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Journal of Biophotonics

Wiley

Preprints posted in the last 90 days, ranked by how well they match Journal of Biophotonics's content profile, based on 16 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.

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Correlative scanning electron and super-resolution structured illumination microscopy

Hamilton, J. R.; Levis, S.; Hagen, G. M.

2026-02-11 biophysics 10.64898/2026.02.09.704937 medRxiv
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Correlative microscopy techniques are used for many different applications in the biological sciences because the comparison of different imaging methods allows researchers to gain more insight and data from samples. Correlative light and electron microscopy (CLEM) methods have been developed to preserve biological samples to withstand the harsh environments necessary for electron microscopy. After first being imaged using widefield (WF) and super-resolution structured illumination fluorescence microscopy (SIM), a NanoSuit chemical treatment was applied to a mammalian testis sample before imaging with scanning electron microscopy (SEM). This was done to compare the image quality and resolution of each technique. SEM yields higher resolution and offers validation of results from SIM.

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Noninvasive Laser SCOS Monitoring of Rat Brain Hemodynamics During Intracerebral Injection

Fernandes, M.; Huang, Y. X.; Xu, I.; Noguera Saigua, C.; Li, J.; Mahler, S.

2026-03-05 biophysics 10.64898/2026.03.03.709425 medRxiv
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Cerebral blood volume (CBV) and blood flow (CBF) constitute key metrics for cerebrovascular monitoring, enabling assessment of stroke severity and risk-prediction, aging-related changes, and neurological diseases. CBF and CBV monitoring are key aspects in diagnosis, treatment triage, and clinical outcome of ischemic and hemorrhagic strokes. In recent years, there have been ongoing efforts toward the development of optical devices for noninvasive monitoring of CBV and CBF. Speckle contrast optical spectroscopy (SCOS) has recently emerged as a strong candidate for clinical translation in monitoring CBF and CBV, due to its affordability, compact and wearable design, and noninvasive nature. However, experimental demonstrations that SCOS can effectively monitor brain hemodynamics remain sparse. This is primarily due to challenges in design experiments that isolate cerebral blood dynamics from those in the scalp and skull. In this paper, we report experiments using SCOS to monitor cerebral hemodynamics in rats during intracerebral blood flow modulation. To modify cerebral blood dynamics, a surgical procedure was performed to insert a catheter for direct injection of flow modulation fluids into the brain. Using the SCOS device, we monitored changes in CBV during deliberate CBF interventions into the brains of five rats. A saline solution was also injected as a sham control of the flow intervention. The results show a significant decrease in CBV during injection, followed by a return to baseline. This behavior is consistent with physiological expectations, as the injected fluids dilute the blood, leading to a transient reduction in blood volume. Notably, the CBV decrease induced by the flow modulation fluid solution required more than twice as long to recover to baseline compared with the saline solution, which is consistent with the delayed clearance of the flow modulation fluid by design. These experimental results demonstrate the effectiveness of SCOS for monitoring cerebral hemodynamics in animal models and highlight its potential for translation to human studies. Moreover, this work paves the way for the testing and characterization of cerebral therapeutic agents intended for blood flow modulation in animal models.

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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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Constructing a single-objective oblique plane microscope (OPM) for fast, multi-colour, high-resolution volumetric fluorescence imaging

Zhang, Z.; Hong, W.; Wu, Y.; Dey, A.; Shevchuk, A.; Klenerman, D.

2026-03-06 biophysics 10.64898/2026.03.04.709686 medRxiv
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Oblique plane microscopy (OPM) is a light sheet microscopy technique that uses a single high numerical aperture (NA) objective for both illuminating the sample and collecting emission fluorescence from a tilted plane within the specimen. OPM has become indispensable in biological and biomedical research, providing rapid, high-resolution volumetric fluorescence imaging of live cells and tissues while minimising phototoxicity and photobleaching. It also overcomes the sample mounting challenges associated with conventional light sheet microscopes that require two orthogonally placed objectives. However, the application of OPM has been limited by the complex design and the intricate optical alignment and characterisation needed, particularly with the remote-refocusing system (RFS) in the emission path. This protocol offers a detailed, step-by-step guide for constructing an OPM setup using commercially available components and for characterising its performance to ensure optimal imaging quality. We aim to deliver the unique merits of OPM to researchers in life science and medicine, enabling them to visualise the spatiotemporal organisation of key biomolecules, structures, and cells in 3D at high resolutions.

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Object Detection Techniques for Live Monitoring of Amoeba in Phase-Contrast Microscopic Images

Chambers, O.; Cadby, A. J.

2026-04-01 biophysics 10.64898/2026.03.30.715415 medRxiv
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In contemporary bio-imaging-based research, computer-based assessment is becoming crucial for the characterisation of biological structures, as it minimises the need for time-consuming human annotation, which is prone to human error. Furthermore, it allows for the use of optical techniques that use lower photon intensities, thereby reducing reliance on high-intensity excitation and mitigating adverse effects on their activities. This study details the development and evaluation of sophisticated deep-learning models for amoeba detection using phase-contrast imaging. Using a single-class annotated dataset comprising 88 images and 4,131 annotations, we developed nine object detection models based on Detectron 2 and six variants based on YOLO v10. The diversity of the dataset, acquired under varying setup parameters, facilitated a comprehensive evaluation of the strengths and limitations of each model. A comparative analysis of speed and accuracy was performed to identify the most efficient models for real-time detection, providing critical insights for future microscopic analyses.

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Dose dependence and neurovascular mechanisms of the fMRI response to pulsed photobiomodulation in humans

Van Lankveld, H.; Chen, J. X.; Zhong, X. Z.; Chen, J. J.

2026-02-27 bioengineering 10.1101/2025.11.20.689588 medRxiv
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BackgroundTranscranial photobiomodulation (tPBM) utilizes near-infrared light to penetrate the skull to stimulate neural tissue. However, the in vivo physiological response and the factors influencing this response in the human brain have yet to be understood. MethodsIn this study, we utilize functional magnetic resonance imaging (fMRI) to evaluate the effect of tPBM on the blood-oxygenation (BOLD) and cerebral blood flow (CBF), while varying stimulation parameters such as wavelength, irradiance, and frequency. We further examine the influence of skin tone and sex. We further model the neurovascular interactions underlying the response. ResultsOur results show that the fMRI responses to tPBM is not restrained to the site of irradiation, but quickly spreads to distal sites. Certain regions display an fMRI response sustained after tPBM cessation. Importantly, the responses are dependent on biological and stimulation parameters. Lastly, biophysical modeling revealed a consistent neurovascular coupling-like behaviour underlying these responses. ConclusionEmpirical characterizations of dose dependence are critically important to brain stimulation methods in general but have yet to be demonstrated in most cases. This is the first tPBM study to do just that, establishing the foundation for precision medicine using tPBM, and sets a valuable precedent for the field of brain stimulation.

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Residual ellipticity in waveplate-compensated polarization-resolved SHG microscopy may arise from femtosecond laser spectral bandwidth

Nguyen, D.; Wilde, J. P.; Uhlmann, V.; Smith, D. J.; Kusch-Wieser, J.; Zanre, V.; Schwiedrzik, J.; Csucs, G.

2026-02-25 bioengineering 10.64898/2026.02.24.707711 medRxiv
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Polarization-resolved second harmonic generation microscopy provides structural information about non-centrosymmetric biological samples such as collagen. It involves illuminating the sample with a focused laser beam having a variable linear polarization angle and recording the second harmonic signal as a function of this angle. However, accurate linear polarization control is challenging due to ellipticity introduced by reflections from mirrors and dichroic mirrors in the optical path. Waveplate-based compensation has emerged as the standard approach to address these distortions, but its effectiveness for quantitative measurements remains incompletely characterized. Here, we attempt to fill this gap by implementing an established automated waveplate compensation method based on a rotating half-waveplate in combination with a compensating quarter-waveplate. This was done on a commercial Leica TCS SP8 MP multiphoton microscope, making various hardware improvements and carefully documenting important experimental details. Despite significant effort, we consistently observed substantial unwanted residual polarization ellipticity, with amplitudes up to 0.25, persisting under optimal waveplate configurations. Our simulation analysis provides evidence that this limitation may arise from wavelength-dependent dichroic mirror birefringence combined with the broad spectral bandwidth (10nm to 20nm full width at half maximum) of femtosecond laser pulses. While the approach investigated here can compensate a single wavelength, different spectral components within the pulse experience different phase retardations from wavelength-dependent optical elements, potentially resulting in residual ellipticity that cannot be eliminated. Our simulations qualitatively reproduced key features of the experimental observations. These findings have important implications for quantitative polarization-resolved second harmonic generation microscopy and suggest that alternative approaches, including specimen rotation or picosecond laser sources with narrower bandwidth, should be investigated for applications requiring precise polarization control. To facilitate community investigation of these effects, we provide open-source analysis code and simulation files.

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Micro-elastography of biopsies

Gregoire, S.; Giammarinaro, B.; Le Quere, D.; Devissi, M.; BRULPORT, A.; Catheline, S.

2026-03-18 biophysics 10.64898/2026.03.17.712283 medRxiv
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Micro-elastography is an optical technique that studies elastic waves for the mechanical characterisation of micrometric objects, such as cells. We propose to adapt this technique for the characterisation of millimetre-sized samples using a white light microscope. The objective is to perform a rapid, global characterisation of the elasticity of a biopsy. The millimetre-sized samples to be characterized are embedded in an agarose gel. A vibrator generates shear waves in this gel that transmit naturally inside the sample. This technique removes the need for precise manipulation of the wave source. A high-speed camera records the propagation of the waves in the sample. Their velocity is calculated using a noise correlation approach. Due to the lack of millimetric phantoms of calibrated elasticity, we choose to validate this method with a three step process. The experimental setup is first validated on homogeneous gels, then on biological samples of increasing elasticity, biopsies of beef liver hardened by heating, and finally on biological samples of clinical interest: biopsies of mouse endometrium. This method can be applied to all types of biological tissue, paving the way for rapid mechanical characterization of biopsies.

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Comparison of Deep Learning Approaches for Extreme Low-SNR Image Restoration

Buhn, N. E.; Adunur, S. R.; Hamilton, J.; Levis, S.; Hagen, G. M.; Ventura, J.

2026-01-20 bioinformatics 10.64898/2026.01.16.700026 medRxiv
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BackgroundLive-cell fluorescence microscopy enables the study of dynamic cellular processes. However, fluorescence microscopy can damage cells and disrupt these dynamic processes through photobleaching and phototoxicity. Reducing light exposure mitigates the effects of photobleaching and phototoxicity but results in low signal-to-noise ratio (SNR) images. Deep learning provides a solution for restoring these low-SNR images. However, these deep learning methods require large, representative datasets for training, testing, and benchmarking, as well as substantial GPU memory, particularly for denoising large images. ResultsWe present a new fluorescence microscopy dataset designed to expand the range of imaging conditions and specimens currently available for evaluating denoising methods. The dataset contains 324 paired high/low-SNR images ranging from four to 282 megapixels across 12 sub-datasets that vary in specimen, objective used, staining type, excitation wavelength, and exposure time. The dataset also includes spinning disk confocal microscopy examples and extreme-noise cases. We evaluated three state-of-the-art deep learning denoising models on the dataset: a supervised transformer-based model, a supervised CNN model, and an unsupervised single image model. We also developed an image stitching method that enables large images to be processed in smaller crops and reconstructed. ConclusionsOur dataset provides a diverse benchmark for evaluating deep learning denoising methods, and our stitching method provides a solution to GPU memory constraints encountered when processing large images. Among the evaluated deep learning models, the supervised transformer-based model had the highest denoising performance but required the longest training time.

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Doubling the Field of View in Common-Path Digital Holographic Microscopy via Wavelength Scanning and Polarization Gratings

Piekarska, A.; Rogalski, M.; Stefaniuk, M.; Trusiak, M.; Zdankowski, P.

2026-04-06 biophysics 10.64898/2026.04.03.716314 medRxiv
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Digital holographic microscopy systems in a common-path configuration, compared to systems with a separate reference arm, offer a compact design and resistance to disturbances. They can operate with partially coherent illumination, reducing speckle noise. However, they are limited by the overlapping of the object beam and its laterally shifted replica. As a result, images from different regions of the object overlap on the detector, preventing imaging of dense samples. We present the wavelength-scanning replica-removal method, which solves this problem by enabling the separation of information from both replicas and thereby doubling the effective field of view (FOV). The wavelength-scanning multi-shear replica removal algorithm plays a key role in reconstructing the undisturbed phase from a series of holograms recorded with variable shears. The shear value is controlled by changing the illumination wavelength. This enabled the development of two measurement modes: time-domain wavelength scanning for high-quality imaging, and a single-shot mode with frame division into color channels to improve temporal resolution. The method was validated using resolution tests and biological samples - neurons and dynamic yeast cultures. By combining the advantages of the common-path configuration with dense-structure imaging and dynamic processes, the proposed method constitutes a versatile tool for quantitative phase microscopy.

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Quantitative Phase Imaging of Epithelial Monolayer Dynamics

Lastad, S. B.; Abbasova, N.; Combriat, T.; Dysthe, D. K.

2026-01-20 biophysics 10.64898/2026.01.17.700037 medRxiv
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This study uses two different quantitative phase imaging techniques (QPI) and for the first time measures the height, volume, and mass dynamics of Madin-Darby Canine Kidney (MDCK) monolayers. We demonstrate novel methods to determine the height of confluent monolayers of cells from 2D and 3D QPI data and validate that the two methods agree. We developed a novel cell segmentation method adapted to QPI images of confluent cell layers and present a robust measure of relative error. We also demonstrate that height statistics of cells can be obtained without segmenting the images. We obtain the following precisions of cell density (1 %), height (3 %), area (5 %) and volume (6 %). Cell height varies 15-25 % over a monolayer and increases 50-100 % when cell density doubles. The average refractive index and the dry mass fraction of the cells, on the other hand, are constant over the entire density range.

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Fluorescence Properties of Collagen Types I-V: A Comprehensive Study of Spectral and Lifetime Characteristics

Liu, X.; Adams, A. C.; Zhou, X.; Bec, J.; Marcu, L.

2026-02-23 bioengineering 10.64898/2026.02.21.706506 medRxiv
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SignificanceCollagen autofluorescence provides valuable intrinsic contrast for assessing tissue structure, composition, and pathology. However, a comprehensive understanding of the fluorescence properties across different collagen types remains limited. This knowledge gap may limit the development of advanced label-free fluorescence spectroscopy and imaging techniques for specific tissue characterization and diagnostic applications. AimThis study aims to comprehensively characterize the fluorescence intensity excitation-emission matrices (I-EEMs) and time-resolved excitation-emission matrices (TR-EEMs) of collagen standards from Types I, II, III, IV, and V obtained from various organ sources under both dry and hydrated conditions, to identify optimal excitation-emission parameters for each collagen type discrimination, and to establish a reference dataset that supports future research in label-free tissue characterization. ApproachWe employed a time-resolved fluorescence spectroscopy system equipped with an optical parametric oscillator laser (excitation: 200-2000 nm, pulse width: 30 ps) as an excitation source to generate I-EEMs and TR-EEMs of human and bovine collagen Types I-V. The fluorescence light was obtained by a multichannel plate photomultiplier tube through a monochromator (spectral range: 200-1000 nm). Measurements were conducted using collagen standards, under both dry and hydrated states. Additionally, photobleaching effects were assessed to ensure the reliability and reproducibility of fluorescence data. ResultsEach collagen type exhibited distinct I-EEM and TR-EEM signatures, with fluorescence lifetimes ranging from 2.5 ns (Type III, bovine skin) to 5.3 ns (Types II and V). Fibrillar collagens (Types I and V) displayed broader I-EEMs, whereas basement membrane collagen (Type IV) showed the narrowest spectral distribution. Organ-source-dependent variations were evident within the same collagen type. Type I collagen from human placenta exhibited an inverse lifetime-emission wavelength relationship compared to bovine sources. Hydration consistently red-shifted emission peaks into the 395-420 nm range and reduced fluorescence lifetimes across all collagen types (e.g., Type I bovine Achilles tendon: 3.2-5.0 ns dry vs. 3.0-4.5 ns hydrated). Despite excitation wavelength- and fluence-dependent photobleaching of fluorescence intensity, fluorescence lifetimes remained relatively stable, confirming the robustness of lifetime-based measurements. ConclusionsThis study establishes a comprehensive reference dataset for the fluorescence properties of collagen Types I-V and demonstrates the potential of combined I-EEMs and TR-EEMs analysis for tissue characterization. The results highlight species-, organ-, type-, and environment-specific optical fingerprints of similar collagens, which must be considered before implementing more in-depth studies on how the optical properties of collagen change in different medical applications.

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Time-Resolved Resonance Raman Spectroscopy of Retinal Proteins with Continuous-Wave Excitation. A Fundamental Methodology Revisited.

Hildebrandt, P.; Schaefer, A. L.; Gellini, C.; Diller, R.; Kuhlmann, U.; Forest, K. T.

2026-01-21 biophysics 10.64898/2026.01.18.700169 medRxiv
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Time-resolved resonance Raman spectroscopy with continuous-wave excitation is a fundamental technique that has contributed substantially to the understanding of structure and dynamics of bacteriorhodopsin and related retinal proteins. However, the underlying principles were developed about fifty years ago for instrumentation that is hardly in use any more. Thus, the adaptation of the technique to current state-of-the art equipment is needed to satisfy the increasing demand for the spectroscopic characterization of microbial retinal proteins. In this work, we focus on pump-probe time-resolved resonance Raman experiments with a confocal spectrometer using a rotating cell. We discuss the boundary conditions that fulfill the fresh sample conditions and the photochemical innocence of the probe beam as a prerequisite for studying parent or intermediate states of retinal proteins that undergo a cyclic photoinduced reaction sequence. For the measurements of intermediate states and reaction kinetics, pump-probe experiments are required in which the two laser beams hit the flowing sample with a defined but variable delay time. An appropriate set-up for such two-beam experiments with a confocal spectrometer is proposed and tested in time-resolved experiments of bacteriorhodopsin. The comparison with the results obtained with previous classical slit spectrometers with 90-degree-scattering illustrates the advantages and disadvantages of the confocal arrangement. It is shown that modern confocal spectrometers substantially decrease the spectra acquisition time but require a more demanding optical set-up. Furthermore, the extent of photoconversion by the pump beam is lower than for the 90-degree-scattering arrangement which lowers the accuracy of kinetic measurements.

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MD Biophysics Photobiomodulation Plasma (PPT)/ Very Small Embryonic like (VSEL) Antibody Marker Trend Analysis

DeSylvia, D.; Mitchell, I.

2026-04-01 cell biology 10.64898/2026.03.29.715134 medRxiv
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BackgroundPhotobiomodulation (PBM) therapy has demonstrated therapeutic potential in promoting cellular repair, modulating inflammation, and enhancing mitochondrial function. Platelet-rich plasma (PRP) is widely used in regenerative medicine due to its concentration of growth factors and cytokines. Very small embryonic-like stem cells (VSELs), a rare population of pluripotent stem cells present in adult tissues, have emerged as a potential contributor to tissue regeneration. While PBM and PRP are used in combination, how VSELs or Multi-lineage stress enduring (MUSE) cells are at play, and the biological mechanisms underlying their synergistic effects remain incompletely characterized. ObjectiveThis exploratory pilot study aimed to evaluate whether application of the MD Biophysics laser to autologous PRP is associated with measurable changes in VSEL-related antibody marker expression, and to identify directional trends to inform future controlled studies. MethodsPRP samples were collected from participants across seven test dates (July 2024 to February 2025), yielding 18 participant-session datasets. Samples were analyzed before (Pre) and after (Post) laser application using flow cytometry conducted at a UCLA Flow Cytometry Laboratory. Four VSEL-associated antibody markers were assessed: CD45-CD34+, CXCR4+, CD133+, and SSEA-4+. Analyses were descriptive and focused on paired differences and directional trends due to the exploratory design and absence of a control group. ResultsThree of four VSEL-associated markers (CXCR4+, CD133+, and SSEA-4+) demonstrated a group-level increase in median paired differences following laser application. Directional increases were observed in 12/18 sessions for CXCR4+, 10/18 for CD133+, and 9/18 for SSEA-4+. CD45-CD34+ showed a near-equal distribution of increases and decreases. Ki-67 positivity indicated the presence of viable, proliferative cells. While no findings reached statistical significance due to limited sample size, consistent directional trends were observed across multiple markers. ConclusionApplication of PBM to autologous PRP was associated with directional increases in multiple VSEL-associated antibody markers, suggesting a potential role for stem cell activation or mobilization in the mechanism of action. Although preliminary and not statistically powered, these findings provide hypothesis-generating evidence supporting further investigation. The observed trends informed iterative protocol refinement and establish a foundation for future controlled, adequately powered studies to evaluate clinical efficacy and underlying biological mechanisms.

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Enhanced 2D structured illumination microscopy: super-resolution with optical sectioning and reduced reconstruction artifacts

Steinecker, S. M.; Ortkrass, H.; Schuerstedt-Seher, J. C.; Kiel, A.; Kralemann-Koehler, A.; Schulte am Esch, J.; Huser, T.; Mueller, M.

2026-02-28 biophysics 10.64898/2026.02.26.708245 medRxiv
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Structured Illumination Microscopy (SIM) provides imaging with spatial super-resolution, as well as optical sectioning capability, without relying on specialized fluorescent dyes. 2D and 3D variants of this method exist, but most bespoke implementations are 2D-SIM, because it is easier to realize and modify than 3D-SIM. 2D-SIM systems, however, often experience reconstruction artifacts, especially when pushing for high lateral spatial resolution in thicker samples. We present enhanced 2D-SIM, an approach to 2D-SIM where both, coarse patterns optimized for removing out-of-focus background, and fine patterns optimized for resolution improvement beyond the diffraction limit are used. In combination, this achieves 2D-SIM reconstructions with high contrast, spatial super-resolution, and significantly reduced reconstruction artifacts. We present the theoretical framework of this technique, and provide enhanced 2D-SIM imaging results of liver sinusoidal endothelial cells stained with fluorophores emitting at visible and near-infrared wavelengths. Quantitative comparisons of power spectral distribution and image resolution are provided.

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Detecting visual deficits in retinal degeneration mice using photoacoustic tomography

Xu, G.

2026-02-02 bioengineering 10.64898/2026.01.30.702640 medRxiv
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We established a photoacoustic tomography and ultrasound imaging system capable of resolving visually evoked hemodynamic responses in the cortical and subcortical visual regions of the brains of freely behaving mice. By searching for anatomical landmarks in the US imaging planes, we can locate brain regions of interest and continuously record HR in these regions. The system was examined using a 100-minute-long vision research protocol in wild-type mice and mice with vision deficits. We found that: 1) visually evoked HR amplitudes increase as visual stimulation intensity increases in both scotopic and photopic conditions; and 2) HR amplitudes increase during the light adaptation time course.

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Intranasal photobiomodulation: an energy efficient paradigm for cortical and subcortical stimulation

Van Lankveld, H.; Chen, J. X.; Zhong, X.; Chen, J. J.

2026-03-05 neuroscience 10.64898/2026.03.03.709361 medRxiv
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Previous studies have shown the hemodynamic response to transcranial photobiomodulation (tPBM) in localized cortical regions during and after forehead irradiation. However, it is unclear if tPBM can reach deeper regions such as subcortical tissue. It is also unclear whether the manner of regional neurovascular coupling predominantly studied using tPBM extends to all brain regions. As an alternative to forehead delivery, intranasal PBM (iPBM) uses the pathway of the cribriform plate, which is thin and directly leads to the orbitofrontal cortex, rather than the prefrontal cortex in the case of forehead PBM. Thus, it is possible that iPBM can stimulate the brain more efficiently (i.e. with less power). In this study, healthy young adults underwent different iPBM protocols differing in wavelength, frequency and irradiance. We utilized functional magnetic resonance imaging (fMRI) to quantify regional blood oxygenation (BOLD) and perfusion. We further model the neurovascular interactions underlying the fMRI response. We uncovered three distinct temporal signatures, varying by brain region. Specifically, a significant response in the thalamus was observed, with a time-locked BOLD response. Overall, iPBM was found to be associated with much higher efficiency at eliciting BOLD fMRI responses than its forehead (tPBM) counterpart. Lastly, in addition to the expected dose dependence, there were extensive sex differences in the fMRI response to iPBM, surpassing those observed for tPBM. Collectively, these findings highlight the feasibility and efficacy of iPBM and establish a foundation for personalizing PBM protocols for optimal outcomes.

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MCA-UNet: A Multi-Scale Context and Attention U-Net for Colorectal Polyp Segmentation

Dong, Y.; Fang, G.; Du, R.; Hu, H.; Fang, Z.; Guo, C.; Lu, R.; Jia, Y.; Tian, Y.; Wang, Z.

2026-03-16 gastroenterology 10.64898/2026.03.11.26348049 medRxiv
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IntroductionTo propose an improved U-Net-based segmentation model for colorectal polyp segmentation, aiming to address the challenges of variable lesion morphology, ambiguous boundaries, complex background interference, and insufficient cross-level feature fusion in endoscopic images [5,12]. MethodsAn improved network termed MCA-UNet was developed based on U-Net [5]. The model incorporates a multi-scale context convolution block (MCCB) to enhance multi-scale feature extraction and an attention-guided feature fusion module (AGFF) to optimize skip-feature selection and fusion in the decoder. Experiments were conducted on publicly available colorectal polyp image datasets, including Kvasir-SEG and CVC-ClinicDB [13-15]. Four models, including U-Net, U-Net+MCCB, U-Net+AGFF, and MCA-UNet, were compared, and all models were trained for 100 epochs. Dice, intersection over union (IoU), and mean absolute error (MAE) were used as the main evaluation metrics [20]. ResultsOn the mixed validation set, the Dice scores of U-Net, U-Net+MCCB, U-Net+AGFF, and MCA-UNet were 0.742, 0.771, 0.754, and 0.783, respectively; the corresponding IoU values were 0.603, 0.635, 0.618, and 0.649; and the MAE values were 0.102, 0.090, 0.097, and 0.086. Compared with the baseline U-Net, MCA-UNet improved Dice and IoU by 5.53% and 7.63%, respectively, while reducing MAE by 15.69%. Comparisons on the Kvasir-SEG and CVC-ClinicDB validation subsets further demonstrated the more stable performance of the proposed model. ConclusionBy jointly integrating multi-scale contextual modeling and attention-guided feature fusion, MCA-UNet effectively improves the accuracy and robustness of colorectal polyp segmentation and may provide useful support for intelligent endoscopic image analysis [12,17,18].

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Modeling and optimization of a central diamond shape threefold hexagon metamaterial sensor for glioblastoma cell detection

Foysal, M. R.; Dey, B.; Ahmed, M.; Keya, L.; Haque, S. M. A.

2026-03-13 bioengineering 10.64898/2026.03.11.710974 medRxiv
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The present study introduces a novel design and analysis of a sensor based on a terahertz metamaterial absorber (MMA) to identify Glioblastoma cell by employing microwave imaging techniques. Terahertz (THz) frequencies offer unique advantages for biomedical applications. Computer Simulation Technology (CST) employs a finite integration (FIT) approach to simulate the suggested structure in the resonant frequency (RF) range of 4.5 THz to 6 THz. The crystal structure displays three distinct absorption peaks at resonance frequencies. The MTA can absorb energy in three specific spectral bands: 4.782 THz, 5.30 THz, and 5.7319 THz. At these frequencies, the MTM achieves exceptionally high absorption, reaching 99.99%, 99.98%, and 99.68% peak absorption, respectively. The electric field (E), magnetic field (H), and surface current of the MTM are also examined. Finally, detecting Glioblastoma cells is also being investigated by analyzing the E-field H-field using microwave imaging. The suggested biosensor features a high-quality factor of 143.63, a frequency shifts per refractive index of 1.45 THz/RIU. In this study, the PCR value is measured at 0.95 at a frequency of 4.782 THz, indicating a high efficiency in polarization conversion. Polarization Conversion Ratio (PCR) quantifies the efficiency of a metamaterial in converting the polarization of an incident electromagnetic wave. Extensive simulation studies confirm the sensors capability to distinguish between healthy and cancerous cervical tissue. The suggested MMA-based sensor has numerous advantages and can be utilized for Glioblastoma cell detection.

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Open Fourier Ptychographic Microscopy (OpenFPM)

Walker, L. D.; Copeland, L.; Rooney, L. M.; Bendkowski, C.; Shaw, M. J.; McConnell, G.

2026-03-20 biophysics 10.64898/2026.03.18.711080 medRxiv
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Fourier ptychographic microscopy (FPM) uses sequential multi-angle illumination and iterative phase retrieval to recover a high-resolution complex image from a series of low-resolution brightfield and darkfield images. We present OpenFPM, an open-source FPM platform in which conventional and optomechanical hardware is replaced with compact, low-cost 3D printed components. Illumination, sample and objective positioning, and camera triggering are controlled using a Python-based interface on a Raspberry Pi microcomputer. With a 10 x /0.25 NA objective lens and 636 nm illumination, OpenFPM experimentally achieves amplitude and phase reconstructions with an effective synthetic NA of 0.90 over a 1 mm field-of-view. This platform gives researchers accessible and affordable hardware for developing and testing LED-array microscopy techniques for a range of biomedical imaging applications.