Convolutional dictionary learning for blind deconvolution of optical coherence tomography images
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Three-Dimensional Optical Coherence Tomography
Three-dimensional (3D) optical coherence tomography (OCT) is an advanced method of noninvasive infrared imaging of tissues in depth. Heretofore, commercial OCT systems for 3D imaging have been designed principally for external ophthalmological examination. As explained below, such systems have been based on a one-dimensional OCT principle, and in the operation of such a system, 3D imaging is accomplished partly by means of a combination of electronic scanning along the optical (Z) axis and mechanical scanning along the two axes (X and Y) orthogonal to the optical axis. In 3D OCT, 3D imaging involves a form of electronic scanning (without mechanical scanning) along all three axes. Consequently, the need for mechanical adjustment is minimal and the mechanism used to position the OCT probe can be correspondingly more compact. A 3D OCT system also includes a probe of improved design and utilizes advanced signal- processing techniques. Improvements in performance over prior OCT systems include finer resolution, greater speed, and greater depth of field.
Gutin, Mikhail↗
Computer-aided Veress needle guidance using endoscopic optical coherence tomography and convolutional neural networks
During laparoscopic surgery, the Veress needle is commonly used in pneumoperitoneum establishment. Precise placement of the Veress needle is still a challenge for the surgeon. In this study, a computer-aided endoscopic optical coherence tomography (OCT) system was developed to effectively and safely guide Veress needle insertion. This endoscopic system was tested by imaging subcutaneous fat, muscle, abdominal space, and the small intestine from swine samples to simulate the surgical process, including the situation with small intestine injury. Each tissue layer was visualized in OCT images with unique features and subsequently used to develop a system for automatic localization of the Veress needle tip by identifying tissue layers (or spaces) and estimating the needle-to-tissue distance. We used convolutional neural networks (CNNs) in automatic tissue classification and distance estimation. In conclusion, the average testing accuracy in tissue classification was 98.53 ± 0.39%, and the average testing relative error in distance estimation reached 4.42 ± 0.56% (36.09 ± 4.92 μm).
59 BASIC BIOLOGICAL SCIENCES↗
Optical coherence tomography imaging of plant root growth in soil
Complex interactions between roots and soil provide the nutrients and physical support required for robust plant growth. Yet, visualizing the root-soil interface is challenged by soil’s opaque scattering characteristics. In this paper, we describe methods for using optical coherence tomography (OCT) to provide non-destructive 3D and cross-sectional root imaging not available with traditional bright field microscopy. OCT is regularly used for bioimaging, especially in ophthalmology where it can detect retinal abnormalities. Prior use of OCT in plant biology has focused on surface defects of above ground tissues, predominantly in food crops. Our results show OCT is also viable for detailed, in situ study of living plant roots.
59 BASIC BIOLOGICAL SCIENCES↗
From pixels to patterns: Coupling Optical Coherence Tomography and machine learning for monitoring coastal wetland root systems
Coastal wetlands are crucial in shoreline stabilization, carbon sequestration, and storm protection. Yet, due to limitations in traditional destructive sampling techniques, the belowground biomass (live root mass) and necromass (dead and decaying roots) remain difficult to assess in coastal wetlands, limiting our understanding on coastal resilience, nutrient cycling, and soil structure. This study employs Optical Coherence Tomography (OCT) as a high-resolution imaging technique to analyze root biomass and necromass in the Terrebonne Basin, Louisiana. A Random Forest (RF) model was developed to classify root health states based on OCT-derived features, achieving an accuracy of 70% in distinguishing live from dead root segments. The results demonstrate that OCT, combined with ML, offers a promising novel approach to root analysis, providing fine-scale insights into root morphology and decay patterns that are not easily captured by conventional methods. This research lays the foundation for future integration of OCT with complementary imaging modalities such as X-ray Computed Tomography (XCT) and advanced ML algorithms to enhance classification accuracy and scalability. Future work aims to expand the dataset diversity across different wetland types and apply the methodology for large-scale, repeatable assessments of root biomass turnover and accumulation, with important implications for wetland monitoring, conservation, and restoration under changing environmental conditions.
AI/ML↗
Integration of Optical Coherence Tomography Scan Patterns to Augment Clinical Data Suite
Vision changes identified in long duration spaceflight astronauts has led Space Medicine at NASA to adopt a more comprehensive clinical monitoring protocol. Optical Coherence Tomography (OCT) was recently implemented at NASA, including on board the International Space Station in 2013. NASA is collaborating with Heidelberg Engineering to increase the fidelity of the current OCT data set by integrating the traditional circumpapillary OCT image with radial and horizontal block images at the optic nerve head. The retinal nerve fiber layer was segmented by two experienced individuals. Intra-rater (N=4 subjects and 70 images) and inter-rater (N=4 subjects and 221 images) agreement was performed. The results of this analysis and the potential benefits will be presented.
Mason, S.↗
3D Optical Coherence Tomography image processing in BISCAP: characterization of biofilm structure and properties
Abstract Motivation BISCAP is a state-of-the-art tool for automatically characterizing biofilm images obtained from Optical Coherence Tomography. Limited availability of other software tools is reported in the field. BISCAP’s first version processes 2D images only. Processing 3D images is a problem of greater scientific relevance since it deals with the entire structure of biofilms instead of their 2D slices. Results Building on the image-processing principles and algorithms proposed earlier for 2D images, these were adapted to the 3D case, and a more general implementation of BISCAP was developed. The primary goal concerns the extension of the initial methodology to incorporate the depth axis in 3D images; multiple improvements were also made to boost computational performance. The calculation of structural properties and visual outputs was extended to offer new insights into the 3D structure of biofilms. BISCAP was tested using 3D images of biofilms with different morphologies, consistently delivering accurate characterizations of 3D structures in a few minutes using standard laptop machines. Low user dependency is required for image analysis. Availability and implementation BISCAP is available from https://github.com/diogonarciso/BISCAP. All images used in the tutorials and the validation examples are available from https://web.fe.up.pt/∼fgm/biscap3d.
Narciso, Diogo A. C. (ORCID:0000000227767477)↗
Development of polarization-sensitive optical coherence tomography imaging platform and metrics to quantify electrostimulation-induced peripheral nerve injury in vivo in a small animal model
Neuromodulation devices are rapidly evolving for the treatment of neurological diseases and conditions. Injury from implantation or long-term use without obvious functional losses is often only detectable through terminal histology. New technologies are needed that assess the peripheral nervous system (PNS) under normal and diseased or injured conditions. We aim to demonstrate an imaging and stimulation platform that can elucidate the biological mechanisms and impacts of neurostimulation in the PNS and apply it to the sciatic nerve to extract imaging metrics indicating electrical overstimulation. A sciatic nerve injury model in a 15-rat cohort was observed using a newly developed imaging and stimulation platform that can detect electrical overstimulation effects with polarization-sensitive optical coherence tomography. The sciatic nerve was electrically stimulated using a custom-developed nerve holder with embedded electrodes for 1 h, followed by a 1-h recovery period, delivered at above-threshold Shannon model k-values in experimental groups: sham control (SC, n = 5, 0.0 mA / 0 Hz), stimulation level 1 (SL1, n = 5, 3.4 mA / 50 Hz, and k = 2.57), and stimulation level 2 (SL2, n = 5, 6.8 mA / 100 Hz, and k = 3.17). The stimulation and imaging system successfully captured study data across the cohort. When compared to a SC after a 1-week recovery, the fascicle closest to the stimulation lead showed an average change of +4 % / – 309 % (SL1/SL2) in phase retardation and –79 % / – 148 % in optical attenuation relative to SC. Analysis of immunohistochemistry (IHC) shows a +1 % / – 36 % difference in myelin pixel counts and –13 % / + 29 % difference in axon pixel counts, and an overall increase in cell nuclei pixel count of +20 % / + 35 % . These metrics were consistent with IHC and hematoxylin/eosin tissue section analysis. The poststimulation changes observed in our study are manifestations of nerve injury and repair, specifically degeneration and angiogenesis. Optical imaging metrics quantify these processes and may help evaluate the safety and efficacy of neuromodulation devices.
60 APPLIED LIFE SCIENCES↗
Epidural anesthesia needle guidance by forward-view endoscopic optical coherence tomography and deep learning
Epidural anesthesia requires injection of anesthetic into the epidural space in the spine. Accurate placement of the epidural needle is a major challenge. To address this, we developed a forward-view endoscopic optical coherence tomography (OCT) system for real-time imaging of the tissue in front of the needle tip during the puncture. We tested this OCT system in porcine backbones and developed a set of deep learning models to automatically process the imaging data for needle localization. A series of binary classification models were developed to recognize the five layers of the backbone, including fat, interspinous ligament, ligamentum flavum, epidural space, and spinal cord. The classification models provided an average classification accuracy of 96.65%. During puncture, it is important to maintain a safe distance between the needle tip and the dura mater. Regression models were developed to estimate that distance based on the OCT imaging data. Based on the Inception architecture, our models achieved a mean absolute percentage error of 3.05% ± 0.55%. Overall, our results validated the technical feasibility of using this novel imaging strategy to automatically recognize different tissue structures and measure the distances ahead of the needle tip during the epidural needle placement.
60 APPLIED LIFE SCIENCES↗
Exploratory Analysis of Carbon Dioxide Levels, Ultrasound and Optical Coherence Tomography Measures of the Eye During ISS Missions
Enhanced screening for the Visual Impairment/Intracranial Pressure (VIIP) syndrome has been implemented to better characterize the ocular and vision changes observed in some long-duration crewmembers. This includes implementation of in-flight ultrasound in 2010 and optical coherence tomography (OCT) in 2013. Potential risk factors for VIIP include cardiovascular health, diet, anatomical and genetic factors, and environmental conditions. Carbon dioxide (CO2), a potent vasodilator, is chronically elevated on the International Space Station (ISS) relative to ambient levels on Earth, and is a plausible risk factor for VIIP. In an effort to understand the possible associations between CO2 and VIIP, this study explores the relationship of ambient CO2 levels on ISS compared to inflight ultrasound and OCT measures of the eye obtained from ISS crewmembers. CO2 measurements were aggregated from Operational Data Reduction Complex and Node 3 major constituent analyzers (MCAs) on ISS or from sensors located in the European Columbus module, as available. CO2 levels in the periods between each ultrasound and OCT session are summarized using timeseries metrics, including time-weighted means and variances. Partial least squares regression analyses are used to quantify the complex relationship between specific ultrasound and OCT measures and the CO2 metrics simulataneously. These analyses will enhance our understanding of the possible associations between CO2 levels and structural changes to the eye which will in turn inform future analysis of inflight VIIP data.
Schaefer, C.↗
Deep-learning-aided forward optical coherence tomography endoscope for percutaneous nephrostomy guidance
Percutaneous renal access is the critical initial step in many medical settings. In order to obtain the best surgical outcome with minimum patient morbidity, an improved method for access to the renal calyx is needed. In our study, we built a forward-view optical coherence tomography (OCT) endoscopic system for percutaneous nephrostomy (PCN) guidance. Porcine kidneys were imaged in our experiment to demonstrate the feasibility of the imaging system. Three tissue types of porcine kidneys (renal cortex, medulla, and calyx) can be clearly distinguished due to the morphological and tissue differences from the OCT endoscopic images. To further improve the guidance efficacy and reduce the learning burden of the clinical doctors, a deep-learning-based computer aided diagnosis platform was developed to automatically classify the OCT images by the renal tissue types. Convolutional neural networks (CNN) were developed with labeled OCT images based on the ResNet34, MobileNetv2 and ResNet50 architectures. Nested cross-validation and testing was used to benchmark the classification performance with uncertainty quantification over 10 kidneys, which demonstrated robust performance over substantial biological variability among kidneys. ResNet50-based CNN models achieved an average classification accuracy of 82.6%±3.0%. The classification precisions were 79%±4% for cortex, 85%±6% for medulla, and 91%±5% for calyx and the classification recalls were 68%±11% for cortex, 91%±4% for medulla, and 89%±3% for calyx. Interpretation of the CNN predictions showed the discriminative characteristics in the OCT images of the three renal tissue types. The results validated the technical feasibility of using this novel imaging platform to automatically recognize the images of renal tissue structures ahead of the PCN needle in PCN surgery.
Wang, Chen↗
Exploratory Analysis of Carbon Dioxide Levels, Ultrasound and Optical Coherence Tomography Measures of the Eye During ISS Missions
Carbon dioxide (CO2) levels on board the International Space Station (ISS) have typically averaged 2.3 to 5.3 mmHg, with large fluctuations occurring over periods of hours and days. CO2 has effects on cerebral vascular tone, resulting in vasodilation and alteration of cerebral blood flow (CBF). Increased CBF leads to elevated intracranial pressure (ICP), a factor leading to visual disturbances, headaches, and other central nervous system symptoms. Ultrasound of the optic nerve and optical coherence tomography (OCT) provide surrogate measurements of ICP; in-flight measurements of both were implemented as enhanced screening tools for the Visual Impairment/Intracranial Pressure (VIIP) syndrome. This analysis examines the relationships between ambient CO2 levels on ISS, ultrasound and OCT measures of the eye in an effort to understand how CO2 may possibly be associated with VIIP and to inform future analysis of in-flight VIIP data.
Schaefer, C.↗
Ovarian cancer detection using optical coherence tomography and convolutional neural networks
Not provided.
Computer Science↗
Anterior-segment spectral domain optical coherence tomography in epidermolysis bullosa
Not Available
Chen, Vicki M.↗
Contrast enhanced spectroscopic optical coherence tomography
A method of forming an image of a sample includes performing SOCT on a sample. The sample may include a contrast agent, which may include an absorbing agent and/or a scattering agent. A method of forming an image of tissue may include selecting a contrast agent, delivering the contrast agent to the tissue, acquiring SOCT data from the tissue, and converting the SOCT data into an image. The contributions to the SOCT data of an absorbing agent and a scattering agent in a sample may be quantified separately.
Boppart, Stephen A.↗
Measurement of Acute Changes in Choroid Thickness in Healthy Eyes During Posture Change Using Optical Coherence Tomography
The Visual Impairment and Intracranial Pressure (VIIP) syndrome affects 60% of astronauts returning from long-duration missions and is characterized by structural and functional changes of the eye (3). Upon entry into weightlessness, approximately two liters of fluid translocates from the lower body to the thorax and cephalad regions, potentially contributing to elevated intracranial and intraocular pressures. The choroid is the vasculature that supplies blood flow to the posterior part of the retina and has limited autoregulation. As a consequence these vessels may engorge during a cephalad fluid shift, contributing to structural changes in the retina. The purpose of this experiment was to quantify changes in choroid thickness during a fluid shift. In order to fulfill this objective, it was also necessary to improve the measurement technique for assessing choroid thickness.
Ferguson, Connor R.↗
Optical Coherence Tomography in the Evaluation of Anterior Eye Injuries in Spaceflight
No abstract available
Fer, Dan M.↗
Operational Transition from the First-Generation Heidelberg Spectralis Optical Coherence Tomography [OCT("OCT1")] to the Second-Generation Heidelberg Spectralis OCT("OCT2")
The Heidelberg Spectralis "OCT2", which recently became commercially available, is going to be implemented at the Johnson Space Center Flight Medicine Clinic and on board the International Space Station. Due to the increased scan rate of the "OCT2", this upgrade will allow for significant reduction in valuable crew testing time and also allow for additional capabilities, like OCT Angiography and Multi-Color Fundus Imaging. Due to the custom scans used to monitor Space Flight-Associated Neuro-ocular Syndrome (SANS) in our crewmembers, an evaluation to assess the impacts of transitioning from "OCT1" to "OCT2" was performed. An engineering assessment (N=1) was performed to identify any potential impacts of maintaining an "OCT1" on board ISS while implementing an "OCT2" in the JSC Clinic. "OCT2" implementation will lag JSC FMC clinical implementation due to the flight certification/manifestation process. The clinical assessment was performed (n=12) to identify any impacts due to the replacement of the "OCT1" with the "OCT2" to the longitudinal OCT data across a crewmember's mission/lifetime. The qualitative results from the engineering and clinical evaluation will be reported, as well as the quantitative assessment of the clinical variables
Mason, S.↗