spread of tightly confined light due to diffraction. Here, we show that a particular disposition of light illumination and collection paths liberates optical imaging from the restrictions imposed by diffraction. This arrangement, realized by metasurfaces, decouples lateral resolution from depth-of-focus by establishing a one-to-one correspondence (bijection) along a focal line between the incident and collected light. Implementing this approach in optical coherence tomography, we demonstrate tissue imaging at 1.3 μm wavelength with ~ 3.2 μm lateral resolution, maintained nearly intact over 1.25 mm depth-of-focus, with no additional acquisition or computation burden. This method, termed bijective illumination collection imaging, is general and might be adapted across various existing imaging modalities.
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Affiliation(s)
- Masoud Pahlevaninezhad
- Harvard Medical School and Massachusetts General Hospital, Boston, MA, USA
- Department of Electrical and Computer Engineering, Queen’s University, Kingston, Ontario, Canada
- Department of Mechanical and Materials Engineering, Queen’s University, Kingston, Ontario, Canada
| | - Yao-Wei Huang
- Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
| | - Majid Pahlevani
- Department of Electrical and Computer Engineering, Queen’s University, Kingston, Ontario, Canada
| | - Brett Bouma
- Harvard Medical School and Massachusetts General Hospital, Boston, MA, USA
- Harvard-MIT Health Science and Technology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Melissa J. Suter
- Harvard Medical School and Massachusetts General Hospital, Boston, MA, USA
| | - Federico Capasso
- Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
| | - Hamid Pahlevaninezhad
- Harvard Medical School and Massachusetts General Hospital, Boston, MA, USA
- Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
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