Optical coherence tomography follow‐up of patients treated from periodontal disease

Optical coherence tomography (OCT) is one of the most important imaging modalities for biophotonics applications. In this work, an important step towards the clinical use of OCT in dental practice is reported, by following‐up patients treated from periodontal disease (PD). A total of 147 vestibular dental sites from 14 patients diagnosed with PD were evaluated prior and after treatment, using a swept‐source OCT and two periodontal probes (Florida probe and North Carolina) for comparison. The evaluation was performed at four stages: day 0, day 30, day 60 and day 90. Exceptionally one patient was evaluated 1‐year after treatment. It was possible to visualize in the two‐dimensional images the architectural components that compose the periodontal anatomy, and identify the improvements in biofilm and dental calculus upon treatment. In the follow‐up after the treatment, it was observed in some cases decrease of the gingival thickness associated with extinction of gingival calculus. In some cases, the improvement of both depth of probing with the traditional probes and the evidence in the images of the region was emphasized. The study evidenced the ability of OCT in the identification of periodontal structures and alterations, being an important noninvasive complement or even alternative for periodontal probes for treatment follow‐up. OCT system being used in a clinical environment. Above OCT image (left) prior treatment and (right) 30 days after treatment.      

Convolutional neural network‐based malaria diagnosis from focus stack of blood smear images acquired using custom‐built slide scanner

The present paper introduces a focus stacking‐based approach for automated quantitative detection of Plasmodium falciparum malaria from blood smear. For the detection, a custom designed convolutional neural network (CNN) operating on focus stack of images is used. The cell counting problem is addressed as the segmentation problem and we propose a 2‐level segmentation strategy. Use of CNN operating on focus stack for the detection of malaria is first of its kind, and it not only improved the detection accuracy (both in terms of sensitivity [97.06%] and specificity [98.50%]) but also favored the processing on cell patches and avoided the need for hand‐engineered features. The slide images are acquired with a custom‐built portable slide scanner made from low‐cost, off‐the‐shelf components and is suitable for point‐of‐care diagnostics. The proposed approach of employing sophisticated algorithmic processing together with inexpensive instrumentation can potentially benefit clinicians to enable malaria diagnosis.      

Pixel classification method in optical coherence tomography for tumor segmentation and its complementary usage with OCT microangiography

A novel machine‐learning method to distinguish between tumor and normal tissue in optical coherence tomography (OCT) has been developed. Pre‐clinical murine ear model implanted with mouse colon carcinoma CT‐26 was used. Structural‐image‐based feature sets were defined for each pixel and machine learning classifiers were trained using “ground truth” OCT images manually segmented by comparison with histology. The accuracy of the OCT tumor segmentation method was then quantified by comparing with fluorescence imaging of tumors expressing genetically encoded fluorescent protein KillerRed that clearly delineates tumor borders. Because the resultant 3D tumor/normal structural maps are inherently co‐registered with OCT derived maps of tissue microvasculature, the latter can be color coded as belonging to either tumor or normal tissue. Applications to radiomics‐based multimodal OCT analysis are envisioned.      

One‐to‐one registration of en‐face optical coherence tomography attenuation coefficients with histology of a prostatectomy specimen

Optical coherence tomography (OCT), enables high‐resolution 3D imaging of the morphology of light scattering tissues. From the OCT signal, parameters can be extracted and related to tissue structures. One of the quantitative parameters is the attenuation coefficient; the rate at which the intensity of detected light decays in depth. To couple the quantitative parameters with the histology one‐to‐one registration is needed. The primary aim of this study is to validate a registration method of quantitative OCT parameters to histological tissue outcome through one‐to‐one registration of OCT with histology. We matched OCT images of unstained fixated prostate tissue slices with corresponding histology slides, wherein different histologic types were demarcated. Attenuation coefficients were determined by a supervised automated exponential fit (corrected for point spread function and sensitivity roll‐off related signal losses) over a depth of 0.32 mm starting from 0.10 mm below the automatically detected tissue edge. Finally, the attenuation coefficients corresponding to the different tissue types of the prostate were compared. From the attenuation coefficients, we produced the squared relative residue and goodness‐of‐fit metric R². This article explains the method to perform supervised automated quantitative analysis of OCT data, and the one‐to‐one registration of OCT extracted quantitative data with histopathological outcomes.      

Biometry of Anterior Segment of Human Eye on Both Horizontal and Vertical Meridians during Accommodation Imaged with Extended Scan Depth Optical Coherence Tomography

Purpose

To determine the biometry of anterior segment dimensions of the human eye on both horizontal and vertical meridians with extended scan depth optical coherence tomography (OCT) during accommodation.

Methods

Twenty pre-presbyopic volunteers, aged between 24 and 30, were recruited. The ocular anterior segment of each subject was imaged using an extended scan depth OCT under non- and 3.0 diopters (D) of accommodative demands on both horizontal and vertical meridians. All the images were analyzed to yield the following parameters: pupil diameter (PD), anterior chamber depth (ACD), anterior and posterior surface curvatures of the crystalline lens (ASC and PSC) and the lens thickness (LT). Two consecutive measurements were performed to assess the repeatability and reproducibility of this OCT. They were evaluated by calculating the within-subject standard deviation (SD), a paired t-test, intra-class correlation coefficients (ICC) and the coefficient of repeatability/reproducibility (CoR).

Results

There were no significant differences between two consecutive measurements on either horizontal or vertical meridians under both two different accommodative statuses (P>0.05). The ICC for all parameters ranged from 0.775 to 0.998, except for the PSC (0.550) on the horizontal meridian under the non-accommodative status. In addition, the CoR for most of the parameters were excellent (0.004% to 4.89%). In all the parameters, only PD and PSC were found different between the horizontal and vertical meridians under both accommodative statuses (P<0.05). PD, ACD, ASC and PSC under accommodative status were significantly smaller than those under the non-accommodative status, except that the PSC at the vertical meridian did not change. In addition, LT was significantly increased when accommodation.

Conclusion

The extended scan depth OCT successfully measured the dimensions of the anterior eye during accommodation with good repeatability and reproducibility on both horizontal and vertical meridians. The asymmetry of lens posterior surface and oval-shaped pupil were found during accommodation.     

K‐distribution three‐dimensional mapping of biological tissues in optical coherence tomography

Probability density function (PDF) analysis with K‐distribution model of optical coherence tomography (OCT) intensity signals has previously yielded a good representation of the average number of scatterers in a coherence volume for microspheres‐in‐water systems, and has shown initial promise for biological tissue characterization. In this work, we extend these previous findings, based on single point M‐mode or two‐dimenstional slice analysis, to full three‐dimensional (3D) imaging maps of the shape parameter α of the K‐distribution PDF. After selecting a suitably sized 3D evaluation window, and verifying methodology in phantoms, the resultant parametric α images obtained in different animal tissues (rat liver and brain) show new contrasting ability not seen in conventional OCT intensity images.      

In vivo detection of endotracheal tube biofilms in intubated critical care patients using catheter‐based optical coherence tomography

The formation of biofilms in the endotracheal tubes (ETTs) of intubated patients on mechanical ventilation is associated with a greater risk of ventilator‐associated pneumonia and death. New technologies are needed to detect and monitor ETTs in vivo for the presence of these biofilms. Longitudinal OCT imaging was performed in mechanically ventilated subjects at 24‐hour intervals until extubation to detect the formation and temporal changes of in vivo ETT biofilms. OCT‐derived attenuation coefficient images were used to differentiate between mucus and biofilm. Extubated ETTs were examined with optical and electron microscopy, and all imaging results were correlated with standard‐of‐care clinical test reports. OCT and attenuation coefficient images from four subjects were positive for ETT biofilms and were negative for two subjects. The processed and stained extubated ETTs and clinical reports confirmed the presence/absence of biofilms in all subjects. Our findings confirm that OCT can detect and differentiate between biofilm‐positive and biofilm‐negative groups (P < 10^?5). OCT image‐based features may serve as biomarkers for direct in vivo detection of ETT biofilms and help drive investigation of new management strategies to reduce the incidence of VAP.      

High‐definition optical coherence tomography of melanocytic skin lesions

High‐definition optical coherence tomography (HD‐OCT) scanners have recently been developed. We assessed micromorphological HD‐OCT correlates of benign naevi (BN) and malignant melanoma (MM). 28 BN and 20 MM were studied using HD‐OCT and histology. Epidermal honeycomb/cobblestone pattern, regular junctional cell nests, and edged papillae are more often observed in BN, whereas fusion of rete ridges, pagetoid cells and junctional and/or dermal nests with atypical cells are more frequently seen in MM. A high overlap of HD‐OCT features in BN and MM was observed and in 20% of MM we did not find evidence for malignancy in OCT images at all. Using HD‐OCT it is possible to visualize architectural and cellular alterations of melanocytic skin lesions. The overlap of HD‐OCT features seen in BN and MM and the absence of suspicious HD‐OCT features in some MM represents an important limitation of HD‐OCT affecting the sensitivity of HD‐OCT in diagnosing MM.

High‐definition optical coherence tomography and the corresponding vertically sectioned histology of a compound naevus.     

Capsid Mutated Adeno-Associated Virus Delivered to the Anterior Chamber Results in Efficient Transduction of Trabecular Meshwork in Mouse and Rat

Background

Adeno associated virus (AAV) is well known for its ability to deliver transgenes to retina and to mediate improvements in animal models and patients with inherited retinal disease. Although the field is less advanced, there is growing interest in AAV’s ability to target cells of the anterior segment. The purpose of our study was to fully articulate a reliable and reproducible method for injecting the anterior chamber (AC) of mice and rats and to investigate the transduction profiles of AAV2- and AAV8-based capsid mutants containing self-complementary (sc) genomes in the anterior segment of the eye.

Methodology/Principle Findings

AC injections were performed in C57BL/6 mice and Sprague Dawley rats. The cornea was punctured anterior of the iridocorneal angle. To seal the puncture site and to prevent reflux an air bubble was created in the AC. scAAVs expressing GFP were injected and transduction was evaluated by immunohistochemistry. Both parent serotype and capsid modifications affected expression. scAAV2- based vectors mediated efficient GFP-signal in the corneal endothelium, ciliary non-pigmented epithelium (NPE), iris and chamber angle including trabecular meshwork, with scAAV2(Y444F) and scAAV2(triple) being the most efficient.

Conclusions/Significance

This is the first study to semi quantitatively evaluate transduction of anterior segment tissues following injection of capsid-mutated AAV vectors. scAAV2- based vectors transduced corneal endothelium, ciliary NPE, iris and trabecular meshwork more effectively than scAAV8-based vectors. Mutagenesis of surface-exposed tyrosine residues greatly enhanced transduction efficiency of scAAV2 in these tissues. The number of Y-F mutations was not directly proportional to transduction efficiency, however, suggesting that proteosomal avoidance alone may not be sufficient. These results are applicable to the development of targeted, gene-based strategies to investigate pathological processes of the anterior segment and may be applied toward the development of gene-based therapies for glaucoma and acquired or inherited corneal anomalies.     

Automatic counting of birds in a bird deterrence field trial

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Dye free automated cell counting and analysis

We have developed an automated cell counting method that uses images obtained at multiple focal heights to enumerate cells in confluent culture. By taking the derivative of image intensity with respect to focal height using two complementary images, we are able to count high‐density monolayers of cells over a large image area. Our method resists errors arising from variability in the focal plane caused by flatness or tilt non‐uniformities with a minimal amount of focal plane alignment, allowing the automated collection of images across a large area. Biotechnol. Bioeng. © 2013 Wiley Periodicals, Inc.     

General model for depth‐resolved estimation of the optical attenuation coefficients in optical coherence tomography

We present the proof of concept of a general model that uses the tissue sample transmittance as input to estimate the depth‐resolved attenuation coefficient of tissue samples using optical coherence tomography (OCT). This method allows us to obtain an image of tissue optical properties instead of intensity contrast, guiding diagnosis and tissues differentiation, extending its application from thick to thin samples. The performance of our method was simulated and tested with the assistance of a home built single‐layered and multilayered phantoms (~100 μm each layer) with known attenuation coefficient on the range of 0.9 to 2.32 mm^?1. It is shown that the estimated depth‐resolved attenuation coefficient recovers the reference values, measured by using an integrating sphere followed by the inverse adding doubling processing technique. That was corroborated for all situations when the correct transmittance value is used with an average difference of 7%. Finally, we applied the proposed method to estimate the depth‐resolved attenuation coefficient for a thin biological sample, demonstrating the ability of our method on real OCT images.     

A low‐cost,automated parasite diagnostic system via a portable,robotic microscope and deep learning

Manual hand counting of parasites in fecal samples requires costly components and substantial expertise, limiting its use in resource‐constrained settings and encouraging overuse of prophylactic medication. To address this issue, a cost‐effective, automated parasite diagnostic system that does not require special sample preparation or a trained user was developed. It is composed of an inexpensive (~US$350), portable, robotic microscope that can scan over the size of an entire McMaster chamber (100 mm²) and capture high‐resolution (~1 μm lateral resolution) bright field images without need for user intervention. Fecal samples prepared using the McMaster flotation method were imaged, with the imaging region comprising the entire McMaster chamber. These images are then automatically segmented and analyzed using a trained convolution neural network (CNN) to robustly separate eggs from background debris. Simple postprocessing of the CNN output yields both egg species and egg counts. The system was validated by comparing accuracy with hand‐counts by a trained operator, with excellent performance. As a further demonstration of utility, the system was used to conveniently quantify drug response over time in a single animal, showing residual disease due to Anthelmintic resistance after 2 weeks.     

Biocompatibility evaluation of bioprinted decellularized collagen sheet implanted in vivo cornea using swept‐source optical coherence tomography

Corneal transplantation by full‐thickness penetrating keratoplasty with human donor tissue is a widely accepted treatment for damaged or diseased corneas. Although corneal transplantation has a high success rate, a shortage of high‐quality donor tissue is a considerable limitation. Therefore, bioengineered corneas could be an effective solution for this limitation, and a decellularized extracellular matrix comprises a promising scaffold for their fabrication. In this study, three‐dimensional bioprinted decellularized collagen sheets were implanted into the stromal layer of the cornea of five rabbits. We performed in vivo noninvasive monitoring of the rabbit corneas using swept‐source optical coherence tomography (OCT) after implanting the collagen sheets. Anterior segment OCT images and averaged amplitude‐scans were acquired biweekly to monitor corneal thickness after implantation for 1 month. The averaged cornea thickness in the control images was 430.3 ± 5.9 μm, while the averaged thickness after corneal implantation was 598.5 ± 11.8 μm and 564.5 ± 12.5 μm at 2 and 4 weeks, respectively. The corneal thickness reduction of 34 μm confirmed the biocompatibility through the image analysis of the depth‐intensity profile base. Moreover, hematoxylin and eosin staining supported the biocompatibility evaluation of the bioprinted decellularized collagen sheet implantation. Hence, the developed bioprinted decellularized collagen sheets could become an alternative solution to human corneal donor tissue, and the proposed image analysis procedure could be beneficial to confirm the success of the surgery.      

Performance of a cost‐effective and automated blood counting system for resource‐limited settings operated by trained and untrained users

Current flow‐based blood counting devices require expensive and centralized medical infrastructure and are not appropriate for field use. In this article we report a streamlined, easy‐to‐use method to count red blood cells (RBC), white blood cells (WBC), platelets (PLT) and 3‐part WBC differential through a cost‐effective and automated image‐based blood counting system. The approach consists of using a compact, custom‐built microscope with large field‐of‐view to record bright‐field and fluorescence images of samples that are diluted with a single, stable reagent mixture and counted using automatic algorithms. Sample collection utilizes volume‐controlled capillary tubes, which are then dropped into a premixed, shelf‐stable solution to stain and dilute in a single step. Sample measurement and analysis are fully automated, requiring no input from the user. Cost of the system is minimized through the use of custom‐designed motorized components. We compare the performance of our system, as operated by trained and untrained users, to the clinical gold standard on 120 adult blood samples, demonstrating agreement within Clinical Laboratory Improvement Amendments guidelines, with no statistical difference in performance among different operator groups. The system's cost‐effectiveness, automation and performance indicate that it can be successfully translated for use in low‐resource settings where central hematology laboratories are not accessible.      

OCT layered tomography of the cornea provides new insights on remodeling after photorefractive keratectomy

OCT (optical coherence tomography) of corneal layers was generated to analyze the remodeling of the epithelium and stroma after photorefractive keratectomy (PRK). Myopic PRK was performed in 15 patients. One eye underwent manual scraping of epithelium while the other was treated with Epi clear. Epi clear allowed a gentler removal of the epithelium compared to manual scraping. Scheimpflug (Pentacam, OCULUS Optikgerate Gmbh, Wetzlar, Germany) and OCT (RTVue, Optovue Inc., Fremont, California, USA) scans of the cornea were performed before and after PRK (3 months). The OCT scanner and Pentacam acquired 8 and 25 radial 2‐D scans of the cornea, respectively. The results showed similar topographic changes on the anterior corneal surface between Scheimpflug and OCT imaging. The curvature of the underlying anterior surface of the stroma after PRK was similar to the anterior corneal surface (air‐epithelium interface), when measured with OCT. Aberrometric changes were mostly similar between Scheimpflug and OCT. However, Scheimpflug imaging reported greater changes in spherical aberration and corneal higher order aberrations than OCT after PRK. This is the first study to quantify the curvatures of the stromal layers with OCT after PRK. New insights were gained, which could be useful for refinement of surgical ablation algorithms, refractive procedures and detection of ectasia.      

A Novel Method for Measuring Anterior Segment Area of the Eye on Ultrasound Biomicroscopic Images Using Photoshop

Purpose

To describe a novel method for quantitative measurement of area parameters in ocular anterior segment ultrasound biomicroscopy (UBM) images using Photoshop software and to assess its intraobserver and interobserver reproducibility.

Methods

Twenty healthy volunteers with wide angles and twenty patients with narrow or closed angles were consecutively recruited. UBM images were obtained and analyzed using Photoshop software by two physicians with different-level training on two occasions. Borders of anterior segment structures including cornea, iris, lens, and zonules in the UBM image were semi-automatically defined by the Magnetic Lasso Tool in the Photoshop software according to the pixel contrast and modified by the observers. Anterior chamber area (ACA), posterior chamber area (PCA), iris cross-section area (ICA) and angle recess area (ARA) were drawn and measured. The intraobserver and interobserver reproducibilities of the anterior segment area parameters and scleral spur location were assessed by limits of agreement, coefficient of variation (CV), and intraclass correlation coefficient (ICC).

Results

All of the parameters were successfully measured by Photoshop. The intraobserver and interobserver reproducibilities of ACA, PCA, and ICA were good, with no more than 5% CV and more than 0.95 ICC, while the CVs of ARA were within 20%. The intraobserver and interobserver reproducibilities for defining the spur location were more than 0.97 ICCs. Although the operating times for both observers were less than 3 minutes per image, there was significant difference in the measuring time between two observers with different levels of training (p<0.001).

Conclusion

Measurements of ocular anterior segment areas on UBM images by Photoshop showed good intraobserver and interobserver reproducibilties. The methodology was easy to adopt and effective in measuring.     

TiO2‐coated fluoride nanoparticles for dental multimodal optical imaging

Core‐shell nanostructures associated with photonics techniques have found innumerous applications in diagnostics and therapy. In this work, we introduce a novel core‐shell nanostructure design that serves as a multimodal optical imaging contrast agent for dental adhesion evaluation. This nanostructure consists of a rare‐earth‐doped (NaYF₄:Yb 60%, Tm 0.5%)/NaYF₄ particle as the core (hexagonal prism, ~51 nm base side length) and the highly refractive TiO₂ material as the shell (~thickness of 15 nm). We show that the TiO₂ shell provides enhanced contrast for optical coherence tomography (OCT), while the rare‐earth‐doped core upconverts excitation light from 975 nm to an emission peaked at 800 nm for photoluminescence imaging. The OCT and the photoluminescence wide‐field images of human tooth were demonstrated with this nanoparticle core‐shell contrast agent. In addition, the described core‐shell nanoparticles (CSNps) were dispersed in the primer of a commercially available dental bonding system, allowing clear identification of dental adhesive layers with OCT. We evaluated that the presence of the CSNp in the adhesive induced an enhancement of 67% scattering coefficient to significantly increase the OCT contrast. Moreover, our results highlight that the upconversion photoluminescence in the near‐infrared spectrum region is suitable for image of deep dental tissue.      

Automatic skin lesion area determination of basal cell carcinoma using optical coherence tomography angiography and a skeletonization approach: Preliminary results

Cutaneous blood flow plays a key role in numerous physiological and pathological processes and has significant potential to be used as a biomarker to diagnose skin diseases such as basal cell carcinoma (BCC). The determination of the lesion area and vascular parameters within it, such as vessel density, is essential for diagnosis, surgical treatment and follow‐up procedures. Here, an automatic skin lesion area determination algorithm based on optical coherence tomography angiography (OCTA) images is presented for the first time. The blood vessels are segmented within the OCTA images and then skeletonized. Subsequently, the skeleton is searched over the volume and numerous quantitative vascular parameters are calculated. The vascular density is then used to segment the lesion area. The algorithm is tested on both nodular and superficial BCC, and comparing with dermatological and histological results, the proposed method provides an accurate, non‐invasive, quantitative and automatic tool for BCC lesion area determination.     

Automated assessment of breast cancer margin in optical coherence tomography images via pretrained convolutional neural network

The benchmark method for the evaluation of breast cancers involves microscopic testing of a hematoxylin and eosin (H&E)‐stained tissue biopsy. Resurgery is required in 20% to 30% of cases because of incomplete excision of malignant tissues. Therefore, a more accurate method is required to detect the cancer margin to avoid the risk of recurrence. In the recent years, convolutional neural networks (CNNs) has achieved excellent performance in the field of medical images diagnosis. It automatically extracts the features from the images and classifies them. In the proposed study, we apply a pretrained Inception‐v3 CNN with reverse active learning for the classification of healthy and malignancy breast tissue using optical coherence tomography (OCT) images. This proposed method attained the sensitivity, specificity and accuracy is 90.2%, 91.7% and 90%, respectively, with testing datasets collected from 48 patients (22 normal fibro‐adipose tissue and 26 Invasive ductal carcinomas cancerous tissues). The trained network utilizes for the breast cancer margin assessment to predict the tumor with negative margins. Additionally, the network output is correlated with the corresponding histology image. Our results lay the foundation for the future that the proposed method can be used to perform automatic intraoperative identification of breast cancer margins in real‐time and to guide core needle biopsies.