Livelayer: a semi-automatic software program for segmentation of layers and diabetic macular edema in optical coherence tomography images

Comparative Analysis of Deep Learning Architectures for Macular Hole Segmentation in OCT Images: A Performance Evaluation of U-Net Variants

This study presents a comprehensive comparison of U-Net variants with different backbone architectures for Macular Hole (MH) segmentation in optical coherence tomography (OCT) images. We evaluated eleven architectures, including U-Net combined with InceptionNetV4, VGG16, VGG19, ResNet152, DenseNet121, EfficientNet-B7, MobileNetV2, Xception, and Transformer. Models were assessed using the Dice coefficient and HD95 metrics on the OIMHS dataset. While HD95 proved unreliable for small regions like MH, often returning 'nan' values, the Dice coefficient provided consistent performance evaluation. InceptionNetV4 + U-Net achieved the highest Dice coefficient (0.9672), demonstrating superior segmentation accuracy. Although considered state-of-the-art, Transformer + U-Net showed poor performance in MH and intraretinal cyst (IRC) segmentation. Analysis of computational resources revealed that MobileNetV2 + U-Net offered the most efficient performance with minimal parameters, while InceptionNetV4 + U-Net balanced accuracy with moderate computational demands. Our findings suggest that CNN-based backbones, particularly InceptionNetV4, are more effective than Transformer architectures for OCT image segmentation, with InceptionNetV4 + U-Net emerging as the most promising model for clinical applications.

Assessment of area and structural irregularity of retinal layers in diabetic retinopathy using machine learning and image processing techniques

Diabetes retinopathy prevention necessitates early detection, monitoring, and treatment. Non-invasive optical coherence tomography (OCT) shows structural changes in the retinal layer. OCT image evaluation necessitates retinal layer segmentation. The ability of our automated retinal layer segmentation to distinguish between normal, non-proliferative (NPDR), and proliferative diabetic retinopathy (PDR) was investigated in this study using quantifiable biomarkers such as retina layer smoothness index (SI) and area (S) in horizontal and vertical OCT images for each zone (fovea, superior, inferior, nasal, and temporal). This research includes 84 eyes from 57 individuals. The study shows a significant difference in the Area (S) of inner nuclear layer (INL) and outer nuclear layer (ONL) in the horizontal foveal zone across the three groups (p < 0.001). In the horizontal scan, there is a significant difference in the smoothness index (SI) of the inner plexiform layer (IPL) and the upper border of the outer plexiform layer (OPL) among three groups (p < 0.05). There is also a significant difference in the area (S) of the OPL in the foveal zone among the three groups (p = 0.003). The area (S) of the INL in the foveal region of horizontal slabs performed best for distinguishing diabetic patients (NPDR and PDR) from normal individuals, with an accuracy of 87.6%. The smoothness index (SI) of IPL in the nasal zone of horizontal foveal slabs was the most accurate at 97.2% in distinguishing PDR from NPDR. The smoothness index of the top border of the OPL in the nasal zone of horizontal slabs was 84.1% accurate in distinguishing NPDR from PDR. Smoothness index of IPL in the temporal zone of horizontal slabs was 89.8% accurate in identifying NPDR from PDR patients. In conclusion, optical coherence tomography can assess the smoothness index and irregularity of the inner and outer plexiform layers, particularly in the nasal and temporal regions of horizontal foveal slabs, to distinguish non-proliferative from proliferative diabetic retinopathy. The evolution of diabetic retinopathy throughout severity levels and its effects on retinal layer irregularity need more study.

The effect of optical degradation from cataract using a new Deep Learning optical coherence tomography segmentation algorithm

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.

Loss-Modified Transformer-Based U-Net for Accurate Segmentation of Fluids in Optical Coherence Tomography Images of Retinal Diseases

Background

Optical coherence tomography (OCT) imaging significantly contributes to ophthalmology in the diagnosis of retinal disorders such as age-related macular degeneration and diabetic macular edema. Both diseases involve the abnormal accumulation of fluids, location, and volume, which is vitally informative in detecting the severity of the diseases. Automated and accurate fluid segmentation in OCT images could potentially improve the current clinical diagnosis. This becomes more important by considering the limitations of manual fluid segmentation as a time-consuming and subjective to error method.

Methods

Deep learning techniques have been applied to various image processing tasks, and their performance has already been explored in the segmentation of fluids in OCTs. This article suggests a novel automated deep learning method utilizing the U-Net structure as the basis. The modifications consist of the application of transformers in the encoder path of the U-Net with the purpose of more concentrated feature extraction. Furthermore, a custom loss function is empirically tailored to efficiently incorporate proper loss functions to deal with the imbalance and noisy images. A weighted combination of Dice loss, focal Tversky loss, and weighted binary cross-entropy is employed.

Results

Different metrics are calculated. The results show high accuracy (Dice coefficient of 95.52) and robustness of the proposed method in comparison to different methods after adding extra noise to the images (Dice coefficient of 92.79).

Conclusions

The segmentation of fluid regions in retinal OCT images is critical because it assists clinicians in diagnosing macular edema and executing therapeutic operations more quickly. This study suggests a deep learning framework and novel loss function for automated fluid segmentation of retinal OCT images with excellent accuracy and rapid convergence result.

Discrimination of multiple sclerosis using OCT images from two different centers

BACKGROUND

Multiple sclerosis (MS) is one of the most prevalent chronic inflammatory diseases caused by demyelination and axonal damage in the central nervous system. Structural retinal imaging via optical coherence tomography (OCT) shows promise as a noninvasive biomarker for monitoring of MS. There are successful reports regarding the application of Artificial Intelligence (AI) in the analysis of cross-sectional OCTs in ophthalmologic diseases. However, the alteration of thicknesses of various retinal layers in MS is noticeably subtle compared to other ophthalmologic diseases. Therefore, raw cross-sectional OCTs are replaced with multilayer segmented OCTs for discrimination of MS and healthy controls (HCs).

METHODS

To conform to the principles of trustworthy AI, interpretability is provided by visualizing the regional layer contribution to classification performance with the proposed occlusion sensitivity approach. The robustness of the classification is also guaranteed by showing the effectiveness of the algorithm while being tested on the new independent dataset. The most discriminative features from different topologies of the multilayer segmented OCTs are selected by the dimension reduction method. Support vector machine (SVM), random forest (RF), and artificial neural network (ANN) are used for classification. Patient-wise cross-validation (CV) is utilized to evaluate the performance of the algorithm, where the training and test folds contain records from different subjects.

RESULTS

The most discriminative topology is determined to square with a size of 40 pixels and the most influential layers are the ganglion cell and inner plexiform layer (GCIPL) and inner nuclear layer (INL). Linear SVM resulted in 88% Accuracy (with standard deviation (std) = 0.49 in 10 times of execution to indicate the repeatability), 78% precision (std=1.48), and 63% recall (std=1.35) in the discrimination of MS and HCs using macular multilayer segmented OCTs.

CONCLUSION

The proposed classification algorithm is expected to help neurologists in the early diagnosis of MS. This paper distinguishes itself from other studies by employing two distinct datasets, which enhances the robustness of its findings in comparison with previous studies with lack of external validation. This study aims to circumvent the utilization of deep learning methods due to the limited quantity of the available data and convincingly demonstrates that favorable outcomes can be achieved without relying on deep learning techniques.

Optimal Deep Learning Architecture for Automated Segmentation of Cysts in OCT Images Using X-Let Transforms

The retina is a thin, light-sensitive membrane with a multilayered structure found in the back of the eyeball. There are many types of retinal disorders. The two most prevalent retinal illnesses are Age-Related Macular Degeneration (AMD) and Diabetic Macular Edema (DME). Optical Coherence Tomography (OCT) is a vital retinal imaging technology. X-lets (such as curvelet, DTCWT, contourlet, etc.) have several benefits in image processing and analysis. They can capture both local and non-local features of an image simultaneously. The aim of this paper is to propose an optimal deep learning architecture based on sparse basis functions for the automated segmentation of cystic areas in OCT images. Different X-let transforms were used to produce different network inputs, including curvelet, Dual-Tree Complex Wavelet Transform (DTCWT), circlet, and contourlet. Additionally, three different combinations of these transforms are suggested to achieve more accurate segmentation results. Various metrics, including Dice coefficient, sensitivity, false positive ratio, Jaccard index, and qualitative results, were evaluated to find the optimal networks and combinations of the X-let's sub-bands. The proposed network was tested on both original and noisy datasets. The results show the following facts: (1) contourlet achieves the optimal results between different combinations; (2) the five-channel decomposition using high-pass sub-bands of contourlet transform achieves the best performance; and (3) the five-channel decomposition using high-pass sub-bands formations out-performs the state-of-the-art methods, especially in the noisy dataset. The proposed method has the potential to improve the accuracy and speed of the segmentation process in clinical settings, facilitating the diagnosis and treatment of retinal diseases.

Automated assessment of the smoothness of retinal layers in optical coherence tomography images using a machine learning algorithm

Quantifying the smoothness of different layers of the retina can potentially be an important and practical biomarker in various pathologic conditions like diabetic retinopathy. The purpose of this study is to develop an automated machine learning algorithm which uses support vector regression method with wavelet kernel and automatically segments two hyperreflective retinal layers (inner plexiform layer (IPL) and outer plexiform layer (OPL)) in 50 optical coherence tomography (OCT) slabs and calculates the smoothness index (SI). The Bland-Altman plots, mean absolute error, root mean square error and signed error calculations revealed a modest discrepancy between the manual approach, used as the ground truth, and the corresponding automated segmentation of IPL/ OPL, as well as SI measurements in OCT slabs. It was concluded that the constructed algorithm may be employed as a reliable, rapid and convenient approach for segmenting IPL/OPL and calculating SI in the appropriate layers.

Synthetic OCT data in challenging conditions: three-dimensional OCT and presence of abnormalities

Nowadays, retinal optical coherence tomography (OCT) plays an important role in ophthalmology and automatic analysis of the OCT is of real importance: image denoising facilitates a better diagnosis and image segmentation and classification are undeniably critical in treatment evaluation. Synthetic OCT was recently considered to provide a benchmark for quantitative comparison of automatic algorithms and to be utilized in the training stage of novel solutions based on deep learning. Due to complicated data structure in retinal OCTs, a limited number of delineated OCT datasets are already available in presence of abnormalities; furthermore, the intrinsic three-dimensional (3D) structure of OCT is ignored in many public 2D datasets. We propose a new synthetic method, applicable to 3D data and feasible in presence of abnormalities like diabetic macular edema (DME). In this method, a limited number of OCT data is used during the training step and the Active Shape Model is used to produce synthetic OCTs plus delineation of retinal boundaries and location of abnormalities. Statistical comparison of thickness maps showed that synthetic dataset can be used as a statistically acceptable representative of the original dataset (p > 0.05). Visual inspection of the synthesized vessels was also promising. Regarding the texture features of the synthesized datasets, Q-Q plots were used, and even in cases that the points have slightly digressed from the straight line, the p-values of the Kolmogorov–Smirnov test rejected the null hypothesis and showed the same distribution in texture features of the real and the synthetic data. The proposed algorithm provides a unique benchmark for comparison of OCT enhancement methods and a tailored augmentation method to overcome the limited number of OCTs in deep learning algorithms.