Biomedical Optics Express
● Optica Publishing Group
All preprints, ranked by how well they match Biomedical Optics Express's content profile, based on 84 papers previously published here. The average preprint has a 0.06% match score for this journal, so anything above that is already an above-average fit. Older preprints may already have been published elsewhere.
Azimipour, M.; Valente, D.; Werner, J. S.; Zawadzki, R. J.; Jonnal, R. S.
Show abstract
In vivo functional imaging of human photoreceptors is an emerging field, with compelling potential applications in basic science, translational research, and clinical management of ophthalmic disease. Measurements of light-evoked changes in the photoreceptors has been successfully demonstrated using adaptive optics (AO) coherent flood illumination (CFI), AO scanning light ophthalmoscopy (SLO), AO optical coherence tomography (OCT), and full-field OCT with digital AO (dAO). While the optical principles and data processing of these systems differ greatly, and while these differences manifest in the resulting measurements, we believe that the underlying physiological processes involved in each of those techniques are likely the same. AO-CFI and AO-SLO systems are more widely used than OCT systems. However, those systems produce only two-dimensional images and so, less can be said about the anatomical and physiological origins of the observed signal. OCT signal, on the other hand, provides 3D imaging but at a cost of high volume of data, making it impractical to clinical purposes. In light of this, we employed a combined AO-OCT-SLO system-with point-for-point correspondence between the OCT and SLO images-to measure functional responses simultaneously with both and investigate SLO retinal functional biomarkers based on OCT response. The resulting SLO images reveal reflectance changes in the cones which are consistent with those previously reported using AO-CFI and AO-SLO. The resulting OCT volumes show phase changes in the cone outer segment (OS) consistent with those previously reported by us and others. We recapitulate a model of the cone OS previously proposed to explain AO-CFI reflectance changes, and show how this model can be used to predict the signal in AO-SLO. The limitations of the model is also discussed in this manuscript.
Teranikar, T.; Villarreal, C.; Salehin, N.; Lim, J.; Ijaseun, T.; Cao, H.; Chuong, C.-J.; Lee, J.
Show abstract
In vivo quantitative assessment of structural and functional biomarkers is essential for understanding pathophysiology and identifying novel therapies for congenital heart disorders. Cardiac defect analysis through fixed tissue and histology has offered revolutionary insights into the tissue architecture, but section thickness limits the tissue penetration. This study demonstrated the potential of Light Sheet Fluorescence Microscopy (LSFM) for analyzing in vivo 4D (3d + time) cardiac contractility. Furthermore, we have described the utility of an improved feature detection framework for localizing cardiomyocyte nuclei in the zebrafish atrium and ventricle. Using the Hessian Difference of Gaussian (HDoG) scale space in conjunction with the watershed algorithm, we were able to quantify a statistically significant increase in cardiomyocyte nuclei count across different developmental stages. Furthermore, we assessed individual volumes and surface areas for the cardiomyocyte nuclei in the ventricles innermost and outermost curvature during cardiac systole and diastole. Using the segmented nuclei volumes from the feature detection, we successfully performed local area ratio analysis to quantify the degree of deformation suffered by the outermost ventricular region compared to the innermost ventricular region. This paper focuses on the merits of our segmentation and demonstrates its efficacy for cell counting and morphology analysis in the presence of anisotropic illumination across the field-of-view (FOV).
Matsuyama, M.
Show abstract
The combination of tissue-clearing techniques with light-sheet microscopy has enabled detailed visualization of histological changes from the micrometer to millimeter scale, deepening understanding of various disease processes. However, these protocols are not fully optimized for animal species beyond mice or for organs outside the brain. Additionally, the lack of suitable fluorescent probes for target molecules limits their broader application. In this study, we present a protocol for whole-organ clearing of rat hearts in a myocardial infarction model, achieving complete transparency and enabling label-free imaging of collagen fibers in the myocardial wall up to a depth of [~]5 mm using Second Harmonic Generation (SHG) microscopy. For the first time, we successfully compared collagen fiber orientations between infarcted and healthy myocardial regions. Our approach facilitates high-resolution tissue remodeling analysis in cardiovascular research without the need for antibody staining, demonstrating that tissue-clearing techniques are feasible even in animal species with limited available antibodies. Summary statementWe present a novel method for visualizing collagen fibers deep within the heart using a combination of tissue clearing and advanced microscopy, providing valuable data for cardiac research.
Cai, Y. N.; Druszkiewicz, E.; Patterson, S. S.; Parkins, K.; McGregor, J. E.; William, M. H.; Fienup, J. R.; Williams, D. R.
Show abstract
The quality of retinal images is compromised by aberrations that remain uncorrected even in confocal adaptive optics imaging. This study demonstrates phase diversity (PD), a computational imaging technique, to address residual aberrations and enhance image quality in adaptive optics scanning laser ophthalmoscopy (AOSLO). By using images of the same object obtained with and without deliberately added aberrations, PD computes and compensates for the effects of existing residual aberrations beyond those corrected by a closed-loop AO system. Experimental validation demonstrates that PD improves visualization of retinal microstructures, including cone mosaics and dendrites of fluorescently labeled retinal ganglion cells (RGCs).
Lee, C.-Y.; Li, X.
Show abstract
We present an effective approach to compensate for multiple scattering effects in Quantitative Optical Coherence Tomography (qOCT) imaging, with the goal of accurately extracting tissue attenuation coefficients, which is crucial for precise clinical diagnosis. In clinical practice, especially for intra-operative imaging, an increased working distance is often necessary to avoid interference with surgical instruments and workflow. However, this increased working distance corresponds to an increased beam spot size, leading to more multiply scattered photons in the OCT signal and thereby underestimating the optical attenuation. To address this challenge, we investigated errors in attenuation coefficient quantification under different beam spot sizes. Monte Carlo simulations were employed to generate virtual OCT signals for two distinct beam spot sizes, enabling us to quantify the errors induced by multiple scattering across a range of true optical attenuation coefficients. Based on this analysis, we developed a compensation function to correct these errors. The proposed method was validated through experimental measurements using tissue-mimicking phantoms and demonstrated a significant improvement in the accuracy of attenuation coefficient quantification. Our results underscore the potential of this easy-to-implement technique to enhance the diagnostic reliability of qOCT, facilitating its broader application in clinical settings for accurate tissue characterization.
Else, T.; Loreno, C.; Groves, A.; Cox, B.; Gröhl, J.; Modolell, I.; Bohndiek, S.; Roshan, A.
Show abstract
Skin colour is known to confound readouts from optical devices that make measurements through the skin, which can adversely impact the care of patients with darker skin. Photoacoustic imaging (PAI) is making its way from the laboratory to the clinic, however, combining optics and ultrasound for deep tissue imaging leads to a complex relationship between photoacoustic-derived imaging biomarkers and skin melanin concentration. Furthermore, no generalisable correction of the confounding effects of skin colour in PAI has been demonstrated. We sought to overcome this limitation by recruiting a healthy volunteer cohort with the most diverse range of skin tones ever assembled in the field, with participants from Fitzpatrick types I to VI and with vitiligo. From this comprehensive dataset, we identified and characterised two physical mechanisms responsible for skin colour-dependent degradation in both image quality and biomarker quantification. Accompanied by detailed theoretical modelling, we demonstrated that strong light absorption by melanin leads to spectral colouring, which dominates in individuals with low skin melanin pigmentation. We further identified the backscattering of ultrasound waves generated in the skin as a major source of image artefacts for individuals with high skin melanin pigmentation. With this improved understanding of the physical basis, we were able to develop a fast and practicable correction method for spectral colouring and adapted a plane-wave ultrasound reconstruction algorithm to reveal the ultrasound scatterer distribution encoded in the photoacoustic timeseries. Our findings highlight the need for more advanced image reconstruction methods to enable equitable clinical application of PAI. One Sentence SummaryPhotoacoustic imaging is proven to suffer from measurement inaccuracies in people with darker skin, which could adversely impact patient care if not appropriately corrected.
Ruiz, A.; Robledo, E. A.; Littler, E. A.
Show abstract
SignificanceFluorescence imaging remains largely qualitative and device-specific, limiting reproducibility and intersystem comparisons. Advancing toward quantitative imaging requires a radiometric characterization framework that provides SI-traceable units while explicitly addressing the interdependent factors that govern image formation. AimEstablish and evaluate a radiometric characterization framework that converts device-native counts to SI-traceable imaged radiance ({micro}W{middle dot}cm-2{middle dot}sr-1) and aggregate fluorescence yield (sr-1) while accounting for interdependent factors that influence fluorescence image formation. ApproachA calibrated Lambertian solid-state radiometric emitter target (RET) was combined with a three-step radiometric framework consisting of the Radiance Transfer Curve (RTC), the Radiance Imaging Transform (RIT), and the Fluorescence Imaging Transform (FIT). The RTC establishes system responsivity as a function of radiance; the RIT applies this calibration at the pixel level to map digital counts to SI-traceable radiance; and the FIT performs pixel-wise excitation normalization of the RIT image to produce an aggregate fluorescence yield image. The framework was tested through distance and aperture invariance, digital-vs-physical ROI analyses, RTC acquisition, and application of the RIT and FIT to an ICG concentration target and a breast lumpectomy phantom. ResultsThe RET exhibited Lambertian behavior, with no significant dependence of the measured radiance on distance or aperture; imager responsivity (R{lambda}) also remained invariant within uncertainty across working distances and f-numbers. Digitally masked ROIs reproduced R{lambda} obtained with matched physical apertures, enabling ROI and pixel-level radiance transfer. RTCs acquired over 49 radiances captured sensor and processing nonlinearities. The RIT provided a per-pixel mapping from counts to radiance ({micro}W{middle dot}cm-2{middle dot}sr-1). Applying pipeline-specific RTCs, the RIT and FIT reconciled large discrepancies across RAW, 8-bit, and log10 image processing pipelines, yielding closely aligned radiance-concentration curves and improved SBR/SNR/CNR agreement. In a breast lumpectomy phantom, FIT produced SI-traceable aggregate fluorescence yield (sr-1) images and absolute contrast metrics in an anthropomorphic geometry. ConclusionsThe combined framework converts device-native counts into SI-traceable radiance and aggregate fluorescence yield at the pixel level, providing a practical basis for reproducible quantitative fluorescence imaging. The feasibility results across distance/aperture tests, ROI analyses, image pipelines, and phantom imaging indicate readiness for broader evaluation. Future work will establish formal uncertainty budgets and assess robustness across devices, geometries, and excitation conditions to support adoption as a quantitative reporting standard.
Rubinoff, I.; Miller, D. A.; Kuranov, R.; Wang, Y.; Fang, R.; Volpe, N. J.; Zhang, H. F.
Show abstract
Increases in speed and sensitivity enabled rapid clinical adoption of optical coherence tomography (OCT) in ophthalmology. Recently visible-light OCT (vis-OCT) achieved ultrahigh axial resolution, improved tissue contrast, and new functional imaging capabilities, demonstrating the potential to improve clincal care further. However, limited speed and sensitivity caused by the high relative intensity noise (RIN) in supercontinuum lasers impeded the clinical adoption of vis-OCT. To overcome these limitations, we developed balanced-detection vis-OCT (BD-vis-OCT), which uses two calibrated spectrometers to cancel noises common to sample and reference arms, including RIN. We analyzed the RIN to achieve a robust pixel-to-pixel calibration between the two spectrometers and showed that BD-vis-OCT enhanced system sensitivity by up to 22.2 dB. We imaged healthy volunteers at an A-line rate of 125 kHz and a field-of-view as large as 10 mm x 4 mm. We found that BD-vis-OCT revealed retinal anatomical features previously obscured by the noise floor.
Dong, Z.; Mahler, S.; Readhead, C.; Chen, X.; Dickson, M.; Bronner, M. E.; Yang, C.
Show abstract
Imaging blood vessels in early-stage avian embryos has a wide range of practical applications for developmental biology studies, drug and vaccine testing, and early sex determination. Optical imaging such as brightfield transmission imaging offers a compelling solution due to its safe non-ionizing radiation, and operational benefits. However, it comes with challenges such as eggshell opacity and light scattering. To address these, we have revisited an approach based on laser speckle contrast imaging (LSCI) and demonstrated a high quality, comprehensive and non-invasive visualization of blood vessels in few-days-old chicken eggs, with blood vessel as small as 100 {micro}m in diameter (with LSCI profile full-width-at-half-maximum of 275 {micro}m). We present its non-invasive use for monitoring blood flow, measuring the embryos heartbeat, and determining the embryos developmental stages using machine learning with 85% accuracy from stage HH15 to HH22. This method can potentially be used for non-invasive longitudinal studies of cardiovascular development and angiogenesis, as well as egg screening for the poultry industry.
Cai, Y.; Grieve, K.; Mece, P.
Show abstract
High-resolution ophthalmic imaging devices including spectral-domain and full-field optical coherence tomography (SDOCT and FFOCT) are adversely affected by the presence of continuous involuntary retinal axial motion. Here, we thoroughly quantify and characterize retinal axial motion with both high temporal resolution (200,000 A-scans/s) and high axial resolution (4.5 {micro}m), recorded over a typical data acquisition duration of 3 s with an SDOCT device over 14 subjects. We demonstrate that although breath-holding can help decrease large-and-slow drifts, it increases small-and-fast fluctuations, which is not ideal when motion compensation is desired. Finally, by simulating the action of an axial motion stabilization control loop, we show that a loop rate of 1.2 kHz is ideal to achieve 100% robust clinical in-vivo retinal imaging.
Nguyen, D.; Wilde, J. P.; Uhlmann, V.; Smith, D. J.; Kusch-Wieser, J.; Zanre, V.; Schwiedrzik, J.; Csucs, G.
Show abstract
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.
Han, S.; No, H.; Baek, Y.; Park, H.; Lee, K.; Yang, S.; Park, Y.
Show abstract
Antimicrobial susceptibility testing (AST) is crucial for providing appropriate choices and doses of antibiotics to patients. However, standard ASTs require a time-consuming incubation of about 16-20 h for visual accumulation of bacteria, limiting the use of AST for an early prescription. In this study, we propose a rapid AST based on laser speckle formation (LSF) that enables rapid detection of bacterial growth, with the same sample preparation protocol as in solid-based ASTs. The proposed method exploits the phenomenon that well-grown bacterial colonies serve as optical diffusers, which convert a plane-wave laser beam into speckles. The generation of speckle patterns indicates bacterial growth at given antibiotic concentrations. Speckle formation is evaluated by calculating the spatial autocorrelation of speckle images, and bacterial growth is determined by tracking the autocorrelation value over time. We demonstrated the performance of the proposed method for several combinations of bacterial species and antibiotics to achieve the AST in 2-4.5 hours. Furthermore, we also demonstrated the sensitivity of the technique for low bacterial density. The proposed method can be a powerful tool for rapid, simple, and low-cost AST. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=160 SRC="FIGDIR/small/853168v1_ufig1.gif" ALT="Figure 1"> View larger version (48K): org.highwire.dtl.DTLVardef@8ee314org.highwire.dtl.DTLVardef@de47c5org.highwire.dtl.DTLVardef@13a0103org.highwire.dtl.DTLVardef@118ad36_HPS_FORMAT_FIGEXP M_FIG C_FIG
Gofas, E.; Rui, Y.; Mece, P.; Zhang, M.; Snyder, V. C.; Vienola, K. V.; Lee, D.; Sahel, J.-A.; Rossi, E. A.
Show abstract
Previous work has shown that multi-offset detection in adaptive optics scanning laser ophthalmoscopy (AOSLO) can be used to image retinal ganglion cells (RGCs) in monkeys and humans. However, though images of RGCs in anesthetized monkeys with high light levels produced high contrast images of RGCs, images from humans failed to reach the same contrast due to several drawbacks in the previous dual-wavelength multi-offset approach. Our aim here was to design and build a multi-offset detection pattern for humans at safe light levels that could reveal the retinal ganglion cell layer neurons with a contrast, robustness and acquisition time approaching results only previously obtained in monkeys. Here, we present a new imaging system using only one light source, compared to the previous dual-wavelength used on monkeys. Our single-wavelength solution allows for increased light power and eliminates problematic chromatic aberrations. Then, we demonstrate that a radial multi-offset detection pattern with an offset distance of 8-10 Airy Disk Diameter (ADD) is optimal to detect photons multiply scattered in all directions from RGCs thereby enhancing their contrast. This new setup and image processing pipeline led to improved imaging of retinal ganglion cells using multi-offset imaging in AOSLO.
Wang, J.; Nolen, S.; Song, W.; Shao, W.; Yi, W.; Yi, J.
Show abstract
Visible light optical coherence tomography (VIS-OCT) is an emerging ophthalmic imaging method uniquely featured by ultrahigh depth resolution, retinal microvascular oximetry, and distinct scattering contrast in the visible spectral range. However, the clinical utility of VIS-OCT is impeded by the fundamental trade-off between the imaging depth range and axial resolution, determined by the spectral resolution and bandwidth respectively. While the full potential of VIS-OCT is leveraged by a broad bandwidth, the imaging depth is inversely sacrificed. The effective depth range is further limited by the wavelength-dependent roll-off that the signal-to-noise ratio (SNR) reduces in the deeper imaging range, more so in shorter wavelength. To address this trade-off, we developed a second-generation dual-channel VIS-OCT system including the first linear-in-k VIS-OCT spectrometer, reference pathlength modulation, and per A-line noise cancellation. All combined, we have achieved 7.2dB roll-off over the full 1.74 mm depth range (water) with shot-noise limited performance. The system uniquely enables >60{degrees} wide-field imaging over large retinal curvature at peripheral retina and optic nerve head, as well as high-definition imaging at ultrahigh 1.3 um depth resolution (water). The dual-channel design includes a conventional near infrared (NIR) channel, compatible with Doppler OCT and OCT angiography (OCTA). The comprehensive structure-function measurement by 2nd-Gen VIS-OCT system is a significant advance towards broader adaptation of VIS-OCT in clinical applications.
Vicente, J. R.; Durkin, A.; Shrestha, K.; Balu, M.
Show abstract
Melanin plays a significant role in the regulation of epidermal homeostasis and photoprotection of human skin. The assessment of its epidermal distribution and overall content is of great interest due to its involvement in a wide range of physiological and pathological skin processes. Among several spectroscopic and optical imaging methods that have been reported for non-invasive quantification of melanin in human skin, the approach based on the detection of two-photon excited fluorescence lifetime distinguishes itself by enabling selective detection of melanin with sub-cellular resolution, thus facilitating its quantification while also resolving its depth-profile. A key limitation of prior studies on the melanin assessment based on this approach is their inability to account for the skin heterogeneity due to the reduced field of view of the images, which results in high dispersion of the measurement values. Pigmentation in both normal and pathological human skin is highly heterogeneous and its macroscopic quantification is critical for reliable measurements of the epidermal melanin distribution and for capturing melanin-related sensitive dynamic changes as a response to treatment. In this work, we employ a fast large-area multiphoton exoscope (FLAME), recently developed by our group for clinical skin imaging, that has the ability to evaluate the 3D distribution of epidermal melanin content in vivo macroscopically (millimeter scale) with microscopic resolution (sub-micron) and rapid acquisition rates (minutes). We demonstrate significant enhancement in the reliability of the melanin density and distribution measurements across Fitzpatrick skin types I to V by capturing the intra-subject pigmentation heterogeneity enabled by the large volumetric sampling. We also demonstrate the potential of this approach to provide consistent measurement results when imaging the same skin area at different times. These advances are critical for clinical and research applications related to monitoring pigment modulation as a response to therapies against pigmentary skin disorders, skin aging, as well as skin cancers.
Moore, C.; Wayne, M. A.; Ulku, A. C.; Mos, P.; Bruschini, C.; Charbon, E.; Sunar, U.
Show abstract
Diffuse correlation spectroscopy (DCS) is a promising technique for noninvasive measurement of blood flow, especially for cerebral blood flow where other noninvasive techniques have shortcomings. Conventional DCS often requires multiple simultaneous measurements to enhance the signal-to-noise ratio (SNR) especially when probing deep into the brain with large source-detector separations where photons are scarce. However, this limits scalability when using discrete optical detectors. This study demonstrates the application of the 500 x 500 single-photon avalanche diode (SPAD) array, SwissSPAD3, coupled with a custom field-programmable gate array (FPGA) design, which enables significant increases in SNR compared to conventional DCS systems. We validate the fiber-coupled SPAD camera system against a lab-standard CW-DCS system in two-layer liquid phantoms and in human measurements, and demonstrate robust blood-flow tracking at source-detector separations up to 3.25 cm. These results support SPAD-based parallel detection as a scalable route to improved deep-tissue DCS performance in humans.
Orlik, X.; Colin, E.; Plyer, A.
Show abstract
Recent studies have proposed improving Laser Speckle Contrast Imaging (LSCI) by using polarimetric filtering to isolate multiply scattered photons from moving red blood cells (RBCs), an approach referred to as Laser Speckle Orthogonal Contrast Imaging (LSOCI). This reliance on multiple scattering enables the development of a calibration method based on a moving reference sample, chosen to generate dynamic circular Gaussian speckle fields that replicate the statistical properties of RBC scattering in both intensity and the distribution of polarization states. Assuming that multiply scattered photons from both RBCs and the reference sample exhibit a homogeneous distribution of polarization states over the Poincare sphere, the proposed calibration links in vivo speckle contrast reduction in a bijective manner to an equivalent speed of the reference sample. We demonstrate that this equivalent-velocity metric yields consistent in vivo measurements across distinct instruments despite the use of different laser spectral widths, thereby providing a standardized and transferable means to quantify microcirculation activity.
BULLOCH, S.; XU, T.; HERRMANN, D.; TIMPSON, P.; PHAN, T. G.; Lim, Y. J.; Lee, W. M.
Show abstract
Incuscopes, incubator-compatible microscopes, are crucial for live single-cell imaging studies that spans several hours to days. However, traditional microscopy prioritize high-resolution imaging performance over throughput, neglecting efficient live-cell image sampling. This study challenges existing spatial bandwidth product (field of view/optical resolution) criteria for image sampling for live cells. We demonstrate that imaging throughput is fundamentally determined by the minimal pixel count necessary to adequately resolve single cells across the field of view, not spatial bandwidth product. Using an off-the-shelf handheld microscope (5MP, ~0.03 NA) and a scientific microscope (8MP, 4x, 0.4 NA), we revealed a striking disparity. Contrary to expectations, the handheld microscope exhibited ~4-fold higher imaging throughput, highlighting oversampling inherent in many scientific microscopes. This efficiency stems from a more optimized pixel-to-cell ratio for throughput. We validated this concept by deploying the handheld microscopes within a compact 30-liter incubator, enabling continuous imaging over 40 hours using open-source Micro-Manager. A series of experiments, including cell counting, tracking, division, migration, and spheroid dynamics, were successfully performed. The handheld microscopes compactness, ease of use, and cost-effectiveness render it a compelling alternative to high-grade incubator microscopes for routine, non-fluorescence cell culture studies, offering a paradigm shift towards pixel-optimized imaging throughput. Key pointsO_LIImage through handheld microscope is four-fold higher than scientific camera (objective lenses) C_LIO_LIHandheld microscope can conduct single cell imaging in a cell incubator. Routinely imaging 2-3 thousand cells in a single field of view C_LI
Morizet, J.; Chow, D.; Wijesinghe, P.; Schartner, E.; Dwapanyin, G. O.; Dubost, N.; Bruce, G. D.; Anckaert, E.; Dunning, K.; Dholakia, K.
Show abstract
Cellular metabolism is a key regulator of energetics, cell growth, regeneration and homeostasis. Spatially mapping the heterogeneity of cellular metabolic activity is of great importance for unraveling the overall cell and tissue health. In this regard, imaging the endogenous metabolic co-factors NAD(P)H and FAD with sub-cellular resolution and in a non-invasive manner would be useful to determine tissue and cell viability in a clinical environment, but practical use is limited by current imaging techniques. In this article, we demonstrate the use of phasor-based hyperspectral light-sheet (HS-LS) microscopy using a single UVA excitation wavelength as a route to mapping metabolism in three dimensions. We show that excitation solely at a UVA wavelength of 375 nm can simultaneously excite NAD(P)H and FAD autofluorescence, while their relative contributions can be readily quantified using a hardware-based spectral phasor analysis. We demonstrate the potential of our HS-LS system by capturing dynamic changes in metabolic activity during pre-implantation embryo development. To validate our approach, we delineate metabolic changes during pre-implantation embryo development from volumetric maps of metabolic activity. Importantly, our approach overcomes the need for multiple excitation wavelengths, two-photon imaging or significant post-processing of data, paving the way towards clinical translation, such as in situ, non-invasive assessment of embryo viability.
Fan, W.; Xu, F.; Kuranov, R.; Zambrano, R.; Chen, J.; Wu, J.; Lee, S. H.; Trang, K. Q.; Mirza, R.; Simon, S.; Lavinsky, F.; Liu, X.; Goldberg, J. L.; Huang, A. S.; Schuman, J. S.; Zhang, H. F.
Show abstract
Background and objectivesVisible-light optical coherence tomography (vis-OCT) has enabled the visualization of retinal structures and functions beyond the capabilities of conventional OCTs. However, to reconstruct high-quality images, vis-OCT requires special post-processing, including balanced detection. An open-source, standardized vis-OCT data processing software is essential for clinical applications and translation of vis-OCT. MethodsWe developed Vis-OCT Explorer, an open-source, modular Python-based software for processing vis-OCT images. In addition to the standard spectral-domain OCT processing pipeline - including k-space resampling, dispersion compensation, and fast Fourier transformation - Vis-OCT Explorer offers unique dual-spectrometer balanced detection, short-time-Fourier transformation (STFT) based dispersion compensation coefficient optimization, and GPU-accelerated processing. We evaluated the reconstruction performance by quantifying a quality index extracted from individual B-scan images. We also assessed the repeatability of retinal thickness measurements by five operators on images acquired from different testing sites using the intraclass correlation coefficient (ICC) analysis. ResultsBalanced detection and STFT-based dispersion compensation significantly increased the quality index of reconstructed B-scan images. ICC values of the retinal nerve fiber layer (RNFL) and ganglion cell-inner plexiform layer (GCIPL) thickness measurements from four testing sites exceeded 0.8 in 87.5% of the macular-centered images. The ICC of RNFL thickness measurements on all optic nerve head-centered images is above 0.8, showing strong repeatability across users. ConclusionsVis-OCT Explorer provides high-quality image processing and enables highly repeatable measurements on vis-OCT human retinal images. It facilitates future multicenter clinical tests to validate vis-OCTs clinical efficacy.