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Photoacoustics

Elsevier BV

Preprints posted in the last 30 days, ranked by how well they match Photoacoustics's content profile, based on 11 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
Tumour marker analysis using a machine learning assisted vibrational spectroscopy approach

Fatayer, R.; Sammut, S.-J.; Senthil Murugan, G.

2026-03-31 biochemistry 10.64898/2026.03.27.714840 medRxiv
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Tumour biomarkers such as CA125, CA15-3, CA19-9, AFP and CEA are routinely used in the oncology clinic to diagnose cancer, monitor response to therapy, and detect relapse. However, their quantification depends on immunoassay-based methods that are time-consuming, reagent-dependent, and poorly suited to resource-limited settings. Here, we present a machine learning-assisted ATR-FTIR spectroscopy approach for label-free tumour biomarker analysis to enable simple and rapid quantification at the bedside. Using principal component analysis (PCA), we first demonstrate that these five clinically relevant biomarkers are spectrally separable, with the protein-associated region (1200-1700 cm-1) providing the greatest discriminative information. We then develop partial least squares regression (PLSR) models to quantify CA125 in phosphate-buffered saline (R2 = 0.95) and in human serum across a clinically relevant concentration range, achieving reliable predictions at and above the clinical decision threshold of 35 U/mL. A semi-quantitative classification model further demonstrated robust identification of elevated CA125, with a macro-average sensitivity of 0.86 and specificity of 0.92. These results support ATR-FTIR spectroscopy as a rapid, reagent-free platform for cancer biomarker monitoring, with potential utility in resource-limited settings. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=109 SRC="FIGDIR/small/714840v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@1be9c03org.highwire.dtl.DTLVardef@f49e5eorg.highwire.dtl.DTLVardef@1c93e39org.highwire.dtl.DTLVardef@1141e6f_HPS_FORMAT_FIGEXP M_FIG C_FIG

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High-Field Multinuclear MRI Reveals Sodium Relaxation Heterogeneity in Cortical Organoids

Yu, G.; Liu, X.; Hike, D.; Qian, C.; Devor, A.; Zeldich, E.; Thunemann, M.; Zhou, X. A.

2026-04-05 bioengineering 10.64898/2026.04.01.715894 medRxiv
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Sodium magnetic resonance imaging (23Na MRI) provides a unique opportunity to probe ionic microenvironments in neural tissue because sodium ions play central roles in membrane electrophysiology, ion transport, and cellular homeostasis. Unlike conventional proton ({superscript 1}H) MRI, which primarily reflects water distribution and tissue structure, {superscript 2}3Na MRI is sensitive to ionic compartmentation and quadrupolar interactions arising from the spin-3/2 nature of the sodium nucleus. However, sodium MRI remains technically challenging due to intrinsically low signal sensitivity and rapid biexponential relaxation, particularly when imaging small biological systems. Here, we establish a high-field multinuclear MRI platform for imaging human cerebral organoids at 14 Tesla. Cerebral organoids derived from human induced pluripotent stem cells provide a simplified three-dimensional neural tissue model that enables investigation of ionic microenvironments without vascular or systemic confounds. Using a dual-tuned {superscript 1}H/{superscript 2}3Na radiofrequency coil, we performed co-registered structural, diffusion, and sodium imaging of individual fixed organoids. High-resolution {superscript 1}H MRI (33-100 m) revealed pronounced microstructural heterogeneity, while multi-echo {superscript 2}3Na MRI (300-400 m) enabled voxel-wise characterization of quadrupolar relaxation behavior. Bi-exponential analysis of the sodium signal decay identified distinct relaxation components (T2*short {approx} 1 ms and T2*long {approx} 12 ms) and revealed spatial heterogeneity in sodium microenvironments across the organoid tissue. These results demonstrate the feasibility of quantitative sodium relaxometry in cortical organoids and establish a multinuclear imaging platform for investigating ionic microenvironment dynamics in three-dimensional neural tissue models.

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PA-SfM: Tracker-free differentiable acoustic radiation for freehand 3D photoacoustic imaging

Li, S.; Gao, J.; Kim, C.; Choi, S.; Chen, Q.; Wang, Y.; Wu, S.; Zhang, Y.; Huang, T.; Zhou, Y.; Yao, B.; Yao, Y.; Li, C.

2026-04-08 bioengineering 10.64898/2026.04.06.716718 medRxiv
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Three-dimensional (3D) handheld photoacoustic tomography typically relies on bulky and expensive external positioning trackers to correct motion artifacts, which severely limits its clinical flexibility and accessibility. To address this challenge, we present PA-SfM, a tracker-free framework that leverages exclusively single-modality photoacoustic data for both sensor pose recovery and high-fidelity 3D reconstruction via differentiable acoustic radiation modeling. Unlike traditional Structure-from-Motion (SfM) methods that formulate pose estimation as a geometry-driven optimization over visual features, PA-SfM integrates the acoustic wave equation into a differentiable programming pipeline. By leveraging a high-performance, GPU-accelerated acoustic radiation kernel, the framework simultaneously optimizes the 3D photoacoustic source distribution and the sensor array pose via gradient descent. To ensure robust convergence in freehand scenarios, we introduce a coarse-to-fine optimization strategy that incorporates geometric consistency checks and rigid-body constraints to eliminate motion outliers. We validated the proposed method through both numerical simulations and in-vivo rat experiments. The results demonstrate that PA-SfM achieves sub-millimeter positioning accuracy and restores high-resolution 3D vascular structures comparable to ground-truth benchmarks, offering a low-cost, softwaredefined solution for clinical freehand photoacoustic imaging. The source code is publicly available at https://github.com/JaegerCQ/PA-SfM.

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Bioimpedance-assisted characterization of cardiac electroporation and anisotropic homogenization by pulsed field ablation

Jacobs, E. J.; Santos, P. P.; Parizi, S. S.; Dunham, S. N.; Davalos, R. V.

2026-03-20 bioengineering 10.64898/2026.03.18.712769 medRxiv
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ObjectivePulsed field ablation (PFA) relies on irreversible electroporation to create nonthermal cardiac lesions, yet real-time indicators of electroporation progression and validated lethal electric field thresholds remain limited. This study aimed to develop a bioimpedance-based metric for real-time monitoring of cardiac electroporation, evaluate the impact of myocardial anisotropy under electroporation conditions, and derive waveform-specific lethal electric field thresholds. IntroductionCurrent PFA procedures lack direct intraoperative feedback on lesion formation, and uncertainty remains regarding the role of myocardial fiber orientation in shaping electric field distributions. Because electroporation dynamically alters tissue electrical properties, monitoring these changes during treatment may improve prediction of ablation outcomes. MethodsPFA was delivered to fresh ex vivo porcine ventricular tissue using clinically relevant and energy-matched waveforms with pulse widths from 1 to 100 {micro}s. Inter-burst broadband electrical impedance spectroscopy was performed using a low-voltage diagnostic waveform to quantify burst-resolved impedance changes. Lesions were visualized using metabolic staining, then finite element models incorporating nonlinear electroporation-dependent conductivity were used to compare anisotropic and homogenized electric field distributions. Lethal electric field thresholds were estimated by fitting simulated contours to measured lesion areas and validated using uniform electric fields generated by a parallel electrode array. ResultsAcross all waveforms, impedance measurements showed a rapid initial decrease followed by stabilization, indicating early electroporation saturation. Burst-to-burst percent change in impedance slope provided a consistent, waveform-agnostic metric of electroporation progression. Lesion morphology was not systematically influenced by fiber orientation, and modeling demonstrated that electroporation-induced conductivity increases homogenized tissue anisotropy. Lethal electric field thresholds increased with decreasing pulse width, ranging from 517 {+/-} 46 V/cm (100 {micro}s) to 1405 {+/-} 55 V/cm (1 {micro}s), and were validated under uniform field conditions. ConclusionBioimpedance-assisted monitoring enables real-time assessment of cardiac electroporation, while electroporation-induced homogenization supports simplified modeling and standardized PFA treatment design.

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Visual Fidelity-Driven Quality Assessment of Medical Image Translation

Bizjak, Z.; Zagar, J.; Spiclin, Z.

2026-03-20 radiology and imaging 10.64898/2026.03.18.26348721 medRxiv
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Automated and reliable image quality assessment (IQA) is essential for safe use of medical image synthesis in critical applications like adaptive radiotherapy, treatment planning, or missing-modality reconstruction, where unnoticed generative artifacts may adversely affect outcomes. We evaluated image-to-image translation quality by coupling large-scale expert visual quality assessment with explainable automated IQA modeling. Adversarial diffusion-based framework, SynDiff, was applied to four cross-modality synthesis tasks, including three inter-MR and a CBCT-to-CT translation. Using four-fold cross-validation, ten reference-based and eight no-reference IQA metrics were computed for all synthesized images. Visual IQA ratings were independently collected from thirteen expert raters using predetermined protocol and specialized image viewer enabling blinded, randomized six-point Likert scoring. Auto-Sklearn was employed to learn ensemble regression models mapping IQA metrics to visual consensus ratings, with separate models trained on reference-based and no-reference metrics. The models closely reproduced distribution and ordering of expert ratings, typically within +/- 0.5 Likert points. Reference-based models achieved higher agreement with visual ratings than no-reference models (R^2 0.75 vs. 0.59, resp.), although the latter remained unbiased and informative. Explainability analyses highlighted structure- and contrast-sensitive metrics as key predictors. Overall, the results demonstrate that ensemble regression models can provide transparent, scalable, and clinically meaningful quality control for generative medical imaging.

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Left atrial flow and thrombosis risk from 4D CT contrast dynamics by physics-informed neural network and indicator dilution theory

Maidu, B.; Gonzalo, A.; Guerrero-Hurtado, M.; Bargellini, C.; Martinez-Legazpi, P.; Bermejo, J.; Contijoch, F.; Flores, O.; Garcia-Villalba, M.; McVeigh, E.; Kahn, A.; del Alamo, J. C.

2026-04-03 bioengineering 10.64898/2026.03.31.715623 medRxiv
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Atrial fibrillation (AF) promotes blood stasis and thrombus formation, most often within the left atrial appendage (LAA), and can lead to stroke or transient ischemic attack (TIA). Time-resolved contrast-enhanced computed tomography (4D CT) captures left atrial (LA) opacification and washout, but it does not directly provide quantitative stasis metrics such as blood residence time. Patient-specific computational fluid dynamics (CFD) can quantify LA/LAA residence time, yet routine clinical use is limited by computational cost and sensitivity to patient-specific boundary conditions. Here, we present two complementary approaches to infer time-resolved 3D residence time fields directly from contrast dynamics. First, a physics-informed neural network (PINN) treats contrast as a passive scalar and jointly reconstructs velocity and residence time by enforcing the incompressible Navier-Stokes equations and transport equations for contrast concentration and residence time in moving, patient-specific LA anatomies. Second, an indicator dilution theory (IDT) formulation computes voxelwise, time-resolved residence time maps from contrast time curves alone by constructing a PV-referenced impulse response and modeling transport with a tank-in-series model with spatially dependent parameters. Both methods are benchmarked against patient-specific CFD in six cases spanning diverse LA function, including three patients with TIA or thrombus in the LAA and three patients free of events. Both approaches reproduce expected spatial and temporal trends, with higher residence time in the distal LAA and higher LAA residence time in cases with TIA or thrombus. IDT demonstrates the closest agreement with CFD across the full range of residence times and produces maps in seconds, facilitating clinical translation. In contrast, the PINN additionally recovers phase-dependent atrial flow structures, but tends to smooth and underestimate the highest residence-time regions and requires hours of training. Together, these results support a scalable workflow in which IDT enables rapid stasis screening from contrast CT, and PINNs provide a complementary pathway for detailed, patient-specific hemodynamic inference when full-field flow information is needed.

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AI-Assisted Pneumonia Detection, Localisation and Report Generation from Chest X-rays

Boiardi, F. E.; Lain, A. D.; Posma, J. M.

2026-03-23 radiology and imaging 10.64898/2026.03.20.26348879 medRxiv
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Pneumonia detection in chest X-rays (CXRs) is complicated by high inter-observer variability and overlapping radiographic patterns. While deep learning (DL) solutions show promise, limitations in generalisability and explainability hinder clinical adoption. We address these challenges by introducing a holistic DL-based computer-aided diagnosis (CAD) pipeline for pneumonia detection, localisation, and structured report generation from CXRs. We curated the largest composite of publicly available CXRs to date (N=922,634), of which [Formula] were used for training. MIMIC-CXR radiology reports were relabelled using a local large language model (LLM), positing that LLM-derived pneumonia labels would yield higher diagnostic sensitivity than the provided rule-based natural language processing (rNLP) labels. DenseNet-121 classifiers were trained on four configurations: MIMIC-CXR (rNLP), MIMIC-CXR (LLM), and each supplemented with VinDr-CXR data. Gradient-weighted Class Activation Mapping (Grad-CAM) provided visual explainability and lung zone-based localisation. LLM-driven relabelling significantly improved human-label agreement (96.5% vs 72.5%, P=1.66x10-11). The best-performing model (MIMIC-CXR (LLM) + VinDr-CXR) achieved 82.08% sensitivity and 81.97% precision, surpassing both radiologist sensitivity ranges (64-77.7%) and CheXNets pneumonia F1-score (43.5%). Grad-CAM localisation attained a moderate F1-score of 52.9% (sensitivity=65.7%, precision=44.3%), confirming focus alignment with pathological lung regions while highlighting areas for refinement. These findings demonstrate that LLM-driven label curation, combined with DL, can exceed conventional rNLP and radiologist performance, advancing high-quality data integration in predictive medical imaging. Clinically, our pipeline offers rapid triage, automated report drafting, and real-time pneumonia surveillance; tools that can streamline radiology workflows and mitigate diagnostic errors.

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Fluorescent Protein Photobleaching: From molecular processes to spectromicroscopy

Beguin, T.; Wang, K.; Bousmah, Y.; Abou Mrad, N.; Halgand, F.; Pasquier, H.; Erard, M.

2026-04-02 biochemistry 10.64898/2026.03.31.715555 medRxiv
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Fluorescent proteins (FPs) are essential tools for biological imaging but are limited by photobleaching, a light-induced loss of fluorescence intensity that reduces spatial and temporal resolution. Despite extensive use, the molecular mechanisms underlying FP photobleaching remain poorly understood due to the diversity of FPs and the complexity of their photochemistry. Existing approaches either monitor fluorescence decay in live cells, reflecting imaging conditions but lacking molecular detail, or rely on in vitro spectroscopy of purified proteins, providing mechanistic insight but often limited to individual FPs. We introduce a quantitative workflow bridging these approaches by combining live-cell measurements with in vitro spectroscopy. In vitro measurements are performed on a dedicated setup that simultaneously monitors absorption, emission, and fluorescence decay during photobleaching. Applied to six FPs spanning different chromophores, emission ranges and sequences, this approach reveals that photobleaching strongly depends on FP. It involves multiple chemical pathways, including oxidation, dimerization, and backbone cleavage. Spectroscopic analysis uncovers a heterogeneous ensemble of photoproducts with distinct photophysical properties that can remain optically active during irradiation, including shortened fluorescence lifetimes or altered absorption spectra. These findings demonstrate that FP photobleaching cannot be described as a simple ON-OFF process but involves complex transformations affecting both fluorescence intensity and lifetime. Such transformations can introduce significant biases in quantitative imaging, particularly in advanced techniques such as FLIM and FRET. Finally, we introduce quantitative indicators enabling robust comparison of FP photostability across experimental conditions. This framework provides a comprehensive approach for understanding and quantifying photobleaching and its implications for fluorescence imaging.

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Decoupling Detection and Classification to Improve Morphological Phenotype Analysis of Sickle Red Blood Cells in Full-Scope Microscopy

Ma, S.; Xu, M.; Dao, M.; Li, H.

2026-04-06 bioengineering 10.64898/2026.03.31.715578 medRxiv
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Microscopy-based analysis of red blood cell (RBC) morphology is widely used to study phenotypes in sickle cell disease (SCD). Although AI models have been developed to automate classification, most are trained on pre-cropped single-cell images and thus struggle with full-scope microscopic images containing densely packed cells and diverse morphologies, which require both accurate detection and fine-grained classification. We propose an end-to-end computational framework to identify individual RBCs in full-scope microscopy images and classify them into five morphological categories: discocytes (DO), echinocytes (E), elongated and sickle-shaped cells (ES), granular cells (G), and reticulocytes (R). We first evaluate advanced detection-classification models, including You Only Look Once (YOLO) and Detection Transformers (DETR), and demonstrate that while these models effectively detect cells, their classification performance falls short of specialized classifiers trained on single-cell images, particularly for minority phenotypes. To address this limitation, we introduce a two-step framework in which a YOLO-based detector localizes and crops individual cells from full-scope images, followed by a fine-tuned DenseNet121 ensemble classifier that assigns each cell to one of the five morphological categories. The proposed framework achieves a detection-level F1-score of 0.9661 and a weighted-average classification F1-score of 0.9708, with an overall classification accuracy of 97.06%. Compared with the single-step YOLO26n baseline, the two-step pipeline yields a macro-average F1-score improvement of +0.1675, with particularly substantial gains for minority classes (E: +0.1623; G: +0.2774; R: +0.2603). Overall, this hybrid framework demonstrates a practical strategy for adapting fast, general-purpose detection models to domain-specific biomedical tasks by combining them with specialized classifiers, delivering both efficiency and high accuracy for scientific and clinical image analysis.

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DNA methylation and hydroxymethylation quantification using vibrational spectroscopy

Fatayer, R.; Sammut, S.-J.; Senthil Murugan, G.

2026-04-05 biochemistry 10.64898/2026.04.02.716174 medRxiv
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Global quantification of DNA cytosine modifications, including 5-methylcytosine (5-mC) and 5-hydroxymethylcytosine (5-hmC), is important for understanding cancer biology, though established methods require multi-step workflows and costly instrumentation. Here we show that attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy combined with regression modelling enables rapid, label-free, and non-destructive quantification of both modifications from DNA samples. Using Adenomatous Polyposis Coli (APC) promoter DNA standards spanning 0-100% modification, we identified modification-sensitive spectral features and observed that 5-hmC produces greater spectral changes than 5-mC. A univariate peak-ratio approach yielded strong linearity for both modifications (R2 = 0.97), while partial least squares regression (PLSR) improved quantification accuracy to R2 = 0.99 (RMSE = 2.6%) for 5-hmC and R2 = 0.97 (RMSE = 5.7%) for 5-mC. In composite mixtures containing all three cytosine states, 5-hmC remained highly quantifiable (R2 = 0.97; RMSE = 5.1%), while 5-mC accuracy decreased (R2 = 0.90; RMSE = 9.6%), consistent with the greater spectral distinctiveness secondary to the hydroxymethyl group. Transferability was assessed using circulating tumour DNA (ctDNA), short cell-free DNA fragments shed from tumour cells into the bloodstream, comprising multiplexed reference material spanning seven genomic regions and a polydisperse fragment-length distribution (155-220 bp). After domain adaptation between synthetic and ctDNA spectra, we obtained a quantitative methylation calibration with R2 = 0.98 and RMSE = 5.2% under cross-validation. These results support ATR-FTIR spectroscopy as a viable platform for global cytosine modification quantification and establish proof-of-concept applicability to ctDNA analysis.

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A Three-dimensional Analytical Framework for Retinal Microvasculature Reveals Layer-associated Vulnerability in Development and Neovascular Remodeling

Shang, W.; Hong, G.; Keller, W. E.; Morton, R. A.; Zeboulon, P.; Kenichi, T.; Duan, X.; Gould, D. B.; Kim, T. N.

2026-03-19 bioengineering 10.64898/2026.03.16.711909 medRxiv
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The neurosensory retina is one of the most metabolically active tissues in the body and a uniquely accessible extension of the central nervous system, where neuronal and vascular structures can be visualized non-invasively. Its accessibility and highly organized laminar architecture make it a powerful model for studying vascular development and a window into systemic health. Although computational analyses of retinal images have enabled risk assessment for ocular and systemic diseases, most vascular studies rely on two-dimensional frameworks with limited resolution of capillary structure and layer-specific organization. Here, we present a high-resolution three-dimensional (3D) imaging and analysis pipeline enabling quantification of retinal microvasculature and extraction of structural and network metrics across vascular layers. We apply this approach to two mouse models of aberrant retinal vascular development: one with spontaneous postnatal chorioretinal neovascularization and another with disrupted neurovascular lattice formation and layered organization in early life. Across both pathologic contexts, 3D analysis provides detailed characterization of vascular architecture and identifies early vulnerability of the intermediate layer plexus (IMP) as a sensitive indicator of abnormal remodeling and neovascularization. This framework enables precise characterization of retinal vasculature and establishes a foundation for identifying new retinal biomarkers with potential relevance to neurovascular and systemic disease.

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Hydrogel Fiber Endomicroscopy

Chen, P.; Han, K.; Gao, Z.; Deng, C. M.; Xu, H.; Ling, Z.; Zheng, C.; Sawant, M.; Cicerone, M.; Kesarwala, A.; Markowitz, J. E.; Jia, S.

2026-03-26 bioengineering 10.64898/2026.03.23.713710 medRxiv
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Multimode fibers enable minimally invasive, high-resolution imaging through ultrathin probes, thereby enhancing diagnostic precision and facilitating real-time monitoring in delicate anatomical regions. In this work, we introduce HYFEN, a hydrogel-based endomicroscopic imaging platform for flexible, biocompatible, and subcellular-scale fluorescence microscopy. HYFEN leverages the unique properties of hydrogel materials, adaptive optics, and pixel-wise image enhancement to address challenges associated with silica-based fibers, including mode scrambling, limited field of view, and mechanical rigidity. The technique achieves precise mode threading, rapid diffraction-limited focusing at kilohertz speeds, and high-fidelity fluorescence signal acquisition with subcellular resolution. Notably, the approach extends fluorescence imaging under enhanced fiber dimensions and bending conditions that are unachievable with conventional modalities. Together, these advances establish HYFEN as a versatile platform for next-generation biointerfacing and minimally invasive imaging across biomedical and clinical settings.

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Quantifying Glycogen And Lipid Droplet Synthesis In Ovarian And Cervical Cancer Cells Using Deuterated Raman Probes With Stimulated Raman Scattering Microscopy

Pierson, R. N.; Gupta, S. A.; Zhang, M.; Kaiser, L. C.; Tumey, L. N.; Lu, F.

2026-03-18 bioengineering 10.64898/2026.03.16.712189 medRxiv
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Epithelial ovarian cancer remains one of the most lethal malignancies among women, with late-stage diagnoses yielding 5-year survival rates below 30%. The metabolic heterogeneity of the tumor microenvironment (TME) highlights the need for methods capable of rapid, chemically specific phenotyping. Stimulated Raman scattering (SRS) microscopy when combined with deuterium labeled metabolites enables the non-invasive high contrast interrogation of cellular metabolic pathways. In this study, we used SRS microscopy to profile fatty acid and glycogen metabolism in epithelial ovarian cancer (SKOV-3) and cervical cancer (HeLa) cell models. Deuterium labeled glucose revealed striking differences in glycogen synthesis and intracellular distribution, with SKOV-3 cells exhibiting markedly greater single-cell heterogeneity than HeLa. Complementary measurements of lipid droplet (LD) synthesis and turnover under nutrient starvation further revealed cell-line-specific metabolic strategies, identifying LD and glycogen dynamics as a potential diagnostic marker of cancer metabolic phenotypes. These results demonstrate that SRS microscopy in the Raman silent region, paired with metabolic labeling, can sensitively resolve metabolic diversity across cancer cell subpopulations. Such metabolic phenotyping may inform both early diagnostic strategies and therapeutic approaches that combine cytotoxic treatment with targeted metabolic disruption.

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Two-photon characterisation of long-Stokes-shift dye ATTO 490LS for single-laser multicolour imaging

Cheung, K. Y.; Wu, Y.; Lee, S. Y.; Zhang, X.; Fukuda, M.; Suresh, D. D.; Claridge-Chang, A.

2026-03-27 neuroscience 10.1101/2025.11.21.689649 medRxiv
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Long-Stokes-shift fluorophores enable high sensitivity and multiplexed imaging with single-wavelength excitation. Under single-photon illumination ATTO 490LS exhibits a 165-nm Stokes shift, but its two-photon properties remain uncharacterised. Emission and excitation spectral analyses of ATTO 490LS in ex vivo Drosophila melanogaster brains identified two-photon excitation sensitivity at 940 nm, with peak emission at 640 nm. We demonstrate successful duplexed imaging of ATTO 490LS alongside Alexa Fluor 488 using a single 920-nm fibre laser and dual photomultiplier tubes, enabling distinct measurement of red and green fluorescence signals. These findings establish ATTO 490LS as suitable for multicolour two-photon microscopy with single-laser systems.

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Quantitative assessment of collagen architecture from routine histopathological images shows concordance with Second Harmonic Generation microscopy

Ingawale, V.; Dandapat, K.; Konkada Manattayil, J.; Gupta, S.; Shashidhara, L. S.; Koppiker, C.; Shah, N.; Raghunathan, V.; Kulkarni, M.

2026-04-06 pathology 10.64898/2026.03.31.26349841 medRxiv
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Collagen organisation within the tumour microenvironment plays a critical role in tumour progression and has emerged as an important structural biomarker in cancer. Second Harmonic Generation (SHG) microscopy enables label-free visualisation and quantitative assessment of fibrillar collagen architecture; however, its high cost, specialised instrumentation, and limited field-of-view restrict routine clinical application. In this study, we evaluated whether collagen features quantified from digitally scanned Masson-Goldners Trichrome-stained histopathological sections can approximate measurements obtained from SHG microscopy. Formalin-fixed paraffin-embedded breast tumour tissues, including benign and invasive ductal carcinoma (IDC) samples with varying collagen content, were analysed using SHG microscopy and whole-slide brightfield imaging. Matched regions of interest were analysed using two independent digital image analysis approaches: a conventional ImageJ-based workflow (TWOMBLI) and a machine learning-based computational pipeline. Collagen structural parameters including collagen deposition area, fibre number, and alignment metrics were quantified and compared across imaging modalities using correlation analysis. SHG signals were consistently detected from trichrome-stained sections, confirming compatibility of SHG imaging. Quantitative comparison demonstrated significant concordance between SHG-derived collagen metrics and those obtained from digital image analysis pipelines, particularly for collagen area and fibre alignment. These findings demonstrate that computational analysis of routine histopathological images can capture key spatial features of collagen organisation comparable to SHG microscopy. Digital pathology-based collagen quantification therefore, represents a scalable and clinically accessible approach for assessing extracellular matrix architecture in tumour tissues.

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Computational aberration-corrected volumetric imaging of single retinal cells in the living eye

Feng, G.; Godinez, D. R.; Li, Z.; Nolen, S.; Cho, H.; Kimball, E.; Duh, E. J.; Johnson, T. V.; Yi, J.

2026-03-24 bioengineering 10.64898/2026.03.21.712744 medRxiv
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The eye offers a unique non-invasive window for accessing single-cell level structures and functions of the central nervous system (CNS) throughout the retina. However, strong and space-varying ocular aberrations, along with limited volume rates, challenge large-scale cellular imaging in living eyes and stymie the full potential of possible biological and pathological studies in retina. Here, we present plenoptic illumination scanning laser ophthalmoscopy (PI-SLO), a 3D fluorescent retinal imaging modality that enables high-speed, widefield, volumetric single-cell imaging with low phototoxicity. By capturing multiple angular images of fluorescence signals from the entire volume, PI-SLO enables digital aberration correction and 3D imaging across a >20{o} FOV with >23 Hz volume rate. We leverage this structural and functional imaging modality to investigate three key aspects of CNS physiology through the living mouse retina, including: microglial process dynamics, vascular perfusion, and light evoked calcium fluxes in inner retinal neurons. PI-SLO is a versatile non-invasive platform for in vivo investigation of retinal and CNS physiology at the cellular level.

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Information-Guided Parameter Optimisation for MR Elastography Radiomics

Djebbara, I.; Yin, Z.; Friismose, A. I.; Poulsen, F. R.; Hojo, E.; Aunan-Diop, J. S.

2026-03-20 radiology and imaging 10.64898/2026.03.17.26348578 medRxiv
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Mechanical properties of biological tissues vary across spatial scales, yet radiomics typically relies on fixed, heuristic choices for neighbourhood size, kernel geometry, and spectral content - choices that can silently reshape the feature space before any modelling begins. We introduce a label-free, information-theoretic framework for selecting extraction parameters in multi-frequency MRE radiomics. For each configuration {theta} - neighbourhood radius r, kernel geometry k (sphere or shell), and frequency subset f - we extract a radiomics feature matrix and score it using an objective J({theta}) that integrates distributional richness (Shannon entropy), cross-frequency coherence (canonical correlation), inter-feature redundancy (Spearman correlation), and bootstrap stability. We evaluate 121 configurations per tissue in multi-frequency MRE (30-60 Hz) of human brain, liver, and a calibrated phantom, and test robustness using 10,000 Dirichlet-sampled objective weightings. Across tissues, neighbourhood aggregation is consistently preferred over voxel-wise extraction, outperforming the no-neighbourhood baseline in 98.4-100% of weightings. External validation in 100 independent brain scans acquired with a different protocol and wider frequency range (20-90 Hz) confirms a reproducible mesoscopic plateau at r = 3-5 (9-15 mm), with a modal optimum at r = 4; omitting neighbourhood analysis reduces J({theta}) by 38% relative to each subject's optimum. Frequency-subset preferences replicate across datasets, with lower frequencies most frequently selected for brain. By turning ad hoc extraction choices into an outcome-free optimisation step, this framework improves reproducibility, reduces sensitivity to heuristic parameter choices, and generalises across acquisition protocols and imaging sites.

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Raybloc: A Marine Bioactive Silica-Microsponge Formulation Confers Superior Protection against Blue Light and Infrared-A Induced Skin Damage in Murine Model

Yu, S.; Ngo, K.; Ovais, M.

2026-03-24 bioengineering 10.64898/2026.03.21.713389 medRxiv
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Long-term exposure to high-energy visible (HEV) blue light and infrared-A (IR-A) radiation accelerates oxidative stress, inflammation, and transepidermal water loss (TEWL), leading to photoaging and damage to the skin barrier. In this study, we developed Raybloc(R), a marine bioactive silica microsponge formulation, and evaluated its protective effects against combined high-energy visible (HEV; 410-480 nm) and infrared-A (IR-A; 700-1400 nm) exposure in a preclinical model. We divided 36 nude BALB/c-nu/nu mice into six groups: one that didnt get any treatment, one that got Raybloc(R) (no radiation), one that got Raybloc(R) 5%, one that got Raybloc(R) 8%, one that got HA 0.5%, and one that got HA 0.8%. Animals underwent topical treatment for 14 days under regulated exposure to HEV (410-480 nm, 100 J/cm2/day) and IR-A (700-1400 nm, 30 mW/cm2). We examined transepidermal water loss (TEWL), skin hydration, oxidative stress, inflammatory cytokines (IL-1{beta}, IL-6, TNF-, IL-10), and histological indicators of collagen preservation through biophysical, biochemical, and histopathological techniques. In the Raybloc(R) 8% group, TEWL dropped by 48.3 {+/-} 4.6% (p < 0.001), and skin hydration went up by 62.7 {+/-} 5.1%. The levels of ROS and MMP-1 expression decreased by 63.4% and 57.2%, respectively, while collagen I increased by 2.1 times compared to HA 0.8%. There was a big drop in the pro-inflammatory cytokines IL-1{beta}, IL-6, and TNF- (-54%, -49%, and -46%), and a big rise in IL-10 (+38%). Histological analysis demonstrated well-preserved epidermal integrity and dense collagen bundles in Raybloc(R)-treated mice, whereas irradiated controls exhibited dermal disorganization and inflammatory infiltration. Raybloc(R) showed better photoprotective, antioxidant, and moisturizing effects than HA-based products. It also helped reduce oxidative and inflammatory skin damage caused by blue light and IR-A. These results support Raybloc(R) as a next-generation multifunctional dermocosmetic that can help stop photoaging caused by digital and solar radiation. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=127 SRC="FIGDIR/small/713389v1_ufig1.gif" ALT="Figure 1"> View larger version (70K): org.highwire.dtl.DTLVardef@54e046org.highwire.dtl.DTLVardef@502f87org.highwire.dtl.DTLVardef@6088daorg.highwire.dtl.DTLVardef@1b8c241_HPS_FORMAT_FIGEXP M_FIG C_FIG

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Improving Glioblastoma Classification Using Quantitative Transport Mapping with a Synthetic Data Trained Deep Neural Network

Romano, D. J.; Roberts, A. G.; Weppner, B.; Zhang, Q.; John, M.; Hu, R.; Sisman, M.; Kovanlikaya, I.; Chiang, G. C.; Spincemaille, P.; Wang, Y.

2026-04-01 radiology and imaging 10.64898/2026.03.31.26349864 medRxiv
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Purpose: To develop a deep neural network-based, AIF-free, perfusion estimation method (QTMnet) for improved performance on glioma classification. Methods: A globally defined arterial input function (AIF) is needed to recover perfusion parameters in the two-compartment exchange model (2CXM). We have developed Quantitative Transport Mapping (QTM) to create an AIF-independent estimation method. QTM estimation can be formulated using deep neural networks trained on synthetic DCE-MRI data (QTMnet). Here, we provide a fluid mechanics-based DCE-MRI simulation with exchange between the capillaries and extravascular extracellular space. We implemented tumor ROI generation to morphologically characterize tissue perfusion. We compared our QTMnet implementation with 2CXM on 30 glioma human subjects, 15 of which had low-grade gliomas, and 15 with high-grade glioblastomas. Results: QTMnet outperforms (best AUC: 0.973) traditional 2CXM (best AUC: 0.911) in a glioma grading task. Conclusion: The AIF-independent QTMnet estimation provides a quantitative delineation between low-grade and high-grade gliomas.

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Red/near-infrared light activates the mitochondrial large-conductance calcium-activated potassium channel in glioblastoma cells.

Bednarczyk, P.; Lewandowska, J.; Kulawiak, B.; Szewczyk, A.

2026-04-05 biochemistry 10.64898/2026.04.02.716077 medRxiv
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Mitochondrial potassium channels, located in the inner mitochondrial membrane, play a crucial role in the cells life/death phenomenon. Activation of mitochondrial potassium channels by potassium channel openers may protect cells against ischemia-reperfusion injury. It is known that mitochondrial large conductance calcium-activated potassium channels interact with various mitochondrial proteins, including enzymes of the respiratory chain. Numerous studies indicate that the mitochondria, especially cytochrome c oxidase, play a crucial role as a chromatophore in the cellular response to red and near-infrared light. In this study, we employ the patch-clamp technique and single-channel recordings to investigate the regulation of glioblastoma mitochondrial large conductance calcium-activated potassium channel activity by infrared light. Specifically, we examined the effects of wavelengths 620 nm, 680 nm, 760 nm, and 820 nm in a redox-controlled environment. Our findings suggest that illuminating the inner mitochondrial membrane with these wavelengths may activate mitochondrial large conductance calcium-activated potassium channels. These results offer new insights into the regulation of mitochondrial potassium channels by cytochrome c oxidase, which may lead to the development of non-pharmacological interventions with potential cytoprotective benefits.