Hybrid Monte Carlo simulation with ray tracing for fluorescence measurements in turbid media.

We present a hybrid Monte Carlo simulation method with geometrical ray tracing (hMC-GRT) to model fluorescence excitation and detection in turbid media by optical imaging or spectroscopy systems employing a variety of optical components. hMC-GRT computational verification was achieved via reflectance and fluorescence simulations on epithelial tissue models in comparison with a standard Monte Carlo code. The mean difference between the two simulations was less than 5%. hMC-GRT experimental verification employed depth-sensitive steady-state fluorescence measurements using an aspherical lens on two-layered tissue phantoms. hMC-GRT predictions agreed well with experimental results, achieving less than 3.5% error for measurements at the phantom surface. Verification results demonstrate that the hMC-GRT simulation has the potential to become a useful computational toolbox for designing tissue fluorescence imaging and spectroscopy systems. In addition, the hMC-GRT approach enables a wide variety of applications for computational modeling of fluorescence in turbid media. The source codes are available at https://github.com/ubioptronics/hMC-GRT.

FRAP, FLIM, and FRET: Detection and analysis of cellular dynamics on a molecular scale using fluorescence microscopy.

The combination of fluorescent-probe technology plus modern optical microscopes allows investigators to monitor dynamic events in living cells with exquisite temporal and spatial resolution. Fluorescence recovery after photobleaching (FRAP), for example, has long been used to monitor molecular dynamics both within cells and on cellular surfaces. Although bound by the diffraction limit imposed on all optical microscopes, the combination of digital cameras and the application of fluorescence intensity information on large-pixel arrays have allowed such dynamic information to be monitored and quantified. Fluorescence lifetime imaging microscopy (FLIM), on the other hand, utilizes the information from an ensemble of fluorophores to probe changes in the local environment. Using either fluorescence-intensity or lifetime approaches, fluorescence resonance energy transfer (FRET) microscopy provides information about molecular interactions, with Ångstrom resolution. In this review, we summarize the theoretical framework underlying these methods and illustrate their utility in addressing important problems in reproductive and developmental systems.

Numerical approach to quantify depth-dependent blood flow changes in real-time using the diffusion equation with continuous-wave and time-domain diffuse correlation spectroscopy.

Diffuse correlation spectroscopy (DCS) is a non-invasive optical technique that can measure brain perfusion by quantifying temporal intensity fluctuations of multiply scattered light. A primary limitation for accurate quantitation of cerebral blood flow (CBF) is the fact that experimental measurements contain information about both extracerebral scalp blood flow (SBF) as well as CBF. Separating CBF from SBF is typically achieved using multiple source-detector channels when using continuous-wave (CW) light sources, or more recently with use of time-domain (TD) techniques. Analysis methods that account for these partial volume effects are often employed to increase CBF contrast. However, a robust, real-time analysis procedure that can separate and quantify SBF and CBF with both traditional CW and TD-DCS measurements is still needed. Here, we validate a data analysis procedure based on the diffusion equation in layered media capable of quantifying both extra- and cerebral blood flow in the CW and TD. We find that the model can quantify SBF and CBF coefficients with less than 5% error compared to Monte Carlo simulations using a 3-layered brain model in both the CW and TD. The model can accurately fit data at a rate of <10 ms for CW data and <250 ms for TD data when using a least-squares optimizer.

Reconstruction of optical coefficients in turbid media using time-resolved reflectance and calibration-free instrument response functions.

Measurements of time-resolved reflectance from a homogenous turbid medium can be employed to retrieve the absolute values of its optical transport coefficients. However, the uncertainty in the temporal shift of the experimentally determined instrument response function (IRF) with respect to the real system response can lead to errors in optical property reconstructions. Instrument noise and measurement of the IRF in a reflectance geometry can exacerbate these errors. Here, we examine three reconstruction approaches that avoid requiring direct measurements of photon launch times. They work by (a) fitting relative shapes of the reflectance profile with a pre-determined constraint on the scattering coefficient, (b) calibrating launch-time differences via a reference sample, and (c) freely fitting for the launch-time difference within the inverse problem. Analysis methods that can place a tight bound on the scattering coefficient can produce errors within 5-15% for both absorption and scattering at source-detector separations of 10 and 15 mm. Including the time-shift in the fitting procedure also recovered optical coefficients to under 20% but showed large crosstalk between extracted scattering and absorption coefficients. We find that the uncertainty in the temporal shift greatly impacts the reconstructed reduced scattering coefficient compared to absorption.

Efficient computation of the steady-state and time-domain solutions of the photon diffusion equation in layered turbid media.

Accurate and efficient forward models of photon migration in heterogeneous geometries are important for many applications of light in medicine because many biological tissues exhibit a layered structure of independent optical properties and thickness. However, closed form analytical solutions are not readily available for layered tissue-models, and often are modeled using computationally expensive numerical techniques or theoretical approximations that limit accuracy and real-time analysis. Here, we develop an open-source accurate, efficient, and stable numerical routine to solve the diffusion equation in the steady-state and time-domain for a layered cylinder tissue model with an arbitrary number of layers and specified thickness and optical coefficients. We show that the steady-state ([Formula: see text] ms) and time-domain ([Formula: see text] ms) fluence (for an 8-layer medium) can be calculated with absolute numerical errors approaching machine precision. The numerical implementation increased computation speed by 3 to 4 orders of magnitude compared to previously reported theoretical solutions in layered media. We verify our solutions asymptotically to homogeneous tissue geometries using closed form analytical solutions to assess convergence and numerical accuracy. Approximate solutions to compute the reflected intensity are presented which can decrease the computation time by an additional 2-3 orders of magnitude. We also compare our solutions for 2, 3, and 5 layered media to gold-standard Monte Carlo simulations in layered tissue models of high interest in biomedical optics (e.g. skin/fat/muscle and brain). The presented routine could enable more robust real-time data analysis tools in heterogeneous tissues that are important in many clinical applications such as functional brain imaging and diffuse optical spectroscopy.

Noninvasive Optical Assessment of Implanted Tissue-Engineered Construct Success In Situ.

Quantitative diffuse reflectance spectroscopy (DRS) was developed for label-free, noninvasive, and real-time assessment of implanted tissue-engineered devices manufactured from primary human oral keratinocytes (six batches in two 5-patient cohorts). Constructs were implanted in a murine model for 1 and 3 weeks. DRS evaluated construct success in situ using optical absorption (hemoglobin concentration and oxygenation, attributed to revascularization) and optical scattering (attributed to cellular density and layer thickness). Destructive pre- and postimplantation histology distinguished experimental control from stressed constructs, whereas noninvasive preimplantation measures of keratinocyte glucose consumption and residual glucose in spent culture media did not. In constructs implanted for 1 week, DRS distinguished control due to stressed and compromised from healthy constructs. In constructs implanted for 3 weeks, DRS identified constructs with higher postimplantation success. These results suggest that quantitative DRS is a promising, clinically compatible technology for rapid, noninvasive, and localized tissue assessment to characterize tissue-engineered construct success in vivo. Impact statement Despite the recent advance in tissue engineering and regenerative medicine, there is still a lack of nondestructive tools to longitudinally monitor the implanted tissue-engineered devices. In this study, we demonstrate the potential of quantitative diffuse reflectance spectroscopy as a clinically viable technique for noninvasive, label-free, and rapid characterization of graft success in situ.

Precise fluorophore lifetime mapping in live-cell, multi-photon excitation microscopy.

Fluorophore excited state lifetime is a useful indicator of micro-environment in cellular optical molecular imaging. For quantitative sensing, precise lifetime determination is important, yet is often difficult to accomplish when using the experimental conditions favored by live cells. Here we report the first application of temporal optimization and spatial denoising methods to two-photon time-correlated single photon counting (TCSPC) fluorescence lifetime imaging microscopy (FLIM) to improve lifetime precision in live-cell images. The results demonstrated a greater than five-fold improvement in lifetime precision. This approach minimizes the adverse effects of excitation light on live cells and should benefit FLIM applications to high content analysis and bioimage informatics.

Photon-tissue interaction model enables quantitative optical analysis of human pancreatic tissues.

A photon-tissue interaction (PTI) model was developed and employed to analyze 96 pairs of reflectance and fluorescence spectra from freshly excised human pancreatic tissues. For each pair of spectra, the PTI model extracted a cellular nuclear size parameter from the measured reflectance, and the relative contributions of extracellular and intracellular fluorophores to the intrinsic fluorescence. The results suggest that reflectance and fluorescence spectroscopies have the potential to quantitatively distinguish among pancreatic tissue types, including normal pancreatic tissue, pancreatitis, and pancreatic adenocarcinoma.

Direct estimation of the reduced scattering coefficient from experimentally measured time-resolved reflectance via Monte Carlo based lookup tables.

A heuristic method for estimating the reduced scattering coefficient (µs') of turbid media using time-resolved reflectance is presented. The technique requires measurements of the distributions of times-of-flight (DTOF) of photons arriving at two identical detection channels placed at unique distances relative to a source. Measured temporal shifts in DTOF peak intensities at the two channels were used to estimate µs' of the medium using Monte Carlo (MC) simulation-based lookup tables. MC simulations were used to compute temporal shifts in modeled reflectance at experimentally employed source-detector separations (SDS) for media spanning a wide range of optical properties to construct look up tables. Experiments in Intralipid (IL) phantoms demonstrated that we could retrieve µs' with errors ranging between 6-25% of expected (literature) values, using reflectance measured across 650-800 nm and SDS of 5-15 mm. Advantages of the technique include direct processing of measured data without requiring iterative non-linear curve fitting. We also discuss applicability of this approach for media with low scattering coefficients where the commonly employed diffusion theory analysis could be inaccurate, with practical recommendations for use.

Needle-compatible miniaturized optoelectronic sensor for pancreatic cancer detection.

Pancreatic cancer is one of the deadliest cancers, with a 5-year survival rate of <10%. The current approach to confirming a tissue diagnosis, endoscopic ultrasound-guided fine-needle aspiration (EUS-FNA), requires a time-consuming, qualitative cytology analysis and may be limited because of sampling error. We designed and engineered a miniaturized optoelectronic sensor to assist in situ, real-time, and objective evaluation of human pancreatic tissues during EUS-FNA. A proof-of-concept prototype sensor, compatible with a 19-gauge hollow-needle commercially available for EUS-FNA, was constructed using microsized optoelectronic chips and microfabrication techniques to perform multisite tissue optical sensing. In our bench-top verification and pilot validation during surgery on freshly excised human pancreatic tissues (four patients), the fabricated sensors showed a comparable performance to our previous fiber-based system. The flexibility in source-detector configuration using microsized chips potentially allows for various light-based sensing techniques inside a confined channel such as a hollow needle or endoscopy.

Optical spectroscopy detects histological hallmarks of pancreatic cancer.

An empirical model was developed to interpret differences in the experimentally measured reflectance and fluorescence spectra of freshly excised human pancreatic tissues: normal, adenocarcinoma, and pancreatitis (inflammation). The model provided the first quantitative links between spectroscopic measurements and histological characteristics in the human pancreas. The reflectance model enabled the first (to our knowledge) extraction of wavelength resolved absorption and reduced scattering coefficients for normal and diseased human pancreatic tissues. The fluorescence model employed reflectance information to extract attenuation free "intrinsic" endogenous fluorescence spectra from normal pancreatic tissue, pancreatic adenocarcinoma, and pancreatitis. The method developed is simple, intuitive, and potentially useful for a range of applications in optical tissue diagnostics. This approach is potentially applicable to in vivo studies, because it can account for the absorptive effects of blood in tissues.

Calibration and validation of an optical sensor for intracellular oxygen measurements.

Calibration of fluorescent optical sensors for accurate, quantitative intracellular measurements in vivo suffers from lack of a representative medium that appropriately simulates the molecular complexity of the cytosol. We present a novel protocol for accurate intracellular oxygen sensing via fluorescence lifetime imaging microscopy (FLIM) using cell lysate-FLIM measurements to correct the in vitro calibration of a fluorescent oxygen sensor, and we describe electron paramagnetic resonance (EPR) validation studies. Lysate-FLIM studies provided biochemical information, while EPR provided a "gold standard" for intracellular oxygen estimation. Oxygen levels were evaluated in living human normal squamous and adenocarcinoma esophageal epithelial cells, and good agreement was observed between oxygen levels derived from the optical protocol and EPR. The proposed protocol introduces the concept of a living cell line as a reference for estimating unknown oxygen levels in other cell lines and accounts for high degrees of variability between different cell lines.

Optical Metric Assessed Engineered Tissues Over a Range of Viability States.

Many conventional methods to assess engineered tissue morphology and viability are destructive techniques with limited utility for tissue constructs intended for implantation in patients. Sterile label-free optical molecular imaging methods analyzed tissue endogenous fluorophores without staining, noninvasively and quantitatively assessing engineered tissue, in lieu of destructive assessment methods. The objective of this study is to further investigate label-free optical metrics and their correlation with destructive methods. Tissue-engineered constructs (n = 33 constructs) fabricated with primary human oral keratinocytes (n = 10 patients) under control, thermal stress, and rapamycin treatment manufacturing conditions exhibited a range of tissue viability states, as evaluated by quantitative histology scoring, WST-1 assay, Ki-67 immunostaining imaging, and label-free optical molecular imaging methods. Both histology sections of fixed tissues and cross-sectioned label-free optical images of living tissues provided quantitative spatially selective information on local tissue morphology, but optical methods noninvasively characterized both local tissue morphology and cellular viability at the same living tissue site. Furthermore, optical metrics noninvasively assessed living tissue viability with a statistical significance consistent with the destructive tissue assays WST-1 and histology. Over the range of cell viability states created experimentally, optical metrics noninvasively and quantitatively characterized living tissue viability and correlated with the destructive WST-1 tissue assay. By providing, under sterile conditions, noninvasive metrics that were comparable with conventional destructive tissue assays, label-free optical molecular imaging has the potential to monitor and assess engineered tissue construct viability before surgical implantation.

Image restoration for fluorescence lifetime imaging microscopy (FLIM).

Computational image restoration finds wide applicability for fluorescence intensity imaging. Relatively little work in this regard has been performed on FLIM images, which also suffer from diminished spatial resolution. In this work, we report two separate approaches to enhance FLIM image quality while maintaining lifetime accuracy. A 2D-image restoration algorithm was employed to improve resolution in gated intensity images of various samples including fluorescent beads, living cells and fixed tissue samples. The restoration approach improved lifetime image quality without significant variation in lifetime. Further, overlaying a restored-intensity image over the native lifetime image provided even better results, where the resulting lifetime map had spatial features similar to the intensity map. 2D and 3D image restoration also benefit from advances in computational power and hence holds potential for enhancing FLIM resolution, particularly in ICCD-based wide-field FLIM systems, without sacrificing vital quantitative information.

Noninvasive Optical Assessment of Implanted Engineered Tissues Correlates with Cytokine Secretion.

Fluorescence lifetime sensing has been shown to noninvasively characterize the preimplantation health and viability of engineered tissue constructs. However, current practices to monitor postimplantation construct integration are either qualitative (visual assessment) or destructive (tissue histology). We employed label-free fluorescence lifetime spectroscopy for quantitative, noninvasive optical assessment of engineered tissue constructs that were implanted into a murine model. The portable system was designed to be suitable for intravital measurements and included a handheld probe to precisely and rapidly acquire data at multiple sites per construct. Our model tissue constructs were manufactured from primary human cells to simulate patient variability based on a standard protocol, and half of the manufactured constructs were stressed to create a range of health states. Secreted amounts of three cytokines that relate to cellular viability were measured in vitro to assess preimplantation construct health: interleukin-8 (IL-8), human ß-defensin 1 (hBD-1), and vascular endothelial growth factor (VEGF). Preimplantation cytokine secretion ranged from 1.5 to 33.5 pg/mL for IL-8, from 3.4 to 195.0 pg/mL for hBD-1, and from 0.1 to 154.3 pg/mL for VEGF. In vivo optical sensing assessed constructs at 1 and 3 weeks postimplantation. We found that at 1 week postimplantation, in vivo optical parameters correlated with in vitro preimplantation secretion levels of all three cytokines (p < 0.05). This correlation was not observed in optical measurements at 3 weeks postimplantation when histology showed that the constructs had re-epithelialized, independent of preimplantation health state, supporting the lack of a correlation. These results suggest that clinical optical diagnostic tools based on label-free fluorescence lifetime sensing of endogenous tissue fluorophores could noninvasively monitor postimplantation integration of engineered tissues.

Picosecond-resolution fluorescence lifetime imaging microscopy: a useful tool for sensing molecular interactions in vivo via FRET.

Fluorescence lifetime imaging microscopy (FLIM) provides a promising, robust method of detecting molecular interaction not not nots in vivo via fluorescence/Förster resonance energy transfer (FRET), by monitoring the variation of donor fluorescence lifetime, which is insensitive to many artifacts influencing convential intensity-based measurements, e.g. fluorophore concentration, photobleaching, and spectral bleed-through. As proof of principle, we demonstrate the capability of a novel picosecond-resolution FLIM system to detect molecular interactions in a well-established FRET assay. We then apply the FLIM system to detect the molecular interaction of a transforming oncogene RhoC with a binding partner RhoGDIgamma in vivo, which is critical to understand and interfere with Rho signaling for cancer therapeutics.

Probing pancreatic disease using tissue optical spectroscopy.

Pancreatic adenocarcinoma, one of the leading causes of cancer death in the United States, has a five-year survival rate of only 4%. Present detection methods do not provide accurate diagnosis in the disease's early stages. To investigate whether optical spectroscopy could potentially aid in early diagnosis and improve survival rates, reflectance and fluorescence spectroscopies were employed for the first time in a limited pilot study to probe freshly excised human pancreatic tissues (normal, pancreatitis, and adenocarcinoma) and in vivo human pancreatic cancer xenografts in nude mice. In human pancreatic tissues, measurements were associated with endogenous fluorophores NAD(P)H and collagen, as well as tissue optical properties, with larger relative collagen content detected in adenocarcinoma and pancreatitis than normal. Good correspondence was observed between spectra from adenocarcinoma and cancer xenograft tissues. Reflectance data indicated that adenocarcinoma had higher reflectance in the 430- to 500-nm range compared to normal and pancreatitis tissues. The observed significant differences between the fluorescence and reflectance properties of normal, pancreatitis, and adenocarcinoma tissues present an opportunity for future statistical validation on a larger patient pool and indicate a potential application of multimodal optical spectroscopy to differentiate between diseased and normal pancreatic tissue states.

High speed imaging of bubble clouds generated in pulsed ultrasound cavitational therapy--histotripsy.

Our recent studies have demonstrated that mechanical fractionation of tissue structure with sharply demarcated boundaries can be achieved using short (< 20 micros), high intensity ultrasound pulses delivered at low duty cycles. We have called this technique histotripsy. Histotripsy has potential clinical applications where noninvasive tissue fractionation and/or tissue removal are desired. The primary mechanism of histotripsy is thought to be acoustic cavitation, which is supported by a temporally changing acoustic backscatter observed during the histotripsy process. In this paper, a fast-gated digital camera was used to image the hypothesized cavitating bubble cloud generated by histotripsy pulses. The bubble cloud was produced at a tissue-water interface and inside an optically transparent gelatin phantom which mimics bulk tissue. The imaging shows the following: (1) Initiation of a temporally changing acoustic backscatter was due to the formation of a bubble cloud; (2) The pressure threshold to generate a bubble cloud was lower at a tissue-fluid interface than inside bulk tissue; and (3) at higher pulse pressure, the bubble cloud lasted longer and grew larger. The results add further support to the hypothesis that the histotripsy process is due to a cavitating bubble cloud and may provide insight into the sharp boundaries of histotripsy lesions.

Quantitative, Label-Free Evaluation of Tissue-Engineered Skeletal Muscle Through Multiphoton Microscopy.

The lack of tools for assessing engineered tissue viability and function in a noninvasive manner is a major regulatory and translational challenge facing tissue engineers. Label-free, nonlinear optical molecular imaging (OMI) has utilized endogenous nicotinamide adenine dinucleotide and flavin adenine dinucleotide fluorescence to indicate metabolic activity. Similarly, second harmonic generation (SHG) signals from myosin and collagen can measure overall muscle structural integrity and function. The purpose of this study was to demonstrate these OMI techniques for the first time in engineered skeletal muscle and to develop a novel method for evaluating our engineered skeletal muscle units (SMUs) before implantation. Three experimental groups were studied: Control, Steroid Supplemented, and Metabolically Stressed SMUs. After imaging and analysis in ImageJ, a redox ratio (RR) metric was calculated to indicate metabolic activity, and a structure ratio metric was calculated to reflect structural composition. In addition, function was evaluated as tetanic force production in response to electrical stimulation. In living tissues, the RRs successfully distinguished control and metabolically stressed SMUs in both monolayer and 3D form. OMI of myosin and collagen SHG similarly differentiated control SMUs from the steroid supplemented group. With respect to function, steroid supplementation significantly increased active force generation. When comparing functional and OMI measures, a significant correlation was present between overall myosin density and active force generation. This work demonstrates the potential for using label-free OMI to evaluate tissue-engineered skeletal muscle constructs. The positive correlation between structural OMI measures and force production suggests that OMI could potentially serve as an accurate predictor of functional behaviors, such as integration and tissue regeneration, after implantation. This noninvasive OMI methodology, demonstrated for the first time in engineered skeletal muscle, could prove invaluable for assessing our tissue engineering technology and confirming release criteria for validation.

Tissue Classification Using Optical Spectroscopy Accurately Differentiates Cancer and Chronic Pancreatitis.

OBJECTIVES: Current pancreatic cancer diagnostics cannot reliably detect early disease or distinguish it from chronic pancreatitis. We test the hypothesis that optical spectroscopy can accurately differentiate cancer from chronic pancreatitis and normal pancreas. We developed and tested clinically compatible multimodal optical spectroscopy technology to measure reflectance and endogenous fluorescence from human pancreatic tissues. METHODS: Freshly excised pancreatic tissue specimens (39 normal, 34 chronic pancreatitis, 32 adenocarcinoma) from 18 patients were optically interrogated, with site-specific histopathology representing the criterion standard. A multinomial logistic model using principal component analysis and generalized estimating equations provided statistically rigorous tissue classification. RESULTS: Optical spectroscopy distinguished pancreatic cancer from normal pancreas and chronic pancreatitis (sensitivity, 91%; specificity, 82%; positive predictive value, 69%; negative predictive value, 95%; area under receiver operating characteristic curve, 0.89). Reflectance alone provided essentially the same classification accuracy as reflectance and fluorescence combined, suggesting that a rapid, low-cost, reduced-footprint, reflectance-based device could be deployed without notable loss of diagnostic power. CONCLUSIONS: Our novel, clinically compatible, label-free optical diagnostic technology accurately characterizes pancreatic tissues. These data provide the scientific foundation demonstrating that optical spectroscopy can potentially improve diagnosis of pancreatic cancer and chronic pancreatitis.