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Optics Letters

Optica Publishing Group

Preprints posted in the last 90 days, ranked by how well they match Optics Letters's content profile, based on 13 papers previously published here. The average preprint has a 0.01% match score for this journal, so anything above that is already an above-average fit.

1
Physics-Driven Zero-Shot Reconstruction of Isotropic 3D Fluorescence Microscopy under Undersampled Acquisition

Cao, R.; Jin, T.; Xin, F.; Hou, Y.; Fu, Y.; Jin, B.; Li, L.; Gao, S.; Wang, H.; Li, Y.; Saimi, D.; Ren, W.; Wang, W.; Xin, G.; Yuan, K.; Chen, Z.; Su, X.; Kim, D.; Li, M.; Xi, P.

2026-06-16 bioinformatics 10.64898/2026.06.13.732100 medRxiv
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Three-dimensional (3D) imaging represents the development of next generation of fluorescence microscopy. However, routine axial down-sampling makes isotropic resolution unrealistic. Here, we propose DeepUI, a physical zero-shot framework designed to achieve isotropic 3D fluorescence images from a low axial sampling rate. DeepUI fully leverages the intrinsic characteristics of 3D images through physics-guided degradation, which incorporates spatial-frequency joint learning to generate a scaled optical transfer function, combined with noise degradation and an up-sampling branch. Typically requiring just 5 minutes for training and 0.5 minutes for high-throughput and fast prediction, we demonstrate the superior performance of DeepUI to get isotropic results, and the exclusivity to axial down-sampling conditions, even in more challenging conditions, including defocused background, noise, and resolution blur.

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3D Passive Cavitation Mapping (3D-PCM) with a Large-aperture Planar Array

Qiu, C.; Li, D.; Huo, H.; Mishra, A.; Li, C.; Yin, K.; Wang, N.; Chen, J.; Yao, R.; Margolin, E. J.; Lipkin, M. E.; Zhong, P.; Ni, X.; Yao, J.

2026-06-25 bioengineering 10.64898/2026.06.20.733547 medRxiv
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Urinary stone disease is a common urological condition with increasing incidence, particularly in developed countries. Laser lithotripsy (LL) has become a preferred minimally invasive treatment due to its high precision and low tissue damage. Recent studies suggest that cavitation plays a critical role in stone damage during LL, and three-dimensional passive cavitation mapping (3D-PCM) has emerged as a promising tool for detecting these events. However, clinical translation of 3D-PCM remains challenging due to limitations in imaging depth, field of view (FOV), and procedural compatibility. Here, we present a large-FOV dual-modality imaging system (3D-PCM and B-mode ultrasound) based on a large-aperture planar ultrasound array. Through array optimization and model-based reconstruction, our system achieves an expanded FOV of ~40*40mm^2 at a clinically relevant imaging depth of ~110mm, while maintaining high spatial resolution of ~0.6 mm laterally and ~0.4 mm axially. In vivo experiments in a porcine model demonstrate that the reconstructed cavitation distribution correlates well with stone damage. Our technology has the potential to provide real-time treatment feedback during LL without disrupting the standard workflow.

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Time-of-flight-resolved interferometric speckle-contrast optical spectroscopy (TOF-iSCOS) for depth-resolved blood-flow sensing

Nowacka-Pieszak, K.; Borycki, D.; Mogharari, N.; Marzejon, M.

2026-07-03 bioengineering 10.64898/2026.07.03.736163 medRxiv
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Significance: Continuous, noninvasive, and depth-resolved monitoring of blood-flow-related tissue dynamics remains an important unmet need. Speckle-contrast optical spectroscopy (SCOS), including interferometric implementations such as iSCOS, provides a scalable optical route to blood-flow sensing, but conventional continuous-wave approaches lack intrinsic depth selectivity. Time-of-flight (TOF) gating offers a way to separate superficial and deeper dynamic contributions in layered tissues, such as skin-muscle or scalp-cortex, by resolving photon path lengths. Aim: We introduce a swept-source, single-channel implementation of interferometric speckle-contrast optical spectroscopy (iSCOS) to obtain TOF-resolved temporal speckle contrast, {kappa}^2, from the measured field autocorrelation g_1, and evaluate its feasibility for depth-resolved blood-flow sensing. Approach: A swept-source iNIRS system operating at 780 nm acquired interferometric signals, which were Fourier-transformed along the optical-frequency axis to recover complex TOF-resolved speckle fields. Temporal speckle contrast was then estimated at each TOF gate indirectly from g_1 using the speckle-visibility relation. Diffusion-based numerical simulations were first used to compare the direct variance-based estimator and the indirect g_1-based estimator under varying reduced scattering coefficient, diffusion coefficient, additive noise level, and bi-layer geometry. Because the simulations showed that the g_1-derived {kappa}^2 estimator was substantially less sensitive to additive noise than the direct estimator, this estimator was used for the main phantom and in vivo analyses, while the direct estimator served as a simulation comparator. The g_1-derived estimator was then applied to liquid and bi-layer phantoms, followed by proof-of-concept in vivo measurements on the human forearm during cuff occlusion and on the forehead during a Sudoku task. Results: TOF-resolved kappa2 curves recovered with the g_1-derived estimator matched DWS theory across scattering coefficients, photon path lengths, and exposure times. The estimator preserved theoretical accuracy for additive noise amplitudes up to 50% of the field amplitude, whereas the direct variance estimator showed substantial noise-induced bias and required correction. Bi-layer simulations and phantom experiments reproduced the predicted direction and onset of TOF-dependent decorrelation-rate trends in layered media. In vivo, the recovered blood-flow index tracked the expected TOF-dependent cuff-occlusion and reactive-hyperemia response in the forearm. During the single-subject Sudoku task, the left-forehead recording showed a TOF-dependent relative blood-flow-index increase of +0.8 {+/-} 1.9% at TOF = 400 ps, +9.8 {+/-} 2.2% at TOF = 600 ps, and +15.2 {+/-} 5.6% at TOF = 800 ps. This pattern is consistent with increased sensitivity to deeper tissue at longer photon path lengths, but requires cohort-level validation before quantitative interpretation as cognitive activation. Conclusions: Coupling temporal speckle-contrast analysis with swept-source iNIRS yields a proof-of-concept, depth-resolved platform for blood-flow sensing. By estimating TOF-resolved speckle contrast through the g_1-derived {kappa}^2 route, TOF-iSCOS suppresses additive-noise bias while preserving sensitivity to deeper dynamic tissue layers. The present single-channel results bridge continuous-wave iSCOS, interferometric NIRS and time-domain diffuse correlation spectroscopy (TD-DCS), and motivate future multi-channel and cohort studies for scalable cortical hemodynamic monitoring.

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In vivo real-time elastography with unmodified commercial endoscopes using noise-correlation-inspired method and laser speckle imaging

Legrand, M.; Dufour, N.; Jonca, F.; Schiffler, J.; Sosa Valencia, L.; Bahlouli, N.; Nahas, A.

2026-06-29 biophysics 10.64898/2026.06.23.733923 medRxiv
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AO_SCPLOWBSTRACTC_SCPLOWEarly tumor detection is critical for improving patient survival and recovery. Clinically, tissue palpation is routinely used to identify regions of abnormal stiffness, a hallmark of many pathological conditions. However, palpation is restricted to anatomically accessible sites and remains highly operator dependent. Here, we introduce a method for real-time quantitative stiffness mapping using an unmodified commercial endoscope, with the goal of enhancing diagnostic capabilities and restoring mechanical feedback during endoscopic procedures. Our approach combines shear wave elastography with speckle imaging and an innovative synchronization strategy that enables the measurement of shear wave propagation using an unmodified commercial endoscope. The resulting wave fields are analyzed with the noise-correlation-inspired (NCI) method[1], providing pixel-wise estimates of shear wave velocity and, consequently, quantitative maps of local tissue stiffness. The method demonstrated robust performance in both benchtop and endoscopic configurations. Validation was achieved on polymer phantoms as well as on ex vivo and in vivo biological tissues, highlighting its potential for minimally invasive biomechanical imaging and real-time tissue characterization.

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APRIL: Adaptive Regression-Based Two-Dimensional Quantitative Anisotropy Imaging Using Acoustic Radiation Force Impulse

Hassan, M. W.; Crook, K.; Gi, Y. J.; Lee, J.; Hossain, M. M.

2026-07-01 bioengineering 10.64898/2026.06.30.735710 medRxiv
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Objective: This study aims to develop and validate a quantitative, depth-resolved anisotropy imaging framework that extends ARFI-based focal degree-of-anisotropy (DoA) estimation into two-dimensional mapping by modeling the depth-dependent relationship between shear modulus ratio (SMR) and peak displacement ratio (PDR). Methods: We propose APRIL (Adaptive Polynomial Regression for anisotropy Imaging via ARFI-induced DispLacements), a framework for quantitative, depth-resolved DoA imaging that adaptively selects polynomial regression or shape-preserving spline interpolation based on excitation PSF asymmetry. Training data were generated using an LS-DYNA3D + Field II simulation pipeline in homogeneous transversely isotropic media (SMR 0.9-4.9). Testing included shifted SMRs under varied acoustic conditions and three heterogeneous inclusion configurations (anisotropic inclusion in isotropic background and vice versa). Experimental validation was performed in an in-vivo murine tumor model over the time, ex-vivo chicken breast, and tissue-mimicking gelatin phantoms, using a Verasonics system with an L11-5v transducer. Results: APRIL achieved depth-resolved SMR prediction errors below 9% over 10-30 mm, with highest accuracy in the focal region (MAE 2.3%, RMSE < 0.1) and stable performance across PSF transition zones. In heterogeneous phantoms, it reconstructed anisotropy maps with SSIM up to 86% and MPE below 7%, accurately delineating inclusion boundaries. Under acoustic parameter variations, mean absolute errors remained below 10%, demonstrating robustness to system and tissue heterogeneity. Conclusion: APRIL enables robust, two-dimensional anisotropy imaging beyond focal estimates. Significance: The method provides a physically grounded and generalizable framework for clinically viable anisotropy biomarkers in muscle, tendon, kidney, tumor and breast tissues.

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Nanobubble-Based Ultrasound Localization Microscopy through Interactive Adaptive Processing

Ilovitsh, T.; Shapiro, G.; Gershman, Y.; Bismuth, M.

2026-07-15 bioengineering 10.64898/2026.07.14.738435 medRxiv
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This study presents the use of sub-micron nanobubbles (NBs) as contrast agents for ultrasound localization microscopy (ULM), a super-resolution imaging technique that visualizes microvascular structure and flow beyond the acoustic diffraction limit. While ULM has traditionally relied on micron-sized microbubbles (MBs), the reduced dimensions and prolonged circulation times of NBs make them attractive candidates for localization-based imaging. However, their weaker acoustic responses present significant challenges for reliable detection and tracking. To address this challenge, we developed the ULM Master GUI, an interactive framework for optimization of the complete ULM processing pipeline. Using custom ultrasound-compatible wall-less gelatin flow phantoms containing vessel-mimicking channels and bifurcations ranging from 100 to 500 m, we demonstrate that NB-based ULM achieves velocity reconstruction and flow partitioning measurements comparable to conventional MB-based ULM. Across all investigated geometries, NBs faithfully reproduced the underlying flow patterns and hemodynamic behavior despite their substantially reduced acoustic scattering. These findings establish the feasibility of NB-based ULM, expand the range of contrast agents available for localization microscopy, and provide a foundation for future super-resolution ultrasound imaging using nanoscale acoustic contrast agents. The ULM processing GUI is publicly available at https://github.com/grisha1998/ulm-super-resolution-toolbox.

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Coherent Structured Illumination Microscopy with Enhanced Optical Sectioning

Crampton, K.; Joly, A.; Nguyen, L. D.; Iqbal, S.; Boyd, R.; Evans, J. E.

2026-06-16 bioengineering 10.64898/2026.06.11.731428 medRxiv
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Coherent structured illumination microscopy (c-SIM) is a synthetic aperture optical technique for sub-diffraction limit imaging that extends the utility of traditional SIM to non-fluorescent samples. Here, we present a complementary 5-beam implementation of c-SIM that provides enhanced optical sectioning compared to conventional quadrupolar illumination. Since our approach detects intensity images due to coherent light scattering, it avoids the complications associated with detecting complex fields. Through comparative measurements on calibration samples and live microalgae, we show that 5-beam c-SIM effectively suppresses coherent defocus effects, improving image quality while simultaneously providing a 2-fold lateral resolution improvement.

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Targeted measurement of blood flow in the Anterior Cerebral Artery using Diffuse Correlation Spectroscopy

Das, S.; Sharma, K.; Sarkar, S.; Gonsalves, K.; Srinivasan, U. S.; VARMA, H.

2026-07-27 bioengineering 10.64898/2026.07.25.740702 medRxiv
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SignificanceDiffuse Correlation Spectroscopy (DCS) is an established technique for non-invasive monitoring of Cerebral Blood Flow (CBF), but existing applications primarily measure CBF changes averaged over cortical tissue volumes. A method capable of targeting blood flow within a particular intracranial artery would expand the utility of DCS for vessel-specific cerebral perfusion monitoring and continuous bedside assessment. AimWe aim to investigate the feasibility of targeted, non-invasive monitoring of blood flow in the Anterior Cerebral Artery (ACA) using DCS through optimization of probe geometry and placement. ApproachA custom-built DCS system operating at 785 nm was used to probe ACA from the glabellar region. Source-detector (SD) separation, probe orientation, and probe location were systematically optimized using lower-limb motor tasks and a mental arithmetic task. The optimized configuration was evaluated using an ACA-mimicking multilayer phantom and validated in forty healthy volunteers during lower-limb activation tasks and postural changes. ResultsAn SD separation of 17 mm, vertical probe orientation, and glabellar placement provided the highest sensitivity to ACA-related blood flow changes. Phantom experiments demonstrated sensitivity to flow changes in a vessel located 45 mm beneath the scalp and showed that the frontal sinus, cerebrospinal fluid, and the absence of cortical tissue beneath the glabella along the longitudinal fissure together provide the best optical window for probing deep ACA flow. Using the optimized probe configuration, significant increases in relative CBF were observed during standing leg marching (66.4 {+/-} 38.6%) and supine leg crunches (39.4 {+/-} 32.2%) (p < 0.01), with consistent responses during supine-to-stand postural transitions. ConclusionThe proposed DCS approach enables targeted measurement of blood flow within the ACA territory. This technique provides a framework for continuous, non-invasive monitoring of ACA perfusion and has potential applications in cerebrovascular monitoring and stroke care.

9
Multimodal 3D light-field and laser-speckle endoscopy

Zheng, C.; Jia, S.

2026-07-01 bioengineering 10.64898/2026.06.30.735698 medRxiv
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Minimally invasive surgery is a powerful technique that enables operations deep within the body while minimizing patient trauma and recovery time. Optical endoscopes are key to providing intraoperative vision but still face challenges due to the loss of essential senses, including depth perception and tactile feedback for tissue evaluation. Thus, it is critical to develop endoscopic imaging technologies that can augment operators with critical information. In this work, we explore a prototype multimodal 3D imaging endoscope that integrates volumetric light-field imaging with laser-speckle contrast imaging to simultaneously capture 3D structure and blood-flow information in a clinically relevant form factor.

10
Receive-Only Coupled Wireless Radiofrequency Probe for Endocavity MR Imaging Using a pTx System

Alipour, A.; Acikel, V.; Gokyar, S.; Algin, O.; Oto, C.; Balchandani, P.; Demir, H. V.; Atalar, E.

2026-06-12 bioengineering 10.64898/2026.06.10.731354 medRxiv
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PurposeTo enhance the SNR in MRI within a localized region of interest using a novel interventional wireless RF resonator probe combined with a dual-drive pTx system. MethodsA dual-drive body birdcage coil was operated in a linearly-polarized mode to decouple a passive RF resonator probe from the transmit field while maintaining the resonator in a receive-only coupled mode. The resonator was fabricated using standard microfabrication techniques and tuned to the Larmor frequency of a 3T MRI system. The 10-g specific absorption rate (SAR) distribution was simulated to identify potential hot spots around the resonator prior to heating experiments. To evaluate the interaction between the resonator probe and the linearly-polarized transmit field, SNR and flip-angle distributions were measured in a phantom. In vivo imaging studies were subsequently performed using the resonator probe in conjunction with the linearly-polarized dual-drive birdcage coil. ResultsTemperature measurements demonstrated a normalized temperature increase of less than 0.10{degrees}C, corresponding to a SAR value below 1.21 W/kg. Experimental flip-angle mapping confirmed effective magnetic decoupling of the resonator probe using linearly-polarized dual-drive transmission. An SNR enhancement factor of 1.6 was achieved within the region of interest in phantom experiments. In vivo imaging demonstrated a 2.0 {+/-} 0.2-fold SNR enhancement in the vicinity of the resonator probe. ConclusionA novel interventional approach for localized SNR enhancement in MRI was demonstrated using a wireless RF resonator probe and a dual-drive pTx system. The proposed technique enables local signal enhancement while minimizing transmit-field interactions, thereby facilitating safe interventional MRI and potentially improving image quality and diagnostic performance.

11
Balancing performance and complexity of dual-wedge prism-based spectroscopic single-molecule localization microscopy

Yeo, W.-H.; Shi, M.; Sun, C.; Zhang, H. F.

2026-08-07 bioengineering 10.64898/2026.08.06.743389 medRxiv
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Spectroscopic single-molecule localization microscopy (sSMLM) enables multiplexed super-resolution imaging by simultaneously acquiring the spatial position and spectral information of individual fluorophores. Dual-wedge prism (DWP)-based implementations provide a compact, alignment-stable approach to spectral dispersion, but trade-offs between localization precision, spectral precision, and experimental complexity remain. We systematically compare five DWP-based sSMLM configurations, including two-dimensional (2D) and three-dimensional (3D) implementations using single DWP (DWP-sSMLM) and symmetrically-dispersed DWP (SDDWP-sSMLM). We evaluate lateral precision, spectral precision, and ease of use. SDDWP configurations acquire spectral images in both channels and utilize both for spatial localization, yielding the highest lateral and spectral precision. However, for applications that do not require axial information, 2D-DWP provides a simple, plug-and-play solution with robust performance. This work offers a guideline for selecting DWP configurations based on experimental needs.

12
In situ pulse dispersion estimation via third-harmonic generation interferometric autocorrelation for multiphoton microscopy

Shaughnessy, L.; Vannell, L.; Fernando-Peiris, S.; Rodriguez, C.

2026-08-05 bioengineering 10.64898/2026.08.04.742801 medRxiv
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Three-photon microscopy enables deep-tissue imaging but is highly sensitive to excitation pulse quality, since three-photon excitation efficiency scales with the cube of instantaneous intensity. Group-delay dispersion (GDD) and third-order dispersion (TOD) accumulated through the laser and microscope optics can substantially reduce peak intensity at the focal plane, yet these quantities are rarely measured where imaging occurs. Here, we use third-harmonic generation (THG) interferometric autocorrelation, together with Dispersion Look-Up-Table Estimation (D-LUTE) and a joint two-measurement fitting procedure validated on synthetic data, to estimate baseline GDD and TOD directly at the objective focal plane, requiring only a compact autocorrelator module added to the microscope beam path. Applying this method at 1300 nm and 1600 nm excitation across two microscope systems equipped with different units of the same laser model, we find pulse durations 1.4- to 1.7-fold longer than the transform limit at every condition, driven predominantly by TOD, which varied by roughly 2.7-fold between the two systems. Using the endogenous THG signal from myelinated fibers, we further demonstrate in vivo pulse characterization in the mouse brain, finding no measurable broadening between the tissue surface and a depth of nearly a millimeter. This low-cost, easily implemented approach enables routine, in situ pulse monitoring across multiphoton microscopy platforms.

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Data-adaptive three-dimensional deconvolution and evaluation for volumetric fluorescence microscopy

Hou, Y.; Fu, Y.; Wang, W.; Cao, R.; Su, X.; Li, M.; Xi, P.

2026-07-01 bioengineering 10.64898/2026.06.29.735443 medRxiv
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Optical fluorescence microscopy enables visualization of biological structures and dynamics. However, the intrinsic diffraction limit, especially axially, and depth-related scattering noise compromise the image resolution and fidelity. Computational 3D deconvolution is a promising approach for mitigating these issues, yet its execution is hindered by inaccurate and cumbersome theoretical modeling or experimental measurement of 3D point spread function (PSF), as well as ineffective 3D noise regularization. Furthermore, in the 3D super-resolution regime, there remains a lack of standardized tools for evaluating 3D super-resolution fidelity. Here, we present the 3D adaptive deconvolution and evaluation (3D-ADE) toolkit, which comprises 3D-Ada deconvolution with physics-oriented automatic 3D-PSF calibration, and 3D-SQUIRREL for 3D super-resolution quality assessment. It effectively resolves noise instability, eliminates the need for 3D-PSF calibration, and reliably assesses the fidelity of 3D resolution extension via deconvolution, physical, and deep-learning-based methods. Accessible via multiple software platforms, 3D-ADE enhances the versatility of 3D deconvolution and fills the gap in 3D super-resolution evaluation tools, and thereby advances volumetric fluorescence imaging applications.

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Multiview-SPIM-{micro}PIV for mapping 3C-3D blood flow within the beating zebrafish heart

Jiang, J.; Ross, K.; Taylor, J. M.

2026-08-21 biophysics 10.64898/2026.08.17.745192 medRxiv
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Cardiac blood flow is a regulator of several important developmental and remodelling processes in the heart, including through fluid shear forces sensed by the endothelial cells lining the heart. However, optically mapping these flow fields in the complex 3D geometry of the heart is challenging even in transparent animal models such as the zebrafish. One of the main challenges is the difficulty in measuring the out-of-plane (axial) velocity component, preventing accurate mapping of the complete 3-component-3-dimension (3C-3D) blood flow velocity field; image-based techniques such as microscopic particle image velocimetry ({micro}PIV) traditionally only provide the in-plane flow components. Here we present a computational approach to achieve full time-varying 3C-3D blood flow vector mapping using a standard selective plane illumination microscope (SPIM), based on robust cardiac phase assignment, precise measurement-driven registration of sequentially acquired z-stacks, and PIV data fusion from multiple sample orientations. Our approach holds the key to understanding the complex dynamic flow fields within the developing heart, and their role in shaping cardiac development.

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Photo-thermal Bidirectional Coupling Model for Transcranial Photobiomodulation

Zhang, T.; Chen, Y.; Zeng, X.; Zhang, G.; Wang, F.; Guo, D.; Yao, D.

2026-07-17 neuroscience 10.64898/2026.07.11.737905 medRxiv
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BackgroundAccurate optical-field simulation is critical for precise dosage delivery in transcranial photobiomodulation (tPBM). Current simulations neglect photon absorption-induced tissue heating which leads to temperature-dependent alterations of the optical field, thus fails to account for the bidirectional photo-thermal coupling effect. ObjectiveThis paper aims to establish a dynamic photo-thermal couple model that rigorously quantifies the bidirectional interaction between tissue heating and light propagation, and improves the optical dose prediction. ModelWe propose a Photo-Thermal bidirectional coupling Model (PTM). First, the Pennes Bioheat Equation (PBE) is employed to model the thermal response induced by photon absorption. Second, a Real-time temperature-dependent Absorption coefficient Model (RAM) is newly developed to quantify the thermal effect. Third, the PBE and RAM are integrated into the photon diffusion equation, forming the PTM. Finally, this coupled framework is solved temporally by an unconditionally stable Crank-Nicolson scheme. SimulationsBenchmarking against an analytical solution (two-layer cylindrical domain) demonstrates that PTM reduces the temperature prediction error by over 2.35% compared to the uncoupled baseline. Simulations using a realistic head model reveal that, compared to PTM, uncoupled modeling underestimates energy deposition by 150 J/m3 and overestimates photon fluence by 3 J/m2 within just one minute, and such discrepancies will be amplified with increasing exposure duration and power. Furthermore, the PTM identifies a 1.43-mm advantage in penetration depth for pulsed-wave over continuous-wave modality under iso-energy conditions, a key insight enabled by the coupled modeling approach. ConclusionThe PTM provides a high-fidelity simulation framework that captures the dynamic, bidirectional photo-thermal coupling in tPBM, explicitly quantifying the thermal feedback ignored by current models and thereby enabling more reliable treatment optimization and safer clinical translation.

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Assessing the fractional contributions of static, slow and fast dynamic scatterer components to the flow index derived by continuous wave diffuse correlation spectroscopy

Mogharari, N.; Kacprzak, M.; Borycki, D.

2026-08-18 bioengineering 10.64898/2026.08.14.744820 medRxiv
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Continuous wave diffuse correlation spectroscopy (cw-DCS) is a noninvasive optical technique to monitor the tissues blood flow changes. This technique measures the tissue blood flow index (BFI) by evaluating the decay rate of the autocorrelation function. The derived BFI is proportional to mean squared displacements of the red blood cells considered as the fast-dynamic scatterer component of tissue in time. However, biological tissue contains static scatterer component and slow-dynamic scatterer component which affect the decay rate of autocorrelation function and as a result the derived BFI. In this study, we assessed the fractional contribution of static, slow-dynamic and fast-dynamic scatterer components of a medium in the flow index derived by cw-DCS. The measurements performed on Agar-based phantom with tube showed that presence of static scatterer component and slow-dynamic scatterer component led to substantial underestimation ({approx} 123%) of the flow index derived by Siegert relation, compared to effective diffusion coefficient of fast-dynamic scatterers components derived by modified Siegert relation and bi-exponential model. The less underestimation was observed for the corresponding parameters obtained from the liquid phantom measurements ({approx} 25%) as well as during the forearm occlusion test and respiratory challenges ({approx} 16% - 26%).

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SNR Enhancement Considerations for Loop Receive Coils at Ultra-High Fields

Lagore, R. L.; Waks, M.; Hasapopoulos, T.; Mercer, T.; Grant, A.; Eryaman, Y.; Ugurbil, K.; Adriany, G.; Sadeghi-Tarakameh, A.

2026-06-19 bioengineering 10.64898/2026.06.18.732714 medRxiv
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PurposeTo quantify parasitic losses in ultra-high field (UHF) magnetic resonance imaging (MRI) receive coils and determine how they contribute to the mismatch between numerically predicted and experimentally realized signal-to-noise ratio (SNR), with the goal of guiding receive-array designs toward ultimate intrinsic SNR (uiSNR). MethodsSNR was measured across multiple field strengths (3T, 7T, 10.5T) using commercial and custom-built arrays. To quantify parasitic losses, unloaded-to-loaded quality factor ratio (QR) measurements were performed on representative loop resonators and practical RF coils. Measured losses were combined with single-loop electromagnetic simulations to separate conductor, radiation, and component losses. These bench-derived loss estimates were then incorporated into full-array electromagnetic simulations of a 128-channel receive array to evaluate their impact on predicted intrinsic SNR. ResultsMeasurements across field strengths supported the expected supralinear increase of SNR with B0. QR analysis showed that, at UHF, radiation loss must be excluded from unloaded-Q measurements to avoid overestimating electronic-noise penalties, and that multiple seemingly modest parasitic losses collectively impose substantial SNR degradation. In the 128-channel array, simulations including only conductor and radiation losses predicted 93% of central uiSNR, whereas inclusion of the full measured parasitic-loss budget reduced predicted performance to 78%, in close agreement with the experimentally measured 77%. ConclusionsThe gap between predicted and realized SNR performance of high-channel-count 10.5T loop arrays can be largely explained by parasitic losses that are not captured in conventional simulations. A bench-measurement-informed simulation framework enables more realistic prediction of coil performance and provides practical guidance for optimizing future UHF receive arrays.

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NIR-II squeezed light-field microscopy enables high-speed volumetric imaging of deep-tissue dynamics in vivo

Kim, D. Y.; Zang, Z.; Lin, E. Y.; Zhao, R.; Wang, J.; Hsiai, T. K.; Sletten, E. M.; Gao, L.

2026-08-18 bioengineering 10.64898/2026.08.13.744709 medRxiv
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High-speed three-dimensional imaging in scattering tissues remains challenging because volumetric microscopy generally requires scanning, whereas snapshot light-field approaches divide limited detector pixels among multiple views. This constraint is particularly severe in the second near-infrared window (NIR-II), where commonly used InGaAs cameras typically have relatively small sensor formats and high detector noise. Here we introduce NIR-II squeezed light-field microscopy (NIR-II SLIM), which optically rotates and compresses multiple perspective views before detection, allowing efficient use of camera pixels while retaining complementary spatial information for three-dimensional reconstruction. NIR-II SLIM acquires volumes at up to 600 volumes s-1 with a reconstructed lateral sampling grid of 512 x 512 pixels. We use the method for label-free four-dimensional imaging of cardiac dynamics in pigmented late-larval zebrafish, resolving chamber deformation and millisecond-scale atrioventricular-valve motion, and for NIR-II fluorescence imaging of vascular and lymphatic transport in mice. NIR-II SLIM provides a detector-efficient approach for high-speed volumetric imaging of rapid biological dynamics in scattering tissues.

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Image transmission through a multimode fibre in reflection mode with physics-guided deep learning towards ultrathin endoscopy

Ye, Z.; He, F.; Zhao, T.; Xia, W.

2026-08-31 radiology and imaging 10.64898/2026.08.28.26361674 medRxiv
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Ultrathin endoscopy is highly attractive for real-time tissue imaging in narrow and hard-to-reach regions of the body. A single multimode fibre (MMF) is an attractive probe because of its small diameter, flexibility, and diffraction-limited spatial resolution enabled by the large number of transverse modes guided within a single core. Because the distal fibre tip is inaccessible during endoscopy, reflection-mode imaging, in which the same fibre delivers illumination and collects backscattered light, is more practical than transmission-mode imaging. However, image recovery from the resulting speckle pattern is challenging because light undergoes double-pass propagation through the MMF, with mode coupling and dispersion; the backscattered signal is weak, and the camera records intensity only, without phase information. Here, we propose a single-shot reflection-mode MMF imaging framework that combines a reflected real-valued intensity transmission matrix (reflected-RVITM) with an image restoration network. The reflected-RVITM is calibrated using intensity-only measurements, without interferometry or phase retrieval, and provides a physics-guided initial reconstruction from a single backscattered speckle frame. A restoration network then refines this initial reconstruction instead of inverting the raw speckle. Four restoration backbones are evaluated: HPM-Attention-UNet, GAM, MambaIRv2, and CICPNet. On matched datasets, hybrid models outperformed corresponding networks trained to map raw speckle directly to images. For example, HPM-Attention-UNet on MNIST improved mean PCC from 0.572 to 0.944 (+65.1%). Under domain shift, with training only on Fashion-MNIST and tested on unseen CIFAR scenes, hybrid models achieved mean PCC of 0.61-0.65, compared with 0.36-0.50 for direct learning. This framework is further demonstrated using physical objects at the distal fibre tip. These results demonstrate that a reflected-RVITM physics prior combined with a restoration network enables single-shot image recovery after intensity-only calibration, offering a phase-retrieval-free and generalisable route towards minimally invasive reflection-mode MMF endoscopy.

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Whole-organ surface mapping using multiview projection reconstruction

Brewer, E. S.; Almasian, M.; Saberigarakani, A.; Liu, D.; Azizi, A.; Ware, S. A.; Karambelkar, K.; Shah, N.; Vadlamudu, M.; Obaid, G.; Tong, D.; Ding, Y.

2026-08-27 bioengineering 10.64898/2026.08.26.747115 medRxiv
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While light-sheet microscopy is emerging as a robust method for volumetric imaging with improved axial resolution, its capability regarding two-dimensional, surface-level mapping is often hindered by limitations in data redundancy and reconstruction efficiency stemming from volumetric registration methods. We demonstrate that a multiview imaging approach in an axially-swept, dithered light-sheet microscope paired with computational image reconstruction of view projections is able to address these trade-offs to enable large-scale mapping of surface structural features, leveraging the advantages of multiview light-sheet in scalable field of view, working distance, and near isotropic resolution across the entire imaging depth. To aid in the acquisition and analysis of two-dimensional surface structures, we present a tailored surface mapping workflow and a Fiji plugin for computational reconstruction, promoting robust and comprehensive visualization of surface features of uncleared volumetric samples. Our strategy, termed projection reconstruction for imaging surface morphology (PRISM), integrates axially swept dithered light-sheet microscopy and post-processing software for multiview imaging. The imaging hardware enables near-isotropic resolution across its entire field of view, while the software implementation leverages rigid and affine transformations to align two-dimensional projections of multiview samples. It is designed to work with the BigStitcher pipeline, leveraging its robust algorithm to provide support for two-dimensional image alignment and stitching. We demonstrate the capability of PRISM in studies of lymphatic network mapping in the epicardial layer of intact mouse hearts, as well as surface profiles of FaDu spheroids labeled with antibody-nanodiamond conjugates. This method allows us to quantify cardiac lymphatic branch numbers, diameters, and lengths of a Prox1-tdTomato mouse cardiac model, as well as cluster number and diameters of epidermal growth factor receptor within a FaDu spheroid labeled with a nanodiamond-antibody conjugate, with a significant reduction of post-processing data size. PRISM leverages multiview image projections to promote studies of cardiac lymphatics in mouse models and surface receptor distributions within spheroid models, enabling efficient surface mapping of large, intact, and uncleared biological samples across a variety of scales.