Segmentation of mouse skin layers in optical coherence tomography image data using deep convolutional neural networks

Semi-supervised assisted multi-task learning for oral optical coherence tomography image segmentation and denoising

Optical coherence tomography (OCT) is promising to become an essential imaging tool for non-invasive oral mucosal tissue assessment, but it faces challenges like speckle noise and motion artifacts. In addition, it is difficult to distinguish different layers of oral mucosal tissues from gray level OCT images due to the similarity of optical properties between different layers. We introduce the Efficient Segmentation-Denoising Model (ESDM), a multi-task deep learning framework designed to enhance OCT imaging by reducing scan time from ∼8s to ∼2s and improving oral epithelium layer segmentation. ESDM integrates the local feature extraction capabilities of the convolution layer and the long-term information processing advantages of the transformer, achieving better denoising and segmentation performance compared to existing models. Our evaluation shows that ESDM outperforms state-of-the-art models with a PSNR of 26.272, SSIM of 0.737, mDice of 0.972, and mIoU of 0.948. Ablation studies confirm the effectiveness of our design, such as the feature fusion methods, which enhance performance with minimal model complexity increase. ESDM also presents high accuracy in quantifying oral epithelium thickness, achieving mean absolute errors as low as 5 µm compared to manual measurements. This research shows that ESDM can notably improve OCT imaging and reduce the cost of accurate oral epithermal segmentation, improving diagnostic capabilities in clinical settings.

Segmentation of 3D OCT Images of Human Skin Using Neural Networks with U-Net Architecture

The aim of the study is a comparative analysis of algorithms for segmentation of three-dimensional OCT images of human skin using neural networks based on U-Net architecture when training the model on two-dimensional and three-dimensional data.

Materials and Methods

Two U-Net-based network architectures for segmentation of 3D OCT skin images are proposed in this work, in which 2D and 3D blocks of 3D images serve as input data. Training was performed on thick skin OCT images acquired from 7 healthy volunteers. For training, the OCT images were semi-automatically segmented by experts in OCT and dermatology. The Sørensen-Dice coefficient, which was calculated from the segmentation results of images that did not participate in the training of the networks, was used to assess the quality of segmentation. Additional testing of the networks' capabilities in determining skin layer thicknesses was performed on an independent dataset from 8 healthy volunteers.

Results

In evaluating the segmentation quality, the values of the Sørensen-Dice coefficient for the upper stratum corneum, ordered stratum corneum, epidermal cellular layer, and dermis were 0.90, 0.94, 0.89, and 0.99, respectively, for training on two-dimensional data and 0.89, 0.94, 0.87, and 0.98 for training on three-dimensional data. The values obtained for the dermis are in good agreement with the results of other works using networks based on the U-Net architecture. The thicknesses of the ordered stratum corneum and epidermal cellular layer were 153±24 and 137±17 μm, respectively, when the network was trained on two-dimensional data and 163±19 and 137±20 μm when trained on three-dimensional data.

Conclusion

Neural networks based on U-Net architecture allow segmentation of skin layers on OCT images with high accuracy, which makes these networks promising for obtaining valuable diagnostic information in dermatology and cosmetology, e.g., for estimating the thickness of skin layers.

LS-Net: lightweight segmentation network for dermatological epidermal segmentation in optical coherence tomography imaging

Optical coherence tomography (OCT) can be an important tool for non-invasive dermatological evaluation, providing useful data on epidermal integrity for diagnosing skin diseases. Despite its benefits, OCT's utility is limited by the challenges of accurate, fast epidermal segmentation due to the skin morphological diversity. To address this, we introduce a lightweight segmentation network (LS-Net), a novel deep learning model that combines the robust local feature extraction abilities of Convolution Neural Network and the long-term information processing capabilities of Vision Transformer. LS-Net has a depth-wise convolutional transformer for enhanced spatial contextualization and a squeeze-and-excitation block for feature recalibration, ensuring precise segmentation while maintaining computational efficiency. Our network outperforms existing methods, demonstrating high segmentation accuracy (mean Dice: 0.9624 and mean IoU: 0.9468) with significantly reduced computational demands (floating point operations: 1.131 G). We further validate LS-Net on our acquired dataset, showing its effectiveness in various skin sites (e.g., face, palm) under realistic clinical conditions. This model promises to enhance the diagnostic capabilities of OCT, making it a valuable tool for dermatological practice.

Deep learning automatically assesses 2-µm laser-induced skin damage OCT images

The present study proposed a noninvasive, automated, in vivo assessment method based on optical coherence tomography (OCT) and deep learning techniques to qualitatively and quantitatively analyze the biological effects of 2-µm laser-induced skin damage at different irradiation doses. Different doses of 2-µm laser irradiation established a mouse skin damage model, after which the skin-damaged tissues were imaged non-invasively in vivo using OCT. The acquired images were preprocessed to construct the dataset required for deep learning. The deep learning models used were U-Net, DeepLabV3+, PSP-Net, and HR-Net, and the trained models were used to segment the damage images and further quantify the damage volume of mouse skin under different irradiation doses. The comparison of the qualitative and quantitative results of the four network models showed that HR-Net had the best performance, the highest agreement between the segmentation results and real values, and the smallest error in the quantitative assessment of the damage volume. Based on HR-Net to segment the damage image and quantify the damage volume, the irradiation doses 5.41, 9.55, 13.05, 20.85, 32.71, 52.92, 76.71, and 97.24 J/cm² corresponded to a damage volume of 4.58, 12.56, 16.74, 20.88, 24.52, 30.75, 34.13, and 37.32 mm³. The damage volume increased in a radiation dose-dependent manner.

Rapid measurement of epidermal thickness in OCT images of skin

Epidermal thickness (ET) changes are associated with several skin diseases. To measure ET, segmentation of optical coherence tomography (OCT) images is essential; manual segmentation is very time-consuming and requires training and some understanding of how to interpret OCT images. Fast results are important in order to analyze ET over different regions of skin in rapid succession to complete a clinical examination and enable the physician to discuss results with the patient in real time. The well-known CNN-graph search (CNN-GS) methodology delivers highly accurate results, but at a high computational cost. Our objective was to build a computational core, based on CNN-GS, able to accurately segment OCT skin images in real time. We accomplished this by fine-tuning the hyperparameters, testing a range of speed-up algorithms including pruning and quantization, designing a novel pixel-skipping process, and implementing the final product with efficient use of core and threads on a multicore central processing unit (CPU). We name this product CNN-GS-skin. The method identifies two defined boundaries on OCT skin images in order to measure ET. We applied CNN-GS-skin to OCT skin images, taken from various body sites of 63 healthy individuals. Compared with CNN-GS, our described method reduced computation time by 130 [Formula: see text] with minimal reduction in ET determination accuracy (from 96.38 to 94.67%).

Deep Learning based Skin-layer Segmentation for Characterizing Cutaneous Wounds from Optical Coherence Tomography Images

Optical coherence tomography (OCT) is a medical imaging modality that allows us to probe deeper sub-structures of skin. The state-of-the-art wound care prediction and monitoring methods are based on visual evaluation and focus on surface information. However, research studies have shown that sub-surface information of the wound is critical for understanding the wound healing progression. This work demonstrated the use of OCT as an effective imaging tool for objective and non-invasive assessments of wound severity, the potential for healing, and healing progress by measuring the optical characteristics of skin components. We have demonstrated the efficacy of OCT in studying wound healing progress in vivo small animal models. Automated analysis of OCT datasets poses multiple challenges, such as limitations in the training dataset size, variation in data distribution induced by uncertainties in sample quality and experiment conditions. We have employed a U-Net-based model for segmentation of skin layers based on OCT images and to study epithelial and regenerated tissue thickness wound closure dynamics and thus quantify the progression of wound healing. In the experimental evaluation of the OCT skin image datasets, we achieved the objective of skin layer segmentation with an average intersection over union (IOU) of 0.9234. The results have been corroborated using gold-standard histology images and co-validated using inputs from pathologists.Clinical Relevance-To monitor wound healing progression without disrupting the healing procedure by superficial, non-invasive means via the identification of pixel characteristics of individual layers.

Multiparametric Quantitative Analysis of Photodamage to Skin Using Optical Coherence Tomography

Ultraviolet (UV) irradiation causes 90% of photodamage to skin and long-term exposure to UV irradiation is the largest threat to skin health. To study the mechanism of UV-induced photodamage and the repair of sunburnt skin, the key problem to solve is how to non-destructively and continuously evaluate UV-induced photodamage to skin. In this study, a method to quantitatively analyze the structural and tissue optical parameters of artificial skin (AS) using optical coherence tomography (OCT) was proposed as a way to non-destructively and continuously evaluate the effect of photodamage. AS surface roughness was achieved based on the characteristic peaks of the intensity signal of the OCT images, and this was the basis for quantifying AS cuticle thickness using Dijkstra's algorithm. Local texture features within the AS were obtained through the gray-level co-occurrence matrix method. A modified depth-resolved algorithm was used to quantify the 3D scattering coefficient distribution within AS based on a single-scattering model. A multiparameter assessment of AS photodamage was carried out, and the results were compared with the MTT experiment results and H&E staining. The results of the UV photodamage experiments showed that the cuticle of the photodamaged model was thicker (56.5%) and had greater surface roughness (14.4%) compared with the normal cultured AS. The angular second moment was greater and the correlation was smaller, which was in agreement with the results of the H&E staining microscopy. The angular second moment and correlation showed a good linear relationship with the UV irradiation dose, illustrating the potential of OCT in measuring internal structural damage. The tissue scattering coefficient of AS correlated well with the MTT results, which can be used to quantify the damage to the bioactivity. The experimental results also demonstrate the anti-photodamage efficacy of the vitamin C factor. Quantitative analysis of structural and tissue optical parameters of AS by OCT enables the non-destructive and continuous detection of AS photodamage in multiple dimensions.

Automated detection and growth tracking of 3D bio-printed organoid clusters using optical coherence tomography with deep convolutional neural networks

Organoids are advancing the development of accurate prediction of drug efficacy and toxicity in vitro. These advancements are attributed to the ability of organoids to recapitulate key structural and functional features of organs and parent tumor. Specifically, organoids are self-organized assembly with a multi-scale structure of 30-800 μm, which exacerbates the difficulty of non-destructive three-dimensional (3D) imaging, tracking and classification analysis for organoid clusters by traditional microscopy techniques. Here, we devise a 3D imaging, segmentation and analysis method based on Optical coherence tomography (OCT) technology and deep convolutional neural networks (CNNs) for printed organoid clusters (Organoid Printing and optical coherence tomography-based analysis, OPO). The results demonstrate that the organoid scale influences the segmentation effect of the neural network. The multi-scale information-guided optimized EGO-Net we designed achieves the best results, especially showing better recognition workout for the biologically significant organoid with diameter ≥50 μm than other neural networks. Moreover, OPO achieves to reconstruct the multiscale structure of organoid clusters within printed microbeads and calibrate the printing errors by segmenting the printed microbeads edges. Overall, the classification, tracking and quantitative analysis based on image reveal that the growth process of organoid undergoes morphological changes such as volume growth, cavity creation and fusion, and quantitative calculation of the volume demonstrates that the growth rate of organoid is associated with the initial scale. The new method we proposed enable the study of growth, structural evolution and heterogeneity for the organoid cluster, which is valuable for drug screening and tumor drug sensitivity detection based on organoids.

Mouse model of selective cryolipolysis

BACKGROUND

Cryolipolysis is a noninvasive method of destroying adipocytes using controlled cooling, thereby enabling localized and targeted fat reduction. Due to their greater vulnerability to cold injury, adipocytes are selectively targeted, while other cell types are spared.

OBJECTIVES

This study aims to develop a mouse model of cryolipolysis to offer a reliable and convenient alternative to human models, providing a methodology to validate clinical hypotheses in-depth with relative ease, low cost, and efficiency. This further facilitates comprehensive studies of the molecular mechanisms involved in cryolipolysis.

MATERIALS AND METHODS

Mice (C57BL/6J) were placed under general anesthesia and were treated using our custom, miniaturized cryolipolysis system. A thermoelectric cooling probe was applied to the inguinal (ING) area for either a cold exposure of -10°C, or for a room temperature exposure for 10 minutes. The thickness of the subcutaneous fat of the mice was quantified using an optical coherence tomography (OCT) imaging system before and after the treatment. Histological analyses were performed before and after cryolipolysis at multiple time points.

RESULTS

OCT analysis showed that mice that underwent cold cryolipolysis treatment induced a significantly greater reduction of subcutaneous fat thickness 1 month after treatment than the control mice. The mice that received cold treatment had no skin injuries. The selective damage of adipocytes stimulated cold panniculitis that was characterized histologically by infiltration of immune cells 2 and 3 days after treatment.

CONCLUSION

This study shows that cryolipolysis performed in mice yields reproducible and measurable subcutaneous fat reduction, consistent with previous studies conducted in humans and pigs. Future studies can utilize the model of selective cryolipolysis developed by our group to further elucidate the cellular and molecular mechanisms of fat cell loss and improve clinical outcomes in humans.

Computer-Aided Diagnosis Methods for High-Frequency Ultrasound Data Analysis: A Review

Over the last few decades, computer-aided diagnosis systems have become a part of clinical practice. They have the potential to assist clinicians in daily diagnostic tasks. The image processing techniques are fast, repeatable, and robust, which helps physicians to detect, classify, segment, and measure various structures. The recent rapid development of computer methods for high-frequency ultrasound image analysis opens up new diagnostic paths in dermatology, allergology, cosmetology, and aesthetic medicine. This paper, being the first in this area, presents a research overview of high-frequency ultrasound image processing techniques, which have the potential to be a part of computer-aided diagnosis systems. The reviewed methods are categorized concerning the application, utilized ultrasound device, and image data-processing type. We present the bridge between diagnostic needs and already developed solutions and discuss their limitations and future directions in high-frequency ultrasound image analysis. A search was conducted of the technical literature from 2005 to September 2022, and in total, 31 studies describing image processing methods were reviewed. The quantitative and qualitative analysis included 39 algorithms, which were selected as the most effective in this field. They were completed by 20 medical papers and define the needs and opportunities for high-frequency ultrasound application and CAD development.

Automatic Segmentation of Laser-Induced Injury OCT Images Based on a Deep Neural Network Model

Optical coherence tomography (OCT) has considerable application potential in noninvasive diagnosis and disease monitoring. Skin diseases, such as basal cell carcinoma (BCC), are destructive; hence, quantitative segmentation of the skin is very important for early diagnosis and treatment. Deep neural networks have been widely used in the boundary recognition and segmentation of diseased areas in medical images. Research on OCT skin segmentation and laser-induced skin damage segmentation based on deep neural networks is still in its infancy. Here, a segmentation and quantitative analysis pipeline of laser skin injury and skin stratification based on a deep neural network model is proposed. Based on the stratification of mouse skins, a laser injury model of mouse skins induced by lasers was constructed, and the multilayer structure and injury areas were accurately segmented by using a deep neural network method. First, the intact area of mouse skin and the damaged areas of different laser radiation doses are collected by the OCT system, and then the labels are manually labeled by experienced histologists. A variety of deep neural network models are used to realize the segmentation of skin layers and damaged areas on the skin dataset. In particular, the U-Net model based on a dual attention mechanism is used to realize the segmentation of the laser-damage structure, and the results are compared and analyzed. The segmentation results showed that the Dice coefficient of the mouse dermis layer and injury area reached more than 0.90, and the Dice coefficient of the fat layer and muscle layer reached more than 0.80. In the evaluation results, the average surface distance (ASSD) and Hausdorff distance (HD) indicated that the segmentation results are excellent, with a high overlap rate with the manually labeled area and a short edge distance. The results of this study have important application value for the quantitative analysis of laser-induced skin injury and the exploration of laser biological effects and have potential application value for the early noninvasive detection of diseases and the monitoring of postoperative recovery in the future.

Semisupervised representative learning for measuring epidermal thickness in human subjects in optical coherence tomography by leveraging datasets from rodent models

SIGNIFICANCE

Morphological changes in the epidermis layer are critical for the diagnosis and assessment of various skin diseases. Due to its noninvasiveness, optical coherence tomography (OCT) is a good candidate for observing microstructural changes in skin. Convolutional neural network (CNN) has been successfully used for automated segmentation of the skin layers of OCT images to provide an objective evaluation of skin disorders. Such method is reliable, provided that a large amount of labeled data is available, which is very time-consuming and tedious. The scarcity of patient data also puts another layer of difficulty to make the model more generalizable.

AIM

We developed a semisupervised representation learning method to provide data augmentations.

APPROACH

We used rodent models to train neural networks for accurate segmentation of clinical data.

RESULT

The learning quality is maintained with only one OCT labeled image per volume that is acquired from patients. Data augmentation introduces a semantically meaningful variance, allowing for better generalization. Our experiments demonstrate the proposed method can achieve accurate segmentation and thickness measurement of the epidermis.

CONCLUSION

This is the first report of semisupervised representative learning applied to OCT images from clinical data by making full use of the data acquired from rodent models. The proposed method promises to aid in the clinical assessment and treatment planning of skin diseases.

Evaluation of a 3.8-µm laser-induced skin injury and their repair with in vivo OCT imaging and noninvasive monitoring

To explore a 3.8-µm laser-induced damage and wound healing effect, we propose using optical coherence tomography (OCT) and a noninvasive monitoring-based in vivo evaluation method to quantitatively and qualitatively analyze the time-dependent biological effect of a 3.8-µm laser. The optical attenuation coefficient (OAC) is computed using a Fourier-domain algorithm. Three-dimensional (3-D) visualization of OCT images has been implemented to visualize the burnt spots. Furthermore, the burnt spots from the 3-D volumetric data was segmented and visualized, and the quantitative parameters of the burnt spots, such as the mean OACs, areas, and volumes, were computed. Then, OCT images and histological sections were analyzed to compare the structural changes. Within a certain radiation range, there is a linear relationship between radiation dose and temperature. Dermoscopic images, OCT images, and histological sections showed that, within a certain dose range, as the radiation doses increased, the cutaneous damage became more serious. One hour after laser radiation, the mean OACs increased and then decreased; the areas of burnt spots always increased and were 0.95 ± 0.07, 1.01 ± 0.06, 1.025 ± 0.07, 0.99 ± 0.07, 0.98 ± 0.07, 1.00 ± 0.07, 0.96 ± 0.05, and 0.98 ± 0.06 mm-1, respectively; the areas were 2.10 ± 0.63, 3.75 ± 1.85, 5.95 ± 1.62, 8.35 ± 0.88, 9.44 ± 1.28, 10.29 ± 0.49, 12.27 ± 0.96, and 13.127 ± 1.90 mm2; and the volumes were 1.54 ± 0.41, 2.86 ± 0.09, 3.73 ± 0.49, 4.14 ± 0.80, 7.21 ± 0.52, 6.77 ± 0.45, 8.36 ± 0.25, and 10.65 ± 0.51 mm3; and 21 days after laser radiation, the volumes were 0.67 ± 0.18, 1.64 ± 0.08, 1.87 ± 0.12, 2.57 ± 0.34, 3.43 ± 0.26, 3.64 ± 0.04, 3.84 ± 0.15, and 4.16 ± 0.53 mm3, respectively. We investigated the time-dependent biological effect of 3.8-µm laser-induced cutaneous damage and wound healing using the quantitative parameters of OCT imaging and noninvasive monitoring. The real-time temperature reflects the photothermal effect during laser radiation of mouse skin. OCT images of burnt spots were segmented to compute the mean OACs, burnt area, and quantitative volumes. This study has the potential for in vivo noninvasive and quantitative clinical evaluation in the future.

Deep-learning approach for automated thickness measurement of epithelial tissue and scab using optical coherence tomography

SIGNIFICANCE

In order to elucidate therapeutic treatment to accelerate wound healing, it is crucial to understand the process underlying skin wound healing, especially re-epithelialization. Epidermis and scab detection is of importance in the wound healing process as their thickness is a vital indicator to judge whether the re-epithelialization process is normal or not. Since optical coherence tomography (OCT) is a real-time and non-invasive imaging technique that can perform a cross-sectional evaluation of tissue microstructure, it is an ideal imaging modality to monitor the thickness change of epidermal and scab tissues during wound healing processes in micron-level resolution. Traditional segmentation on epidermal and scab regions was performed manually, which is time-consuming and impractical in real time.

AIM

We aim to develop a deep-learning-based skin layer segmentation method for automated quantitative assessment of the thickness of in vivo epidermis and scab tissues during a time course of healing within a rodent model.

APPROACH

Five convolution neural networks were trained using manually labeled epidermis and scab regions segmentation from 1000 OCT B-scan images (assisted by its corresponding angiographic information). The segmentation performance of five segmentation architectures was compared qualitatively and quantitatively for validation set.

RESULTS

Our results show higher accuracy and higher speed of the calculated thickness compared with human experts. The U-Net architecture represents a better performance than other deep neural network architectures with 0.894 at F1-score, 0.875 at mean intersection over union, 0.933 at Dice similarity coefficient, and 18.28  μm at an average symmetric surface distance. Furthermore, our algorithm is able to provide abundant quantitative parameters of the wound based on its corresponding thickness maps in different healing phases. Among them, normalized epidermal thickness is recommended as an essential hallmark to describe the re-epithelialization process of the rodent model.

CONCLUSIONS

The automatic segmentation and thickness measurements within different phases of wound healing data demonstrates that our pipeline provides a robust, quantitative, and accurate method for serving as a standard model for further research into effect of external pharmacological and physical factors.

Automated segmentation of epidermis in high-frequency ultrasound of pathological skin using a cascade of DeepLab v3+ networks and fuzzy connectedness

This study proposes a novel, fully automated framework for epidermal layer segmentation in different skin diseases based on 75 MHz high-frequency ultrasound (HFUS) image data. A robust epidermis segmentation is a vital first step to detect changes in thickness, shape, and intensity and therefore support diagnosis and treatment monitoring in inflammatory and neoplastic skin lesions. Our framework links deep learning and fuzzy connectedness for image analysis. It consists of a cascade of two DeepLab v3+ models with a ResNet-50 backbone and a fuzzy connectedness analysis module for fine segmentation. Both deep models are pre-trained on the ImageNet dataset and subjected to transfer learning using our HFUS database of 580 images with atopic dermatitis, psoriasis and non-melanocytic skin tumors. The first deep model is used to detect the appropriate region of interest, while the second stands for the main segmentation procedure. We use the softmax layer of the latter twofold to prepare the input data for fuzzy connectedness analysis: as a reservoir of seed points and a direct contribution to the input image. In the experiments, we analyze different configurations of the framework, including region of interest detection, deep model backbones and training loss functions, or fuzzy connectedness analysis with parameter settings. We also use the Dice index and epidermis thickness to compare our results to state-of-the-art approaches. The Dice index of 0.919 yielded by our model over the entire dataset (and exceeding 0.93 in inflammatory diseases) proves its superiority over the other methods.

Automatic quantitative analysis of structure parameters in the growth cycle of artificial skin using optical coherence tomography

SIGNIFICANCE

Artificial skin (AS) is widely used in dermatology, pharmacology, and toxicology, and has great potential in transplant medicine, burn wound care, and chronic wound treatment. There is a great demand for high-quality AS product and a non-invasive detection method is highly desirable.

AIM

To quantify the constructure parameters (i.e., thickness and surface roughness) of AS samples in the culture cycle and explore the growth regularities using optical coherent tomography (OCT).

APPROACH

An adaptive interface detection algorithm is developed to recognize surface points in each A-scan, offering a rapid method to calculate parameters without constructing OCT B-scan pictures and further achieving realizing real-time quantification of AS thickness and surface roughness. Experiments on standard roughness plates and H&E-staining microscopy were performed as a verification.

RESULTS

As applied on the whole cycle of AS culture, our method's results show that during the air-liquid culture, the surface roughness of the skin first decreases and then exhibits an increase, which implies coincidence with the degree of keratinization under a microscope. And normal and typical abnormal samples can be differentiated by thickness and roughness parameters during the culture cycle.

CONCLUSIONS

The adaptive interface detection algorithm is suitable for high-sensitivity, fast detection, and quantification of the interface with layered characteristic tissues, and can be used for non-destructive detection of the growth regularity of AS sample thickness and roughness during the culture cycle.

Deep Learning-Based High-Frequency Ultrasound Skin Image Classification with Multicriteria Model Evaluation

This study presents the first application of convolutional neural networks to high-frequency ultrasound skin image classification. This type of imaging opens up new opportunities in dermatology, showing inflammatory diseases such as atopic dermatitis, psoriasis, or skin lesions. We collected a database of 631 images with healthy skin and different skin pathologies to train and assess all stages of the methodology. The proposed framework starts with the segmentation of the epidermal layer using a DeepLab v3+ model with a pre-trained Xception backbone. We employ transfer learning to train the segmentation model for two purposes: to extract the region of interest for classification and to prepare the skin layer map for classification confidence estimation. For classification, we train five models in different input data modes and data augmentation setups. We also introduce a classification confidence level to evaluate the deep model’s reliability. The measure combines our skin layer map with the heatmap produced by the Grad-CAM technique designed to indicate image regions used by the deep model to make a classification decision. Moreover, we propose a multicriteria model evaluation measure to select the optimal model in terms of classification accuracy, confidence, and test dataset size. The experiments described in the paper show that the DenseNet-201 model fed with the extracted region of interest produces the most reliable and accurate results.

Real-time deep learning assisted skin layer delineation in dermal optical coherence tomography

We present deep learning assisted optical coherence tomography (OCT) imaging for quantitative tissue characterization and differentiation in dermatology. We utilize a manually scanned single fiber OCT (sfOCT) instrument to acquire OCT images from the skin. The focus of this study is to train a U-Net for automatic skin layer delineation. We demonstrate that U-Net allows quantitative assessment of epidermal thickness automatically. U-Net segmentation achieves high accuracy for epidermal thickness estimation for normal skin and leads to a clear differentiation between normal skin and skin lesions. Our results suggest that a single fiber OCT instrument with AI assisted skin delineation capability has the potential to become a cost-effective tool in clinical dermatology, for diagnosis and tumor margin detection.

Deep learning approach to skin layers segmentation in inflammatory dermatoses

Monitoring skin layers with medical imaging is critical to diagnosing and treating patients with chronic inflammatory skin diseases. The high-frequency ultrasound (HFUS) makes it possible to monitor skin condition in different dermatoses. Accurate and reliable segmentation of skin layers in patients with atopic dermatitis or psoriasis enables the assessment of the treatment effect by the layer thickness measurements. The epidermis and the subepidermal low echogenic band (SLEB) are the most important for further diagnosis since their appearance is an indicator of different skin problems. In medical practice, the analysis, including segmentation, is usually performed manually by the physician with all drawbacks of such an approach, e.g., extensive time consumption and lack of repeatability. Recently, HFUS becomes common in dermatological practice, yet it is barely supported by the development of automated analysis tools. To meet the need for skin layer segmentation and measurement, we developed an automated segmentation method of both epidermis and SLEB layers. It consists of a fuzzy c-means clustering-based preprocessing step followed by a U-shaped convolutional neural network. The network employs batch normalization layers adjusting and scaling the activation to make the segmentation more robust. The obtained segmentation results are verified and compared to the current state-of-the-art methods addressing the skin layer segmentation. The obtained Dice coefficient equal to 0.87 and 0.83 for the epidermis and SLEB, respectively, proves the developed framework's efficiency, outperforming the other approaches.

Self-examination low-cost full-field OCT (SELFF-OCT) for patients with various macular diseases

PURPOSE

The treatment guidelines for many macular diseases rely on frequent monitoring with optical coherence tomography (OCT). However, the burden of frequent disease control leads to low therapy adherence in real life. OCT home monitoring would address this issue but requires an inexpensive and self-operable device. With self-examination low-cost full-field OCT (SELFF-OCT), our group has introduced a novel technology that may fulfill both requirements. In this pilot study, we report the initial experiences with a clinical prototype.

METHODS

Fifty-one patients with different macular diseases were recruited in a cross-sectional study. The most common diseases were age-related macular degeneration (AMD; 39/51), diabetic macular edema (DME; 6/51), and retinal vein occlusion (RVO; 3/51). Patients received a short training in device usage and then performed multiple self-scans with the SELFF-OCT device. For comparison, scans with a standard clinical spectral domain (SD-)OCT were taken.

RESULTS

After a brief training, 77% of the patients were able to successfully acquire images that were clinically gradable. No significant influence on success could be found for age (p = 0.08) or BCVA (p = 0.97). Relevant disease biomarkers in the most common retinal diseases could be detected.

CONCLUSIONS

SELFF-OCT was used successfully for retinal self-examination and in the future could be used for retinal home monitoring. Future improvements in technology are expected to improve success rates and image quality.

TRIAL REGISTRATION

The Trial was registered in the German Trial Register under the number DRKS00013755 on 14.03.2018.

Application of OCT-Derived Attenuation Coefficient in Acute Burn-Damaged Skin

BACKGROUND AND OBJECTIVES

There remains a need to objectively monitor burn wound healing within a clinical setting, and optical coherence tomography (OCT) is proving itself one of the ideal modalities for just such a use. The aim of this study is to utilize the noninvasive and multipurpose capabilities of OCT, along with its cellular-level resolution, to demonstrate the application of optical attenuation coefficient (OAC), as derived from OCT data, to facilitate the automatic digital segmentation of the epidermis from scan images and to work as an objective indicator for burn wound healing assessment.

STUDY DESIGN/MATERIALS AND METHODS

A simple, yet efficient, method was used to estimate OAC from OCT images taken over multiple time points following acute burn injury. This method enhanced dermal-epidermal junction (DEJ) contrast, which facilitated the automatic segmentation of the epidermis for subsequent thickness measurements. In addition, we also measured and compared the average OAC of the dermis within said burns for correlative purposes.

RESULTS

Compared with unaltered OCT maps, enhanced DEJ contrast was shown in OAC maps, both from single A-lines and completed B-frames. En face epidermal thickness and dermal OAC maps both demonstrated significant changes between imaging sessions following burn injury, such as a loss of epidermal texture and decreased OAC. Quantitative analysis also showed that OAC of acute burned skin decreased below that of healthy skin following injury.

CONCLUSIONS

Our study has demonstrated that the OAC estimated from OCT data can be used to enhance imaging contrast to facilitate the automatic segmentation of the epidermal layer, as well as help elucidate our understanding of the pathological changes that occur in human skin when exposed to acute burn injury, which could serve as an objective indicator of skin injury and healing.

Quantitative characterization of human breast tissue based on deep learning segmentation of 3D optical coherence tomography images

In this study, we performed dual-modality optical coherence tomography (OCT) characterization (volumetric OCT imaging and quantitative optical coherence elastography) on human breast tissue specimens. We trained and validated a U-Net for automatic image segmentation. Our results demonstrated that U-Net segmentation can be used to assist clinical diagnosis for breast cancer, and is a powerful enabling tool to advance our understanding of the characteristics for breast tissue. Based on the results obtained from U-Net segmentation of 3D OCT images, we demonstrated significant morphological heterogeneity in small breast specimens acquired through diagnostic biopsy. We also found that breast specimens affected by different pathologies had different structural characteristics. By correlating U-Net analysis of structural OCT images with mechanical measurement provided by quantitative optical coherence elastography, we showed that the change of mechanical properties in breast tissue is not directly due to the change in the amount of dense or porous tissue.

Deep convolutional neural networks: Outperforming established algorithms in the evaluation of industrial optical coherence tomography (OCT) images of pharmaceutical coatings

This paper presents a novel evaluation approach for optical coherence tomography (OCT) image analysis of pharmaceutical solid dosage forms based on deep convolutional neural networks (CNNs). As a proof of concept, CNNs were applied to image data from both, in- and at-line OCT implementations, monitoring film-coated tablets as well as single- and multi-layered pellets. CNN results were compared against results from established algorithms based on ellipse-fitting, as well as to human-annotated ground truth data. Performance benchmarks used include, efficiency (computation speed), sensitivity (number of detections from a defined test set) and accuracy (deviation from the reference method). The results were validated by comparing the output of several algorithms to data manually annotated by human experts and microscopy images of cross-sectional cuts of the same dosage forms as a reference method. In order to guarantee comparability for all results, the algorithms were executed on the same hardware. Since modern OCT systems must operate under real-time conditions in order to be implemented in-line into manufacturing lines, the necessary steps are discussed on how to achieve this goal without sacrificing the algorithmic performance and how to tailor a deep CNN to cope with the high amount of image noise and alterations in object appearance. The developed deep learning approach outperforms static algorithms currently available in pharma applications with respect to performance benchmarks, and represents the next level in real time evaluation of challenging industrial OCT image data.

In vivo assessment of vascular-targeted photodynamic therapy effects on tumor microvasculature using ultrahigh-resolution functional optical coherence tomography

Vascular-targeted photodynamic therapy (VTP) is an emerging treatment for tumors. The change of tumor vasculatures, including a newly-formed microvascular, in response to VTP, is a key assessment parameter for optimizing the treatment effect. However, an accurate assessment of vasculature, particularly the microvasculature's changes in vivo, remains challenging due to the limited resolution afforded by existing imaging modalities. In this study, we demonstrated the in vivo imaging of VTP effects on an A431 tumor-bearing window chamber model of a mouse with an 800-nm ultrahigh-resolution functional optical coherence tomography (UHR-FOCT). We further quantitatively demonstrated the effects of VTP on the size and density of tumor microvasculature before, during, and after the treatment. Our results suggest the promising potential of UHR-FOCT for assessing the tumor treatment with VTP in vivo and in real time to achieve an optimal outcome.

Automatic Segmentation of Epidermis and Hair Follicles in Optical Coherence Tomography Images of Normal Skin by Convolutional Neural Networks

Optical coherence tomography (OCT) is a well-established bedside imaging modality that allows analysis of skin structures in a non-invasive way. Automated OCT analysis of skin layers is of great relevance to study dermatological diseases. In this paper, an approach to detect the epidermal layer along with the follicular structures in healthy human OCT images is presented. To the best of the authors' knowledge, the approach presented in this paper is the only epidermis detection algorithm that segments the pilosebaceous unit, which is of importance in the progression of several skin disorders such as folliculitis, acne, lupus erythematosus, and basal cell carcinoma. The proposed approach is composed of two main stages. The first stage is a Convolutional Neural Network based on U-Net architecture. The second stage is a robust post-processing composed by a Savitzky-Golay filter and Fourier Domain Filtering to fully define the borders belonging to the hair follicles. After validation, an average Dice of 0.83 ± 0.06 and a thickness error of 10.25 μm is obtained on 270 human skin OCT images. Based on these results, the proposed method outperforms other state-of-the-art methods for epidermis segmentation. It demonstrates that the proposed image segmentation method successfully detects the epidermal region in a fully automatic way in addition to defining the follicular skin structures as main novelty.

Phase unwrapping based on a residual en-decoder network for phase images in Fourier domain Doppler optical coherence tomography

To solve the phase unwrapping problem for phase images in Fourier domain Doppler optical coherence tomography (DOCT), we propose a deep learning-based residual en-decoder network (REDN) method. In our approach, we reformulate the definition for obtaining the true phase as obtaining an integer multiple of 2π at each pixel by semantic segmentation. The proposed REDN architecture can provide recognition performance with pixel-level accuracy. To address the lack of phase images that are noise and wrapping free from DOCT systems for training, we used simulated images synthesized with DOCT phase image background noise features. An evaluation study on simulated images, DOCT phase images of phantom milk flowing in a plastic tube and a mouse artery, was performed. Meanwhile, a comparison study with recently proposed deep learning-based DeepLabV3+ and PhaseNet methods for signal phase unwrapping and traditional modified networking programming (MNP) method was also performed. Both visual inspection and quantitative metrical evaluation based on accuracy, specificity, sensitivity, root-mean-square-error, total-variation, and processing time demonstrate the robustness, effectiveness and superiority of our method. The proposed REDN method will benefit accurate and fast DOCT phase image-based diagnosis and evaluation when the detected phase is wrapped and will enrich the deep learning-based image processing platform for DOCT images.