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Journal of Biomedical Optics

SPIE-Intl Soc Optical Eng

Preprints posted in the last 30 days, ranked by how well they match Journal of Biomedical Optics's content profile, based on 28 papers previously published here. The average preprint has a 0.02% match score for this journal, so anything above that is already an above-average fit.

1
Spectral characterisation of short-wave infrared (SWIR) tissue chromophores and tissue-mimicking phantom optical properties

Watt, M. J.; Malouf, L.; Tao, R.; Racicot, I.; Else, T. R.; Groehl, J.; Bohndiek, S. E.

2026-07-07 bioengineering 10.64898/2026.07.07.736740 medRxiv
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Short-wave infrared (SWIR) sensors promise to expand the capabilities of optical sensing technologies but the lack of robust data characterising tissue-constituent optical properties in the SWIR makes instrument design challenging. We characterise and evaluate the optical properties of the dominant chromophores in tissue and tissue-mimicking phantoms, from visible to SWIR wavelengths. Using single-integrating sphere systems, we measured the optical properties of single-component chromophores (H2O, haemoglobin, corn oil, synthetic melanin) and multi-component tissues (whole blood, lard), to decouple contributions from optical scattering, H2O absorption and other contributing chromophores; we also characterised commonly-used phantom materials and investigated their potential to mimic soft tissues in the SWIR range using simulations. We provide a consistent dataset of absorption and reduced scattering coefficients that characterise the dominant tissue chromophores from 450 nm out to 1600 nm. These results were shown to be consistent with literature data, where available. We integrate these data into an open-source Python toolkit, SIMPA, for optical modelling and demonstrate soft tissue simulations that can be probed continuously from visible to SWIR wavelengths. Our findings are compared with tissue-mimicking phantoms, highlighting a need for additives for polymer-based phantoms that mimic SWIR water absorption. By providing this open-source dataset, we aim to enable future studies exploring SWIR light-tissue interactions that facilitate rapid assessment and prototyping of next-generation spectroscopy and imaging techniques.

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Non-invasive in vivo lactate monitoring via NIR spectroscopy

Lehnert, T.; Seidel, S.; Euchner, J.; Thierbach, A.; Schmidt, F.; Ögün, C. M.; Hermes, W.

2026-06-26 biophysics 10.64898/2026.06.23.733906 medRxiv
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We present a non-invasive approach for continuous monitoring of lactate dynamics in-vivo using near-infrared (NIR) spectroscopy. Lactate-related spectral features were measured non-invasively within the overtone region (1600-1850 nm). Several anatomical measurement sites were evaluated, and the middle phalanx of the dorsal finger emerged as the most promising location due to its superior spectral quality and stable tissue perfusion, becoming the exclusive site for all further experiments. Across multiple exercise sessions, predictive models achieved high within-day accuracy (R2[≥] 0.8), while cross-day performance was affected by spectral drift and physiological variability. A dynamic offset-correction procedure effectively mitigated these baseline shifts, enabling stable prediction accuracy across days, weeks, and subjects. These findings demonstrate the feasibility of NIR-based lactate estimation and highlight the importance of adaptive correction strategies for reliable long-term, non-invasive monitoring.

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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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Segmentation and classification of retinal pigment granules in fluorescence lifetime imaging microscopy (FLIM) data

Ali, M.; Ahmad, H. A.; Alderzy, H.; Hammer, M.; Heintzmann, R.; Stranik, O.

2026-07-03 bioinformatics 10.64898/2026.06.29.735375 medRxiv
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Alterations of fluorescence properties in retinal pigment epithelium (RPE) cells caused by diseases such as age-related macular degeneration (AMD) highlight the need for detailed analysis of the fluorescent RPE granules at the individual level. Precise segmentation and classification of these granules remain challenging due to their limited visual separability. In this study, we present Classi4RPE, a computational algorithm designed to accurately segment RPE granules and classify them into three categories -- lipofuscin (L), melanolipofuscin (ML), and melanin (M) -- based on fluorescence lifetime imaging data, which provide distinctive contrast. The method is implemented in a custom Python framework and employs seeded watershed segmentation to isolate individual granules. Lipofuscin granules are identified as hyperfluorescent structures with longer lifetimes, while granules with shorter lifetimes are further analyzed based on their spatial lifetime distribution from the center to edge, enabling discrimination of ML from other melanin-rich granules. Our approach achieves high performance, with mean sensitivities of 0.99 for L granules and 0.90 for ML granules, and corresponding specificities of 0.93 and 0.98, respectively, compared to manually annotated ground truth. These results demonstrate the potential of Classi4RPE to surpass human visual limitations and provide a robust tool for quantitative RPE analysis.

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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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Water as a thermal contrast agent for artificial-intelligence-enhanced in vivo mid-infrared thermography

Xu, S.; Liu, Y.; Xu, D.; Dai, Z.; Ye, W.; Zhan, X.; Wang, F.

2026-07-06 bioengineering 10.64898/2026.07.03.736311 medRxiv
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In vivo infrared thermography is limited by the inherently poor spatial resolution at long wavelengths, low contrast, and the lack of biocompatible contrast agents. Here, we present 3-5 m mid-wave infrared (MWIR) thermography enhanced by an artificial intelligence (AI) network and cold phosphate-buffered saline (PBS) as a thermal contrast agent for noninvasive in vivo imaging with high contrast and resolution. MWIR imaging enabled high thermal sensitivity with microscale spatial resolution, strong relative thermal contrast, and facilitated visualization of the subcutaneous vasculature in the human arm, hand, ankle, the femoral artery and vein in rats, and the femoral vessels in mice, with image contrast further enhanced by AI networks. In a 4T1 tumor-bearing mouse model, AI-enhanced MWIR resolved early-stage tumors of ~2.3 mm and metastases as small as ~1.7 mm. Using cold PBS as a MWIR thermal contrast agent, we achieved precise tumor boundary visualization and real-time imaging-guided tumor resection. AI-enhanced MWIR offers a promising solution for early diagnosis and improved surgical precision.

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Multi-fidelity Bayesian optimization of population-robust near-infrared sensors for skeletal muscle oximetry

Bhattacharyya, K.

2026-07-09 orthopedics 10.64898/2026.07.08.26357539 medRxiv
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Designing transcutaneous skeletal muscle oxygenation (SmO2) sensors requires jointly optimizing source--detector geometry and wavelength selection while guaranteeing performance across populations that vary in subcutaneous fat thickness and skin pigmentation. We present a multi-fidelity Bayesian optimization (MFBO) framework that couples Monte Carlo light-transport simulations at two photon-count fidelities to a distributionally robust design objective. An autoregressive Gaussian-process surrogate learns the correlation between inexpensive low-photon-count and accurate high-photon-count simulations, and a cost-aware acquisition function decides both where and at what fidelity to sample. Robustness across the population is enforced with Conditional Value-at-Risk (CVaR) and entropic-risk (ERM) objectives that target worst-case subjects rather than the population average. On a five-layer forearm tissue model with anthropometric variability we find (i) a fidelity regime that is favorable for MFBO where the low-fidelity surrogate is rank-informative (Spearman {rho} = 0.84) but biased, at 100x lower cost; (ii) MFBO attains 23% higher robust sensitivity than a strong high-fidelity single-fidelity baseline at equal budget (p = 0.035), and avoids the optimistic bias that causes low-fidelity-only optimization to collapse when its designs are validated at high fidelity; (iii) CVaR/ERM objectives improve worst-case tail performance by {approx}23% relative to a mean objective without sacrificing average sensitivity; and (iv) discovered designs improve robust tail sensitivity by roughly 3--6x over commercial and heuristic optode layouts, with the largest gains in the high-fat and high-melanin subpopulations. The methodology bridges stochastic light-transport physics with sample-efficient machine-learning optimization and generalizes to cerebral oximetry, photodynamic therapy planning, and wearable physiological monitors.

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msaGUI: Multispectral Analysis Graphical User Interface for Ratiometric Analysis and Background Correction

Hoy, G. R.; Davis, C. M.

2026-07-03 biophysics 10.64898/2026.06.30.735666 medRxiv
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Chemical imaging is a powerful branch of modern microscopy encumbered by a lack of flexible, high-throughput analysis tools. Bespoke analytical pipelines typically perform ratiometric analysis on two layers in a multispectral image to describe the relative composition of molecules in a sample. This strategy has been implemented across fields, spanning histopathology, cell biology, environmental science, and materials science. The commercialization of chemical imaging microscopes has facilitated the collection of large multispectral datasets, necessitating accessible ways to process them. This paper describes Multispectral Analysis Graphical User Interface (msaGUI), a desktop graphical user interface to analyze individual and batch datasets of multispectral images. Data is loaded as CSV, TSV, or TIFFs and processed through a user-defined sequence of modular image operations that can be flexibly combined, e.g. to reduce spectral crosstalk or background noise. After analysis, data is visualized as exportable images, histograms, and statistics. To yield publication-quality figures, outputted images are fully customizable. Written in Python with open-source libraries, the msaGUI program is packaged into an executable for Windows and Mac for a fully no-code application. Other operating systems are supported via the Python source code. In summary, msaGUI provides a rapid and user-friendly solution for analyzing and visualizing multispectral data.

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.

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Multi-Site Reproducibility Study of 3D High-Content Analysis with Dual-View Oblique Plane Microscopy

Sparks, H.; Alexandrov, Y.; Arias-Garcia, M.; Bakal, C.; Batlle, E.; Bousgouni, V.; Carragher, N.; Colombelli, J.; Culley, J.; Curry, N.; Dent, L.; Dunsby, C.; Dvinskikh, L.; Garcia, E.; Giakoumakis, N. N.; Gustafsson, N.; Llanses, M.; Lee, M.; Mandke, K. N.; Marks, D.; McNeish, I.; Ratcliffe, C.; Sahai, E.; Suckert, T.

2026-07-03 bioengineering 10.64898/2026.06.29.735376 medRxiv
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High content imaging is being applied to achieve quantitative fluorescence readouts in increasingly complex 3-dimensional (3D) cell culture models such as spheroids and organoids. Compared to conventional 2D assays, 3D assays better represent biological heterogeneity but require more complex sample preparation, 3D imaging and 3D image analysis that can affect the accuracy and precision of such assays. We used spheroids formed from the NRAS-activated melanoma cell line 19161 modified to express an ERK kinase translocation reporter (KTR) as an exemplar 3D phenotypic assay carried out in 96-well plates. The spheroids were treated with the ERK activator TPA and a range of concentrations of the MEK inhibitor Binimetinib. 3D live-cell imaging with sub-cellular spatial resolution was performed using a dual-view oblique plane microscope (dOPM) - a form of single-objective light-sheet microscope - and the experiment was performed separately at 4 different institutes. The results were analysed using an identical 3D analysis pipeline and parameters. We assessed the variation in assay readout using a linear mixed effects model. Random variance at the well level was negligible (SD = 0.0048 relative to range of KTR biosensor readout at reference site of 0.17), indicating low technical noise. Treatment effects were dose-dependent and highly statistically significant compared to DMSO control across all sites (Dunnett-corrected p < 0.001). The range in KTR readout between the minimum (3.5 M Binimetinib) and maximum (100 nM TPA) treatments varied between 59 to 96% relative to the reference site. Measured bias in KTR readout between sites was between 6 and 12% of the range of the reference site. This study quantifies the reproducibility of a 3D live spheroid-based assay employing a fluorescence biosensor requiring readout out at the per-cell level using the dOPM platform and discusses areas where experimental protocol could be improved in the future to further improve reproducibility.

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Self-Calibrated Hyperspectral Neural Radiance Fields for 3D Reconstruction of Bone and Bone Analogues

Sigger, N.; Nguyen, T. T.; Ashraf, S.; Tozzi, G.

2026-06-23 bioengineering 10.64898/2026.06.17.732938 medRxiv
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Hyperspectral imaging (HSI) has gained increasing attention for bone assessment because it captures rich wavelength dependent information associated with mineralised tissue. HSI provides detailed spectral information related to material composition, while 3D geometric information supports the analysis of surface morphology and structural detail. However, integrating spectral and geometric information remains challenging, particularly when conventional reconstruction pipelines depend on external pose estimation. To address this challenge, we propose BoNeRF-HS, a self-calibrated hyperspectral neural radiance field for 3D reconstruction. BoNeRF-HS jointly optimises camera intrinsics, volume density, and hyperspectral radiance, removing the need for COLMAP based poses. To improve spectral modelling, we incorporate a gated spectral adapter head that learns wavelength dependent radiance features for hyperspectral view synthesis. We evaluate BoNeRF-HS on a multi-view hyperspectral dataset containing mouse bone, trabecular bone analogue, and cortical bone analogue samples. Experimental results demonstrate that our framework achieves improved reconstruction quality, and better preservation of bone surface details compared with existing approaches.

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Transcranial photobiomodulation influences BOLD responses during finger sequence execution: An fMRI Study in young and older adults

Dole, M.; Auboiroux, V.; Anglade, D.; Cousin, E.; Baciu, M.; Sandre-Ballester, C.; Rebecchi, S.; Cantat-Moltrecht, T.; Mitrofanis, J.

2026-07-09 neurology 10.64898/2026.07.06.26357423 medRxiv
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Transcranial photobiomodulation (PBM) is an emerging non-invasive brain stimulation method that is thought to increase neural metabolism by stimulating ATP production by the mitochondria. However, the mechanisms of action and the effects on the human brain are still unclear. In the present study, we investigated the potential of this method to enhance Blood Oxygen Level Dependent (BOLD) responses during the execution of a motor task in young and aged participants. Sixty young and aged participants were included in this single-blinded, sham-controlled, randomised, crossover study. They underwent an fMRI recording before and after 24-min stimulation with a 80-LEDs helmet emitting transcranially red and near infrared light. Post vs Pre BOLD signal was compared between PBM and SHAM, in each group. At baseline, aged participants showed reduced BOLD signal compared to young ones, in key regions of the sensorimotor processing, principally the left primary motor cortex and striatum. Transcranial PBM did not have a real impact in the young group. However in aged participants it increased BOLD signal in some regions that were underactivated compared to the young group at baseline. In particular, regional analysis showed increased BOLD response in the left primary motor cortex, and right dorsal and ventral premotor regions and striatum. These results suggest that transcranial PBM can increase fMRI BOLD activity in the task-related regions, particularly in aged subjects. Further research are needed to distinguish neural from vascular effects in transcranial PBM.

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VESTA: Machine Learning-Enabled Estimation of ViscoElastic Ratios from On-Axis Spatio-Temporal ARFI Features

Trisha, S. M.; Rahman, M. A.; Hassan, M. W.; Gi, Y. J.; Lee, J.; Hossain, M. M.

2026-07-07 bioengineering 10.64898/2026.07.06.736692 medRxiv
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Viscoelastic characterization of tissue has significant diagnostic value in oncology, as tumor progression alters both elasticity and viscosity in ways that neither property alone can fully capture. Existing acoustic radiation force (ARF)-based methods such as Viscoelastic Response (VisR) ultrasound estimate relative elasticity and viscosity through per-A-line nonlinear model fitting, which is computationally intensive and requires auxiliary simulations to correct elasticity-dependent bias. This work presents VESTA (Machine Learning-Enabled Estimation of ViscoElastic Ratios from On-Axis Spatio-Temporal ARFI Features), a two-stage data-driven pipeline that predicts elasticity ratio (ER) and viscosity ratio (VR) directly from seven normalized ARFI displacement features at the A-line level, without model fitting or compensation. Stage~1 is an MLP classifier that detects inclusion boundaries from normalized peak displacement and negative peak velocity ratios; Stage~2 is a dilated Conv1D regression model that estimates ER and VR along the full axial sequence using the predicted mask alongside displacement features. The pipeline was trained on 500 simulated inclusion scenarios spanning three geometries, five focal depths, two F-numbers, and a broad range of material contrasts. In silico, mean predicted ER and VR were within 12\% of ground truth across all geometries, with performance best when ER and VR were moderate or decoupled. Experimental validation on a chicken breast phantom demonstrated plausible generalization to real tissue heterogeneity. Applied to an in vivo murine 4T1 breast cancer model, the pipeline tracked treatment-related attenuation of mechanical contrast in paclitaxel-treated tumors relative to controls over a 36-day imaging period, supporting its relevance for tumor monitoring.

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Robust thermometry-imaging at sub-micrometer and millisecond-resolution by fluorescence lifetime microscopy allows for additional acquisition of multiple imaging channels

Meethale Mangalassery, B.; Fabiunke, S.; Schmick, M.; Huebinger, J.

2026-06-23 biophysics 10.64898/2026.06.18.733084 medRxiv
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Temperature is a fundamental parameter governing all molecular processes, including those that define life. Fluorescence microscopy is a powerful tool to observe molecular processes in living systems in real time. Precise control and measurement of temperature during fluorescence microscopy is therefore essential. We present here a robust temperature measurement based on the excited-state lifetime of the widely available and relatively inexpensive fluorescent dye pentamethine cyanine (Cy5). The excited-state lifetime of Cy5 shows a monotonic decline in the measurement range of 0 {degrees}C - 80 {degrees}C. The measured dependency is linear until 39 {degrees}C and monoexponential above. The dependance of excited-state lifetime upon temperature is used to measure temperature up to a precision of 0.5 {degrees}C or less, a temporal resolution down to <1 millisecond and to resolve temperature gradients with spatial resolutions that are only diffraction-limited. The far-red excitation and emission of Cy5 leaves bandwidth to simultaneously measure at least 3 additional spectral channels in standard fluorescent microscopes simultaneously. We demonstrate determination of temperature during 4-color live-cell fluorescence microscopy for a temperature-controlled experiment. We also show its applicability in measuring temperature gradients and laser-induced sample heating such as during STED nanoscopy.

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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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Indium Tin Oxide (ITO) Substrates Enable Coating-Free SEM Imaging and Simplified Preparation of Purified Fibrinogen Clots

Cai, C.; Flake, C.; Nameny, A.; Hudson, N. E.; Bannish, B. E.; Guthold, M.

2026-06-30 biophysics 10.64898/2026.06.24.733738 medRxiv
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Background. Scanning electron microscopy (SEM) is widely used to determine fibrin fiber structural properties such as fiber diameter and fiber length. However, conventional SEM preparation protocols are time-consuming and typically require conductive sputter coating. The coating process introduces an additional layer onto the sample surface and may influence measurements of nanoscale fiber structure. Furthermore, preparation of purified fibrinogen clots often follows protocols originally developed for plasma clots, resulting in unnecessary processing steps. Objective. To evaluate indium tin oxide (ITO) as a flat, conductive substrate for SEM imaging of fibrin fibers, investigate the effects of sputter coating on measured fiber diameter, and develop a simplified SEM preparation protocol for purified fibrinogen clots. Methods. Platelet-poor plasma clots and purified fibrinogen clots were formed on ITO substrates and imaged by SEM following 0 s, 45 s, or 90 s sputter coating. Fibrin fiber diameters were quantified and compared across coating conditions. For purified fibrinogen clots, an ITO-based simplified preparation protocol, in which clots were formed and imaged directly on the conductive ITO surface, was compared with a previously developed, standardized SEM protocol, in which clots were formed in microtube lids and subsequently transferred onto carbon tape for imaging. Results. Fiber diameter measurements were affected by sputter coating duration, with increasing coating time resulting in larger apparent fiber diameters. Plasma and purified fibrinogen clots exhibited distinct fiber diameter distributions and coating responses. For purified fibrinogen clots, the simplified ITO-based protocol produced fiber diameter measurements that were not significantly different from those obtained using the standardized lid-to-carbon-tape workflow when identical coating times were applied. Conclusions. ITO provides a practical conductive substrate for SEM imaging of fibrin fibers and enables substantial simplification of purified fibrinogen clot preparation. When coating conditions are matched, the simplified ITO-based protocol yields fiber diameter measurements comparable to those obtained using the previously standardized lid-to-carbon-tape workflow. These findings support the use of ITO as an alternative conductive imaging substrate and provide a simplified workflow for SEM analysis of purified fibrinogen clots. By reducing washing and transfer steps, this workflow may also provide a useful platform for future controlled studies of fibrin interactions with added proteins or other associated components.

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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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Graph-based characterization of in vitro neuronal network maturation using machine learning and digital holographic microscopy

Yazdani, Z.; Belanger, E.; Moreaud, M.; Llinares, J.; Allard, A.; Marquet, P.; Desrosiers, P.

2026-06-23 neuroscience 10.64898/2026.06.18.732973 medRxiv
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SignificanceDigital Holographic Microscopy (DHM) provides label-free quantitative phase images (QPIs) of living cells and has become a powerful tool for studying cellular morphology and dynamics. While most DHM studies have focused on cell-level analysis, the quantitative characterization of neuronal network organization and maturation from DHM images remains largely unexplored, highlighting the need for dedicated computational approaches. AimWe aimed to develop an automated framework combining deep-learning-based image analysis and graph theory to quantitatively characterize the organization, connectivity, and maturation of neuronal networks in primary rat cortical cultures imaged by DHM. ApproachTwo U-Net convolutional neural networks were trained on manually annotated DHM phase images to segment neuronal cell bodies and neurites. The resulting segmentation maps were used to infer putative morphological connections between neurons and generate graph representations of neuronal networks, referred to as graph fingerprints. A panel of 18 connectomics-inspired graph features was then computed to characterize local and global properties of network organization across four stages of culture maturation. ResultsThe mean area under the receiver operating characteristic curves was 0.98 for cell-body and 0.91 for neurite segmentation, indicating near-perfect identification. Graph-theoretical analysis revealed reproducible topological changes during network maturation in vitro, including increased density, reduced modularity, and progressive network integration. Correlation analysis showed that the 18 graph features grouped into two highly correlated families. A Random Forest classifier identified density and modularity as the most informative descriptors, achieving an accuracy of 87% in classifying maturation stages of neuronal cultures. ConclusionsOur results demonstrate that combining DHM, deep-learning-based segmentation, and graphtheoretical analysis enables quantitative characterization of neuronal network organization and maturation from label-free phase images. This framework provides a foundation for future studies of pharmacological experiments, neuronal network phenotyping, and human induced pluripotent stem cell (hiPSC)-derived neuronal cultures, where quantitative assessment of network organization remains a major challenge.

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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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Near-Infrared II Scintillator for High-Resolution X-ray Imaging

Gu, S.; Wu, Z.; Xu, S.; Dai, Z.; Zheng, J.; Li, A.-M.; Choy, W. C. H.; Qu, L.; Dai, H.; Wang, F.

2026-07-02 biophysics 10.64898/2026.06.29.735208 medRxiv
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Light scattering in scintillators is a pervasive problem and a key factor limiting X-ray imaging resolution. Here, we shift scintillator radioluminescence from the traditional visible range into the short-wave infrared (SWIR) or near-infrared II (NIR-II, 1000-3000 nm) window to mitigate light scattering and thereby enhance light penetration and X-ray imaging resolution. We present an NIR II MgGa2O4:Ni2+ scintillator with peak emission at 1340 nm, achieving a threefold improvement in X-ray imaging resolution compared with visible scintillators owing to reduced light scattering. This heavy-metal-free NIR-II scintillator exhibits intense radioluminescence comparable to that of conventional visible-emitting CsI:Tl, achieving a detection limit of 56 nanograys per second, ~100-fold lower than typical doses used in medical imaging. We show that this NIR-II scintillator enables high-resolution X-ray radiography of electronic circuit boards and biological tissues.