Convolutional dictionary learning for blind deconvolution of optical coherence tomography images
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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↗
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↗
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↗
Ovarian cancer detection using optical coherence tomography and convolutional neural networks
Not provided.
Computer Science↗
Tailoring polyvinyl alcohol-sodium alginate (PVA-SA) hydrogel beads by controlling crosslinking pH and time
Abstract Hydrogel-encapsulated catalysts are an attractive tool for low-cost intensification of (bio)-processes. Polyvinyl alcohol-sodium alginate hydrogels crosslinked with boric acid and post-cured with sulfate (PVA-SA-BS) have been applied in bioproduction and water treatment processes, but the low pH required for crosslinking may negatively affect biocatalyst functionality. Here, we investigate how crosslinking pH (3, 4, and 5) and time (1, 2, and 8 h) affect the physicochemical, elastic, and process properties of PVA-SA-BS beads. Overall, bead properties were most affected by crosslinking pH. Beads produced at pH 3 and 4 were smaller and contained larger internal cavities, while optical coherence tomography suggested polymer cross-linking density was higher. Optical coherence elastography revealed PVA-SA-BS beads produced at pH 3 and 4 were stiffer than pH 5 beads. Dextran Blue release showed that pH 3-produced beads enabled higher diffusion rates and were more porous. Last, over a 28-day incubation, pH 3 and 4 beads lost more microspheres (as cell proxies) than beads produced at pH 5, while the latter released more polymer material. Overall, this study provides a path forward to tailor PVA-SA-BS hydrogel bead properties towards a broad range of applications, such as chemical, enzymatic, and microbially catalyzed (bio)-processes.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Characterization and biofouling potential analysis of two cyanobacterial strains isolated from Cape Verde and Morocco
Abstract Cyanobacteria are new sources of value-added compounds but also ubiquitous and harmful microfoulers on marine biofouling. In this work, the isolation and identification of two cyanobacterial strains isolated from Cape Verde and Morocco, as well as their biofilm-forming ability on glass and Perspex under controlled hydrodynamic conditions, were performed. Phylogenetic analysis revealed that cyanobacterial strains isolated belong to Leptothoe and Jaaginema genera (Leptothoe sp. LEGE 181153 and Jaaginema sp. LEGE 191154). From quantitative and qualitative data of wet weight, chlorophyll a content and biofilm thickness obtained by optical coherence tomography, no significant differences were found in biofilms developed by the same cyanobacterial strain on different surfaces (glass and Perspex). However, the biofilm-forming potential of Leptothoe sp. LEGE 181153 proved to be higher compared with Jaaginema sp. LEGE 191154, particularly at the maturation stage of biofilm development. Three-dimensional biofilm images obtained from confocal laser scanning microscopy showed different patterns between both cyanobacterial strains and also among the two surfaces. Because standard methodologies to evaluate cyanobacterial biofilm formation, as well as two different optical imaging techniques, were used, this work also highlights the possibility of integrating different techniques to evaluate a complex phenomenon like cyanobacterial biofilm development.
Romeu, Maria J. (ORCID:0000000210945425)↗
Bayesian Optical Heterodyne Tomography
We introduce a complete workflow for Bayesian quantum state tomography of generic continuous-variable states. We also summarize experimental results applying this workflow to the tomographic reconstruction of thermal and coherent states of light.
Chapman, Joseph↗
Phase-Dependent Squeezing in Dual-Comb Interferometry
Manipulating the quantum noise of continuous-wave lasers through squeezing has reshaped optical interferometry. However, progress in optical frequency comb interferometry with pulsed squeezed sources has been limited, despite the role of frequency combs in ultraprecise optical metrology. Here, we introduce a new time-domain approach to characterizing squeezed femtosecond light pulses using dual-comb interferometry. Time-domain interferograms are generated via multiheterodyne beating between the modes of a Kerr soliton-squeezed frequency comb and a coherent state comb. The interferogram noise reveals phase-dependent squeezing and antisqueezing, dipping as much as 3.8 ± 0.2 dB below the shot noise level at alternating zero crossings. We model this nonstationary quantum noise as a periodic optical displacement of the squeezed comb by the coherent comb. These results support a route toward quantum-enhanced dual-comb timing applications and high-speed quantum state tomography with dual-comb interferometers.
Herman, Daniel Issac [University of Colorado, Boul↗
Probing electromagnetic nonreciprocity with quantum geometry of photonic states
Reciprocal and nonreciprocal effects in dielectric and magnetic materials provide crucial information about the microscopic properties of electrons. However, experimentally distinguishing the two has proven to be challenging, especially when the associated effects are extremely small. To this end, we propose a contactless detection using a cross-cavity device where a material of interest is placed at its center. We show that the optical properties of the material, such as Kerr and Faraday rotation, or birefringence, manifest in the coupling between the cavity's electromagnetic modes and in the shift of their resonant frequencies. By calculating the dynamics of a geometrical photonic state, we formulate a measurement protocol based on the quantum metric and quantum process tomography that isolates the individual components of the material's complex refractive index and minimizes the quantum mechanical Cramér-Rao bound on the variance of the associated parameter estimation. Our approach is expected to be applicable across a broad spectrum of experimental platforms including Fock states in optical cavities, or coherent states in microwave and THz resonators. Published by the American Physical Society 2025
Petrides, Ioannis (ORCID:0000000174842444)↗
Characterization of Quantum Frequency Processors
Frequency-bin qubits possess unique synergies with wavelength-multiplexed lightwave communications, suggesting valuable opportunities for quantum networking with the existing fiber-optic infrastructure. Although the coherent manipulation of frequency-bin states requires highly controllable multi-spectral-mode interference, the quantum frequency processor (QFP) provides a scalable path for gate synthesis leveraging standard telecom components. Here, we summarize the state of the art in experimental QFP characterization. Distinguishing between physically motivated “open box” approaches that treat the QFP as a multiport interferometer, and “black box” approaches that view the QFP as a general quantum operation, we highlight the assumptions and results of multiple techniques, including quantum process tomography of a tunable beamsplitter—to our knowledge the first full process tomography of any frequency-bin operation. Our findings should inform future characterization efforts as the QFP increasingly moves beyond proof-of-principle tabletop demonstrations toward integrated devices and deployed quantum networking experiments.
42 ENGINEERING↗
Qudit Designs and Where to Find Them
Unitary t-designs are some of the most versatile tools in quantum information theory. Their applications range from randomized benchmarking and shadow tomography, to more fundamental ones such as emulating quantum chaos and establishing exponential separations between classical and quantum query complexity. While unitary designs originating from a group structure, such as the Clifford group, have proven to be incredibly useful for qubit systems, unfortunately, this is no longer true for qudits. In fact, the classification of finite-group representations rules out the existence of unitary 2-designs for arbitrary qudit dimensions. This severely limits the applicability of standard quantum information primitives when it comes to qudit systems. We overcome these limitations with a three-fold contribution. First, we introduce a general technique to construct families of weighted state t-designs in arbitrary qudit dimensions. These weighted state-designs generalize classical shadow tomography protocol from qubits to qudits. Second, we introduce a Clifford character RB that allows us to benchmark the qudit Clifford group in any dimension, including non-prime-power dimensions. And third, we establish bounds on the quantum circuit complexity of generating approximate unitary-designs from native gates in existing quantum hardware such as high-spin and cavity-QED qudits. Our work further highlights the analogy between spin and optical coherent states by proving that spin-GKP codewords form a state 2-design while spin coherent states do not; in direct analogy with the optical case. This work is structured as a pedagogical and self-contained introduction to unitary designs and their applications to qudit systems.
Anand, Namit [NASA, Ames; Unlisted, US] (ORCID:000↗
Integrated positron emission particle tracking (PEPT) and X-ray computed tomography (CT) imaging of flow phenomena in twisted tape swirl flow
Abstract A combined positron emission particle tracking (PEPT) and X-ray computed tomography (CT) technique is presented, and its utility is demonstrated through investigation of flow in a pipe with twisted tape swirl insert with varying flow conditions (diameter-based Reynolds numbers 16,300–63,300). A description of this technique is given, as well as data handling practices used to relate geometric information captured by CT to fluid flow data gathered via PEPT. It is found that the CT component is readily capable of capturing the stainless steel insert geometry in this present system, but the use of combined plastic and metal materials leads to artifacts in imaging of the plastic surface. Nonetheless, CT data are related to PEPT flow measurements, and average velocity fields are calculated via a pseudo-framing and interpolation scheme and used to visualize and interrogate key flow phenomena within the system. Radial velocity profiles of the mean flow characteristics are seen to collapse to a nearly common form across all flow conditions considered. Helical vortices are seen propagating through the flow field, generated by bypass flow around the gap between the insert and pipe wall, with additional coherent secondary flow structures seen in the higher Reynolds number cases. These findings enhance the understanding of the mixing mechanisms in these swirl flows and encourage the continued development of PEPT-CT methodologies for 3D flow measurements in optically inaccessible systems.
42 ENGINEERING↗
Experimental generation of polarization entanglement from spontaneous parametric down-conversion pumped by spatiotemporally highly incoherent light
Here, we investigate the cross influence of the pump coherence on the entanglement produced from spontaneous parametric down-conversion (SPDC) in different degrees of freedom (DOFs). We experimentally demonstrate the generation of polarization entanglement from SPDC pumped by a spatiotemporally highly incoherent (STHI) light-emitting diode. Our quantum state tomography measurements using multimode collection fibers to avoid postselection yield a two-qubit state with the concurrence of 0.531 ± 0.006 and purity of 0.647 ± 0.005, in excellent agreement with our theoretically predicted concurrence of 0.552 and purity of 0.652. We find that using an STHI pump reduces the entanglement and purity of the output polarization two-qubit state due to a coupling between the spatiotemporal and polarization DOFs introduced by the birefringence and dispersion of the nonlinear crystal. The viability of SPDC with STHI pumps is important for two reasons: (i) STHI sources are ubiquitous and available at a wider range of wavelengths than lasers, and (ii) the generated STHI polarization-entangled two-photon states could potentially be useful in long-distance quantum communication schemes due to their robustness to scattering.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
Quantum coherence tomography of light-controlled superconductivity
The coupling between superconductors and oscillation cycles of light pulses, i.e., lightwave engineering, is an emerging control concept for superconducting quantum electronics. Although progress has been made towards terahertz-driven superconductivity and supercurrents, the interactions able to drive non-equilibrium pairing are still poorly understood, partially due to the lack of measurements of high-order correlation functions. In particular, the sensing of exotic collective modes that would uniquely characterize light-driven superconducting coherence, in a way analogous to the Meissner effect, is very challenging but much needed. Here we report the discovery of parametrically driven superconductivity by light-induced order-parameter collective oscillations in iron-based superconductors. The time-periodic relative phase dynamics between the coupled electron and hole bands drives the transition to a distinct parametric superconducting state out-of-equalibrium. This light-induced emergent coherence is characterized by a unique phase–amplitude collective mode with Floquet-like sidebands at twice the Higgs frequency. We measure non-perturbative, high-order correlations of this parametrically driven superconductivity by separating the terahertz-frequency multidimensional coherent spectra into pump–probe, Higgs mode and bi-Higgs frequency sideband peaks. We find that the higher-order bi-Higgs sidebands dominate above the critical field, which indicates the breakdown of susceptibility perturbative expansion in this parametric quantum matter.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗