scholarly journals Real-time noise reduction based on ground truth free deep learning for optical coherence tomography

2021 ◽  
Vol 12 (4) ◽  
pp. 2027
Author(s):  
Yong Huang ◽  
Nan Zhang ◽  
Qun Hao
Keyword(s):  
Optical Coherence Tomography ◽  
Deep Learning ◽  
Noise Reduction ◽  
Real Time ◽  
Ground Truth ◽  
Optical Coherence

743Combining deep learning method with optical coherence tomography for ablation lesion assessment

EP Europace ◽  
2020 ◽  
Vol 22 (Supplement_1) ◽  
Author(s):  
D Liang ◽  
A Haeberlin
Keyword(s):  
Neural Network ◽  
Optical Coherence Tomography ◽  
Deep Learning ◽  
Convolutional Neural Network ◽  
Medical Image Analysis ◽  
Ground Truth ◽  
Optical Coherence ◽  
Learning Method ◽  
Ablation Lesion ◽  
Learning Methods

Abstract Background The immediate effect of radiofrequency catheter ablation (RFA) on the tissue is not directly visualized. Optical coherence tomography (OCT) is an imaging technique that uses light to capture histology-like images with a penetration depth of 1-3 mm in the cardiac tissue. There are two specific features of ablation lesions in the OCT images: the disappearance of birefringence artifacts in the lateral and sudden decrease of signal at the bottom (Figure panel A and D). These features can not only be used to recognize the ablation lesions from the OCT images by eye, but also be used to train a machine learning model for automatic lesion segmentation. In recent years, deep learning methods, e.g. convolutional neural networks, have been used in medical image analysis and greatly increased the accuracy of image segmentation. We hypothesize that using a convolutional neural network, e.g. U-Net, can locate and segment the ablation lesions in the OCT images. Purpose To investigate whether a deep learning method such as a convolutional neural network optimized for biomedical image processing, could be used to segment ablation lesions in OCT images automatically. Method 8 OCT datasets with ablation lesions were used for training the convolutional neural network (U-Net model). After training, the model was validated by two new OCT datasets. Dice coefficients were calculated to evaluate spatial overlap between the predictions and the ground truth segmentations, which were manually segmented by the researchers (its value ranges from 0 to 1, and "1" means perfect segmentation). Results The U-Net model could predict the central parts of lesions automatically and accurately (Dice coefficients are 0.933 and 0.934), compared with the ground truth segmentations (Figure panel B and E). These predictions could reveal the depths and diameters of the ablation lesions correctly (Figure panel C and F). Conclusions  Our results showed that deep learning could facilitate ablation lesion identification and segmentation in OCT images. Deep learning methods, integrated in an OCT system, might enable automatic and precise ablation lesion visualization, which may help to assess ablation lesions during radiofrequency ablation procedures with great precision. Figure legend Panel A and D: the central OCT images of the ablation lesions. The blue arrows indicate the lesion bottom, where the image intensity suddenly decreases. The white arrows indicate the birefringence artifacts (the black bands in the grey regions). Panel B and E: the ground true segmentations of lesions in panel A and D. Panel C and F: the predictions by U-Net model of the lesions in panel A and D. A scale bar representing 500 μm is shown in each panel. Abstract Figure

scholarly journals Generation of Augmented Capillary Network Optical Coherence Tomography Image Data of Human Skin for Deep Learning and Capillary Segmentation

Diagnostics ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 685
Author(s):  
Bitewulign Kassa Mekonnen ◽  
Tung-Han Hsieh ◽  
Dian-Fu Tsai ◽  
Shien-Kuei Liaw ◽  
Fu-Liang Yang ◽  
...  
Keyword(s):  
Optical Coherence Tomography ◽  
Deep Learning ◽  
Human Skin ◽  
Gaussian Function ◽  
Image Data ◽  
Ground Truth ◽  
Medical Image Segmentation ◽  
Optical Coherence Tomography Image ◽  
Optical Coherence ◽  
Capillary Networks

The segmentation of capillaries in human skin in full-field optical coherence tomography (FF-OCT) images plays a vital role in clinical applications. Recent advances in deep learning techniques have demonstrated a state-of-the-art level of accuracy for the task of automatic medical image segmentation. However, a gigantic amount of annotated data is required for the successful training of deep learning models, which demands a great deal of effort and is costly. To overcome this fundamental problem, an automatic simulation algorithm to generate OCT-like skin image data with augmented capillary networks (ACNs) in a three-dimensional volume (which we called the ACN data) is presented. This algorithm simultaneously acquires augmented FF-OCT and corresponding ground truth images of capillary structures, in which potential functions are introduced to conduct the capillary pathways, and the two-dimensional Gaussian function is utilized to mimic the brightness reflected by capillary blood flow seen in real OCT data. To assess the quality of the ACN data, a U-Net deep learning model was trained by the ACN data and then tested on real in vivo FF-OCT human skin images for capillary segmentation. With properly designed data binarization for predicted image frames, the testing result of real FF-OCT data with respect to the ground truth achieved high scores in performance metrics. This demonstrates that the proposed algorithm is capable of generating ACN data that can imitate real FF-OCT skin images of capillary networks for use in research and deep learning, and that the model for capillary segmentation could be of wide benefit in clinical and biomedical applications.

scholarly journals Development and validation of a deep learning system to screen vision-threatening conditions in high myopia using optical coherence tomography images

2020 ◽  
pp. bjophthalmol-2020-317825
Author(s):  
Yonghao Li ◽  
Weibo Feng ◽  
Xiujuan Zhao ◽  
Bingqian Liu ◽  
Yan Zhang ◽  
...  
Keyword(s):  
Optical Coherence Tomography ◽  
Deep Learning ◽  
High Myopia ◽  
Large Scale ◽  
Learning System ◽  
Youden Index ◽  
Optical Coherence ◽  
Test Dataset ◽  
Independent Test ◽  
Independent Test Dataset

Background/aimsTo apply deep learning technology to develop an artificial intelligence (AI) system that can identify vision-threatening conditions in high myopia patients based on optical coherence tomography (OCT) macular images.MethodsIn this cross-sectional, prospective study, a total of 5505 qualified OCT macular images obtained from 1048 high myopia patients admitted to Zhongshan Ophthalmic Centre (ZOC) from 2012 to 2017 were selected for the development of the AI system. The independent test dataset included 412 images obtained from 91 high myopia patients recruited at ZOC from January 2019 to May 2019. We adopted the InceptionResnetV2 architecture to train four independent convolutional neural network (CNN) models to identify the following four vision-threatening conditions in high myopia: retinoschisis, macular hole, retinal detachment and pathological myopic choroidal neovascularisation. Focal Loss was used to address class imbalance, and optimal operating thresholds were determined according to the Youden Index.ResultsIn the independent test dataset, the areas under the receiver operating characteristic curves were high for all conditions (0.961 to 0.999). Our AI system achieved sensitivities equal to or even better than those of retina specialists as well as high specificities (greater than 90%). Moreover, our AI system provided a transparent and interpretable diagnosis with heatmaps.ConclusionsWe used OCT macular images for the development of CNN models to identify vision-threatening conditions in high myopia patients. Our models achieved reliable sensitivities and high specificities, comparable to those of retina specialists and may be applied for large-scale high myopia screening and patient follow-up.

scholarly journals Automatic Segmentation of Choroid Layer Using Deep Learning on Spectral Domain Optical Coherence Tomography

2021 ◽  
Vol 11 (12) ◽  
pp. 5488
Author(s):  
Wei Ping Hsia ◽  
Siu Lun Tse ◽  
Chia Jen Chang ◽  
Yu Len Huang
Keyword(s):  
Optical Coherence Tomography ◽  
Deep Learning ◽  
Choroidal Thickness ◽  
Automatic Segmentation ◽  
Average Error ◽  
Good Prediction ◽  
Optical Coherence ◽  
Learning Method ◽  
Subfoveal Choroidal Thickness ◽  
Fully Connected

The purpose of this article is to evaluate the accuracy of the optical coherence tomography (OCT) measurement of choroidal thickness in healthy eyes using a deep-learning method with the Mask R-CNN model. Thirty EDI-OCT of thirty patients were enrolled. A mask region-based convolutional neural network (Mask R-CNN) model composed of deep residual network (ResNet) and feature pyramid networks (FPNs) with standard convolution and fully connected heads for mask and box prediction, respectively, was used to automatically depict the choroid layer. The average choroidal thickness and subfoveal choroidal thickness were measured. The results of this study showed that ResNet 50 layers deep (R50) model and ResNet 101 layers deep (R101). R101 U R50 (OR model) demonstrated the best accuracy with an average error of 4.85 pixels and 4.86 pixels, respectively. The R101 ∩ R50 (AND model) took the least time with an average execution time of 4.6 s. Mask-RCNN models showed a good prediction rate of choroidal layer with accuracy rates of 90% and 89.9% for average choroidal thickness and average subfoveal choroidal thickness, respectively. In conclusion, the deep-learning method using the Mask-RCNN model provides a faster and accurate measurement of choroidal thickness. Comparing with manual delineation, it provides better effectiveness, which is feasible for clinical application and larger scale of research on choroid.

scholarly journals Foveal avascular zone segmentation in optical coherence tomography angiography images using a deep learning approach

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Reza Mirshahi ◽  
Pasha Anvari ◽  
Hamid Riazi-Esfahani ◽  
Mahsa Sardarinia ◽  
Masood Naseripour ◽  
...  
Keyword(s):  
Optical Coherence Tomography ◽  
Diabetic Retinopathy ◽  
Deep Learning ◽  
Healthy Subjects ◽  
Optical Coherence Tomography Angiography ◽  
Validation Dataset ◽  
Diabetic Patients ◽  
Dice Similarity Coefficient ◽  
Optical Coherence ◽  
Avascular Zone

AbstractThe purpose of this study was to introduce a new deep learning (DL) model for segmentation of the fovea avascular zone (FAZ) in en face optical coherence tomography angiography (OCTA) and compare the results with those of the device’s built-in software and manual measurements in healthy subjects and diabetic patients. In this retrospective study, FAZ borders were delineated in the inner retinal slab of 3 × 3 enface OCTA images of 131 eyes of 88 diabetic patients and 32 eyes of 18 healthy subjects. To train a deep convolutional neural network (CNN) model, 126 enface OCTA images (104 eyes with diabetic retinopathy and 22 normal eyes) were used as training/validation dataset. Then, the accuracy of the model was evaluated using a dataset consisting of OCTA images of 10 normal eyes and 27 eyes with diabetic retinopathy. The CNN model was based on Detectron2, an open-source modular object detection library. In addition, automated FAZ measurements were conducted using the device’s built-in commercial software, and manual FAZ delineation was performed using ImageJ software. Bland–Altman analysis was used to show 95% limit of agreement (95% LoA) between different methods. The mean dice similarity coefficient of the DL model was 0.94 ± 0.04 in the testing dataset. There was excellent agreement between automated, DL model and manual measurements of FAZ in healthy subjects (95% LoA of − 0.005 to 0.026 mm2 between automated and manual measurement and 0.000 to 0.009 mm2 between DL and manual FAZ area). In diabetic eyes, the agreement between DL and manual measurements was excellent (95% LoA of − 0.063 to 0.095), however, there was a poor agreement between the automated and manual method (95% LoA of − 0.186 to 0.331). The presence of diabetic macular edema and intraretinal cysts at the fovea were associated with erroneous FAZ measurements by the device’s built-in software. In conclusion, the DL model showed an excellent accuracy in detection of FAZ border in enfaces OCTA images of both diabetic patients and healthy subjects. The DL and manual measurements outperformed the automated measurements of the built-in software.

scholarly journals Characterization of Optical Coherence Tomography Images for Colon Lesion Differentiation under Deep Learning

2021 ◽  
Vol 11 (7) ◽  
pp. 3119
Author(s):  
Cristina L. Saratxaga ◽  
Jorge Bote ◽  
Juan F. Ortega-Morán ◽  
Artzai Picón ◽  
Elena Terradillos ◽  
...  
Keyword(s):  
Optical Coherence Tomography ◽  
Deep Learning ◽  
Data Augmentation ◽  
Optical Biopsy ◽  
Colon Polyps ◽  
Optical Coherence ◽  
Colon Lesion ◽  
Patient Prognosis ◽  
B Scan Images

(1) Background: Clinicians demand new tools for early diagnosis and improved detection of colon lesions that are vital for patient prognosis. Optical coherence tomography (OCT) allows microscopical inspection of tissue and might serve as an optical biopsy method that could lead to in-situ diagnosis and treatment decisions; (2) Methods: A database of murine (rat) healthy, hyperplastic and neoplastic colonic samples with more than 94,000 images was acquired. A methodology that includes a data augmentation processing strategy and a deep learning model for automatic classification (benign vs. malignant) of OCT images is presented and validated over this dataset. Comparative evaluation is performed both over individual B-scan images and C-scan volumes; (3) Results: A model was trained and evaluated with the proposed methodology using six different data splits to present statistically significant results. Considering this, 0.9695 (±0.0141) sensitivity and 0.8094 (±0.1524) specificity were obtained when diagnosis was performed over B-scan images. On the other hand, 0.9821 (±0.0197) sensitivity and 0.7865 (±0.205) specificity were achieved when diagnosis was made considering all the images in the whole C-scan volume; (4) Conclusions: The proposed methodology based on deep learning showed great potential for the automatic characterization of colon polyps and future development of the optical biopsy paradigm.

Sign in / Sign up

Export Citation Format

Share Document