Three‐dimensional mapping of the attenuation coefficient in optical coherence tomography to enhance breast tissue microarchitecture contrast

Effective intraoperative tumor margin assessment is needed to reduce re‐excision rates in breast‐conserving surgery (BCS). Mapping the attenuation coefficient in optical coherence tomography (OCT) throughout a sample to create an image (attenuation imaging) is one promising approach. For the first time, three‐dimensional OCT attenuation imaging of human breast tissue microarchitecture using a wide‐field (up to ~45 × 45 × 3.5 mm) imaging system is demonstrated. Representative results from three mastectomy and one BCS specimen (from 31 specimens) are presented with co‐registered postoperative histology. Attenuation imaging is shown to provide substantially improved contrast over OCT, delineating nuanced features within tumors (including necrosis and variations in tumor cell density and growth patterns) and benign features (such as sclerosing adenosis). Additionally, quantitative micro‐elastography (QME) images presented alongside OCT and attenuation images show that these techniques provide complementary contrast, suggesting that multimodal imaging could increase tissue identification accuracy and potentially improve tumor margin assessment.     

A feasibility study of OCT for anatomical and vascular phenotyping of mouse embryo

The embryo phenotyping of genetic murine model is invaluable when investigating functions of genes underlying embryonic development and birth defect. Although traditional imaging technologies such as ultrasound are very useful for evaluating phenotype of murine embryos, the use of advanced techniques for phenotyping is desirable to obtain more information from genetic research. This letter tests the feasibility of optical coherence tomography (OCT) as a high‐throughput phenotyping tool for murine embryos. Three‐dimensional OCT imaging is performed for live and cleared mouse embryos in the late developmental stage (embryonic day 17.5). By using a dynamic focusing method and OCT angiography (OCTA) approach, our OCT imaging of the embryo exhibits rapid and clean visualization of organ structures deeper than 5 mm and complex microvasculature of perfused blood vessels in the murine embryonic body. This demonstration suggests that OCT imaging can be useful for comprehensively assessing embryo anatomy and angiography of genetically engineered mice.     

Detecting mouse squamous cell carcinoma from submicron full-field optical coherence tomography images by deep learning

The standard medical practice for cancer diagnosis requires histopathology, which is an invasive and time-consuming procedure. Optical coherence tomography (OCT) is an alternative that is relatively fast, noninvasive, and able to capture three-dimensional structures of epithelial tissue. Unlike most previous OCT systems, which cannot capture crucial cellular-level information for squamous cell carcinoma (SCC) diagnosis, the full-field OCT (FF-OCT) technology used in this paper is able to produce images at sub-micron resolution and thereby facilitates the development of a deep learning algorithm for SCC detection. Experimental results show that the SCC detection algorithm can achieve a classification accuracy of 80% for mouse skin. Using the sub-micron FF-OCT imaging system, the proposed SCC detection algorithm has the potential for in-vivo applications.     

Noninvasive multimodal imaging by integrating optical coherence tomography with autofluorescence imaging for dental applications

We report the development of an integrated multifunctional imaging system capable of providing anatomical (optical coherence tomography, OCT), functional (OCT angiography, OCTA) and molecular imaging (light‐induced autofluorescence, LIAF) for in vivo dental applications. Blue excitation light (405 nm) was used for LIAF imaging, while the OCT was powered by a 1310 nm swept laser source. A red‐green‐blue digital camera, with a 450 nm cut‐on broadband optical filter, was used for LIAF detection. The exciting light source and camera were integrated directly with the OCT scanning probe. The integrated system used two noninvasive imaging modalities to improve the speed of in vivo OCT data collection and to better target the regions of interest. The newly designed system maintained the ability to detect differences between healthy and hypomineralized teeth, identify dental biofilm and visualize the microvasculature of gingival tissue. The development of the integrated OCT‐LIAF system provides an opportunity to conduct clinical studies more efficiently, examining changes in oral conditions over time.     

Preclinical mouse model of optical coherence tomography for subcortical brain imaging without dissection

The purpose of this study was to investigate the feasibility of using optical coherence tomography (OCT) to identify internal brain lesions, specifically intracerebral hemorrhage, without dissection. Mice with artificially injected brain hematomas were used to test the OCT system, and the recorded images were compared with microscopic images of the same mouse brains after hematoxylin and eosin staining. The intracranial structures surrounding the hematomas were clearly visualized by the OCT system without dissection. These images reflect the ability of OCT to determine the extent of a lesion in several planes. OCT is a useful technology, and these findings could be used as a starting point for future research in intraoperative imaging.     

Noninvasive detection of nanoscale structural changes in cornea associated with cross‐linking treatment

Corneal cross‐linking (CXL) using ultraviolet‐A (UVA) irradiation with a riboflavin photosensitizer has grown from an interesting concept to a practical clinical treatment for corneal ectatic diseases globally, such as keratoconus. To characterize the corneal structural changes, existing methods such as X‐ray microscopy, transmission electron microscopy, histology and optical coherence tomography (OCT) have been used. However, these methods have various drawbacks such as invasive detection, the impossibility for in vivo measurement, or limited resolution and sensitivity to structural alterations. Here, we report the application of oversampling nanosensitive OCT for probing the corneal structural alterations. The results indicate that the spatial period increases slightly after 30 minutes riboflavin instillation but decreases significantly after 30 minutes UVA irradiation following the Dresden protocol. The proposed noninvasive method can be implemented using existing OCT systems, without any additional components, for detecting nanoscale changes with the potential to assist diagnostic assessment during CXL treatment, and possibly to be a real‐time monitoring tool in clinics.     

The use of optical coherence tomography and convolutional neural networks to distinguish normal and abnormal oral mucosa

Incomplete surgical resection of head and neck squamous cell carcinoma (HNSCC) is the most common cause of local HNSCC recurrence. Currently, surgeons rely on preoperative imaging, direct visualization, palpation and frozen section to determine the extent of tissue resection. It has been demonstrated that optical coherence tomography (OCT), a minimally invasive, nonionizing near infrared mesoscopic imaging modality can resolve subsurface differences between normal and abnormal head and neck mucosa. Previous work has utilized two‐dimensional OCT imaging which is limited to the evaluation of small regions of interest generated frame by frame. OCT technology is capable of performing rapid volumetric imaging, but the capacity and expertise to analyze this massive amount of image data is lacking. In this study, we evaluate the ability of a retrained convolutional neural network to classify three‐dimensional OCT images of head and neck mucosa to differentiate normal and abnormal tissues with sensitivity and specificity of 100% and 70%, respectively. This method has the potential to serve as a real‐time analytic tool in the assessment of surgical margins.     

Distinguishing metastatic triple‐negative breast cancer from nonmetastatic breast cancer using second harmonic generation imaging and resonance Raman spectroscopy

Triple‐negative breast cancer (TNBC) is an aggressive subset of breast cancer that is more common in African‐American and Hispanic women. Early detection followed by intensive treatment is critical to improving poor survival rates. The current standard to diagnose TNBC from histopathology of biopsy samples is invasive and time‐consuming. Imaging methods such as mammography and magnetic resonance (MR) imaging, while covering the entire breast, lack the spatial resolution and specificity to capture the molecular features that identify TNBC. Two nonlinear optical modalities of second harmonic generation (SHG) imaging of collagen, and resonance Raman spectroscopy (RRS) potentially offer novel rapid, label‐free detection of molecular and morphological features that characterize cancerous breast tissue at subcellular resolution. In this study, we first applied MR methods to measure the whole‐tumor characteristics of metastatic TNBC (4T1) and nonmetastatic estrogen receptor positive breast cancer (67NR) models, including tumor lactate concentration and vascularity. Subsequently, we employed for the first time in vivo SHG imaging of collagen and ex vivo RRS of biomolecules to detect different microenvironmental features of these two tumor models. We achieved high sensitivity and accuracy for discrimination between these two cancer types by quantitative morphometric analysis and nonnegative matrix factorization along with support vector machine. Our study proposes a new method to combine SHG and RRS together as a promising novel photonic and optical method for early detection of TNBC.     

Towards quantitative assessment of burn based on photoacoustic and optical coherence tomography

Accurate and timely assessment of the severity of burn is essential for the treatment of burns. Currently, although most first‐degree and third‐degree burns are easily diagnosed through visual inspection or auxiliary diagnostic methods, the second‐degree burn is still difficult to distinguish due to the ambiguity boundaries of second‐degree with first‐degree and third‐degree burns. In this study, we proposed a non‐invasive technique by combing photoacoustic imaging (PAI) and optical coherence tomography (OCT) to multi‐parameter quantitatively assess the burns. The feasibility and capacity of the dual‐mode PAT/OCT for assessing the burns was first testified by tissue‐mimicking phantom and burn wounds in mouse pinna in vivo. The further experiments conducted on the back of rats showed that the changes in skin scattering structure, vascular morphology and blood flow provided by the dual‐mode PAI/OCT system can determine distinct boundaries and depth of the burns. The experimental results prove that combined PAI/OCT as a novel method can be used to assess the severity of burn, which has the potential to diagnose the burns in clinic.     

Development a flexible light‐sheet fluorescence microscope for high‐speed 3D imaging of calcium dynamics and 3D imaging of cellular microstructure

We report a flexible light‐sheet fluorescence microscope (LSFM) designed for studying dynamic events in cardiac tissue at high speed in 3D and the correlation of these events to cell microstructure. The system employs two illumination‐detection modes: the first uses angle‐dithering of a Gaussian light sheet combined with remote refocusing of the detection plane for video‐rate volumetric imaging; the second combines digitally‐scanned light‐sheet illumination with an axially‐swept light‐sheet waist and stage‐scanned acquisition for improved axial resolution compared to the first mode. We present a characterisation of the spatial resolution of the system in both modes. The first illumination‐detection mode achieves dual spectral‐channel imaging at 25 volumes per second with 1024 × 200 × 50 voxel volumes and is demonstrated by time‐lapse imaging of calcium dynamics in a live cardiomyocyte. The second illumination‐detection mode is demonstrated through the acquisition of a higher spatial resolution structural map of the t‐tubule network in a fixed cardiomyocyte cell.     

Quantitative assessment of optical coherence tomography angiography algorithms for neuroimaging

Optical coherence tomography (OCT) angiography can noninvasively map microvascular networks and quantify blood flow in a cerebral cortex with a resolution of 1 to 10 μm and a penetration depth of 2 to 3 mm incorporating OCT signals and angiography algorithms. Different angiography algorithms have been developed in recent years; however, the performance of the algorithms has not been assessed quantitatively for neuroimaging applications. In this paper, we developed four metrics including vascular connectivity, contrast‐to‐noise ratio, signal‐to‐noise ratio and processing time to quantitatively assess the performance of OCT angiography algorithms in image quality and computation speed. After the imaging of a rat cortex using an OCT system, the cerebral microvascular networks were visualized by seven algorithms, and the performance of the algorithms was quantified and compared. Quantitative performance assessment of the algorithms can provide suggestions for the selection of appropriate OCT angiography algorithms in neuroimaging.     

Optical coherence hyperspectral microscopy with a single supercontinuum light source

In the paper, we have developed an optical coherence hyperspectral microscopy with a single supercontinuum light source. The microscopy consists of optical coherence tomography (OCT) and hyperspectral imaging (HSI), which can visualize the structural and functional characteristics of biological tissues. The 500 to 700 nm band is selected for HSI and OCT imaging, where HSI enables imaging of oxygen saturation and hemoglobin (Hb) content, while OCT acquires structural characteristics to assess the morphology of biological tissues. The system performance of the optical coherence hyperspectral microscopy is verified by normal mice ears, and the practical applications of the microscopy is further performed in 4T1 and inflammation Balb/c mice ears in vivo. The experimental results demonstrate that the microscopy has potential to provide complementary information for clinical applications.     

Evaluation of corneal structures in myopic eyes more than twenty‐two years after photorefractive keratectomy

The aim of this study is to evaluate corneal epithelial thickness (CET), corneal densitometry (CD) in 84 myopic eyes (57 patients) more than 22 years after photorefractive keratectomy, using anterior segment‐optical coherence tomography (AS‐OCT) and Scheimpflug imaging system. The CET was significantly higher in all operated eyes than in unoperated eyes in central sector. A statistically significant increase in CD in corneal anterior layer of central sector was shown in groups of operated eyes with greater ablation depth respect to unoperated eyes. While there was no significant difference in CD between the operated eyes groups with lower ablation depth and unoperated eyes. A significant trend toward higher values in anterior CD with deeper ablations in central sector was found. These noninvasive imaging techniques allow to better understand the corneal remodeling process after photoablation and to monitor the patients over time.     

Determination and correction of aberrations in full field optical coherence tomography using phase gradient autofocus by maximizing the likelihood function

A method for numerical estimation and correction of aberrations of the eye in fundus imaging with optical coherence tomography (OCT) is presented. Aberrations are determined statistically by using the estimate based on likelihood function maximization. The method can be considered as an extension of the phase gradient autofocusing algorithm in synthetic aperture radar imaging to 2D optical aberration correction. The efficacy of the proposed method has been demonstrated in OCT fundus imaging with 6λ aberrations. After correction, single photoreceptors were resolved. It is also shown that wave front distortions with high spatial frequencies can be determined and corrected.     

Optical coherence tomography as a noninvasive 3D real time imaging tool for the rapid evaluation of phenotypic variations in insect embryonic development

Noninvasive visualization of embryos at different development stages is crucial for the understanding of the basic developmental biology. It is therefore desirable to have an imaging tool capable of rapidly evaluating the effects of gene manipulation or genome editing in developing embryos for the studies of gene functions and genetic engineering. Here, we propose and demonstrate a novel use of optical coherence tomography (OCT) to noninvasively exam the embryonic development of the migratory locusts in real time with 3‐dimensional (3D) view capability. In particular, we obtain the sufficiently high spatial resolution tomographic 2D and 3D images of live locust embryos throughout their development processes. We show that not only we are able to noninvasively observe all previously known forms of blastokinesis as an embryo develops, such as anatrepsis, katatrepsis, revolution, rotation and diapauses, and determine their precise occurring time or duration, but also discover an unreported rotation form we named “twist.” In addition, with the OCT images we determined the exact occurring time of diapauses of the locusts from Tibetan plateau for the first time. Finally, we demonstrate that OCT systems can be used to rapidly capture the development defects of genetically modified embryos in which certain genes essential for embryonic development were suppressed by RNA interference. Our work shows that OCT is an enabling imaging tool with sufficient spatial resolution for the rapid evaluation of embryonic variations of small animals.     

A waveguide imaging platform for live‐cell TIRF imaging of neurons over large fields of view

Large fields of view (FOVs) in total internal reflection fluorescence microscopy (TIRFM) via waveguides have been shown to be highly beneficial for single molecule localisation microscopy on fixed cells [1,2] and have also been demonstrated for short‐term live‐imaging of robust cell types [3‐5], but not yet for delicate primary neurons nor over extended periods of time. Here, we present a waveguide‐based TIRFM set‐up for live‐cell imaging of demanding samples. Using the developed microscope, referred to as the ChipScope, we demonstrate successful culturing and imaging of fibroblasts, primary rat hippocampal neurons and axons of Xenopus retinal ganglion cells (RGCs). The high contrast and gentle illumination mode provided by TIRFM coupled with the exceptionally large excitation areas and superior illumination homogeneity offered by photonic waveguides have potential for a wide application span in neuroscience applications.     

Delineating papillary dermis around basal cell carcinomas by high and ultrahigh resolution optical coherence tomography—A pilot study

Bedside diagnosis of skin cancer remains a challenging task. The real-time noninvasive technology of optical coherence tomography (OCT) masters a high diagnostic accuracy in basal cell carcinoma (BCC) but a lower specificity in recognizing imitators and other carcinomas. We investigate the delicate signal of papillary dermis using an in-house developed ultrahigh resolution OCT (UHR-OCT) system with shadow compensation and a commercial multi-focus high resolution OCT (HR-OCT) system for clinical BCC imaging. We find that the HR-OCT system struggled to resolve the dark band signal of papillary dermis where the UHR-OCT located this in all cases and detected changes in signal width. UHR-OCT is able to monitor extension and position of papillary dermis suggesting a novel feature for delineating superficial BCCs in pursuit of a fast accurate diagnosis. Comprehensive studies involving more patients are imperative in order to corroborate results.     

Tissue clearing‐based method for unobstructed three‐dimensional imaging of mouse penis with subcellular resolution

Although mice are widely used to elucidate factors contributing to penile disorders and develop treatment options, quantification of tissue changes upon intervention is either limited to minuscule tissue volume (histology) or acquired with limited spatial resolution (MRI/CT). Thus, imaging method suitable for expeditious acquisition of the entire mouse penis with subcellular resolution is described that relies on both aqueous‐ (clear, unobstructed brain imaging cocktails and computational analysis) and solvent‐based (fluorescence‐preserving capability imaging of solvent‐cleared organs) tissue optical clearing (TOC). The combined TOC approach allows to image mouse penis innervation and vasculature with unprecedented detail and, for the first time, reveals the three‐dimensional structure of murine penis fibrocartilage.     

Optical coherence tomography image denoising using a generative adversarial network with speckle modulation

Optical coherence tomography (OCT) is widely used for biomedical imaging and clinical diagnosis. However, speckle noise is a key factor affecting OCT image quality. Here, we developed a custom generative adversarial network (GAN) to denoise OCT images. A speckle‐modulating OCT (SM‐OCT) was built to generate low speckle images to be used as the ground truth. In total, 210 000 SM‐OCT images were used for training and validating the neural network model, which we call SM‐GAN. The performance of the SM‐GAN method was further demonstrated using online benchmark retinal images, 3D OCT images acquired from human fingers and OCT videos of a beating fruit fly heart. The denoise performance of the SM‐GAN model was compared to traditional OCT denoising methods and other state‐of‐the‐art deep learning based denoise networks. We conclude that the SM‐GAN model presented here can effectively reduce speckle noise in OCT images and videos while maintaining spatial and temporal resolutions.     

N2NSR-OCT: Simultaneous denoising and super-resolution in optical coherence tomography images using semisupervised deep learning

Optical coherence tomography (OCT) imaging shows a significant potential in clinical routines due to its noninvasive property. However, the quality of OCT images is generally limited by inherent speckle noise of OCT imaging and low sampling rate. To obtain high signal-to-noise ratio (SNR) and high-resolution (HR) OCT images within a short scanning time, we presented a learning-based method to recover high-quality OCT images from noisy and low-resolution OCT images. We proposed a semisupervised learning approach named N2NSR-OCT, to generate denoised and super-resolved OCT images simultaneously using up- and down-sampling networks (U-Net (Semi) and DBPN (Semi)). Additionally, two different super-resolution and denoising models with different upscale factors (2× and 4× ) were trained to recover the high-quality OCT image of the corresponding down-sampling rates. The new semisupervised learning approach is able to achieve results comparable with those of supervised learning using up- and down-sampling networks, and can produce better performance than other related state-of-the-art methods in the aspects of maintaining subtle fine retinal structures.