Three-dimensional simulation of near-infrared diffusion in tissue: boundary condition and geometry analysis for finite-element image reconstruction

Objective Numerical Evaluation of Diffuse, Optically Reconstructed Images Using Structural Similarity Index

Diffuse optical tomography is emerging as a non-invasive optical modality used to evaluate tissue information by obtaining the optical properties' distribution. Two procedures are performed to produce reconstructed absorption and reduced scattering images, which provide structural information that can be used to locate inclusions within tissues with the assistance of a known light intensity around the boundary. These methods are referred to as a forward problem and an inverse solution. Once the reconstructed image is obtained, a subjective measurement is used as the conventional way to assess the image. Hence, in this study, we developed an algorithm designed to numerically assess reconstructed images to identify inclusions using the structural similarity (SSIM) index. We compared four SSIM algorithms with 168 simulated reconstructed images involving the same inclusion position with different contrast ratios and inclusion sizes. A multiscale, improved SSIM containing a sharpness parameter (MS-ISSIM-S) was proposed to represent the potential evaluation compared with the human visible perception. The results indicated that the proposed MS-ISSIM-S is suitable for human visual perception by demonstrating a reduction of similarity score related to various contrasts with a similar size of inclusion; thus, this metric is promising for the objective numerical assessment of diffuse, optically reconstructed images.

Quantitative photoacoustic image reconstruction improves accuracy in deep tissue structures

Photoacoustic imaging (PAI) is emerging as a potentially powerful imaging tool with multiple applications. Image reconstruction for PAI has been relatively limited because of limited or no modeling of light delivery to deep tissues. This work demonstrates a numerical approach to quantitative photoacoustic image reconstruction that minimizes depth and spectrally derived artifacts. We present the first time-domain quantitative photoacoustic image reconstruction algorithm that models optical sources through acoustic data to create quantitative images of absorption coefficients. We demonstrate quantitative accuracy of less than 5% error in large 3 cm diameter 2D geometries with multiple targets and within 22% error in the largest size quantitative photoacoustic studies to date (6cm diameter). We extend the algorithm to spectral data, reconstructing 6 varying chromophores to within 17% of the true values. This quantitiative PA tomography method was able to improve considerably on filtered-back projection from the standpoint of image quality, absolute, and relative quantification in all our simulation geometries. We characterize the effects of time step size, initial guess, and source configuration on final accuracy. This work could help to generate accurate quantitative images from both endogenous absorbers and exogenous photoacoustic dyes in both preclinical and clinical work, thereby increasing the information content obtained especially from deep-tissue photoacoustic imaging studies.

Combined Diffuse Optical Tomography (DOT) and MRI System for Cancer Imaging in Small Animals

Recently, there has been a great amount of interest in developing multi-modality imaging techniques for oncologic research and clinical studies with the aim of obtaining complementary information and, thus, improving the detection and characterization of tumors. In this present work, the details of a combined MR-diffuse optical imaging system for dual-modality imaging of small animals are given. As a part of this effort, a multi-spectral frequency domain diffuse optical tomography system is integrated with an MRI system. Here, a network analyzer provides the rf modulation signal for the laser diodes and measures the amplitude and the phase of the detected signals. Photomultiplier tubes are utilized to measure low-level signals. The integration of this optical imaging system with the 4T MRI system is realized by incorporating a fiber adaptive interface inside the MR magnet. Coregistration is achieved by a special probe design utilizing fiducial markers. A finite element algorithm is used to solve the diffusion equation and an inverse solver based on this forward solver is implemented to calculate the absorption and scattering maps from the acquired data. The MR a priori information is used to guide the optical reconstruction algorithm. Phantom studies show that the absorption coefficient of a 7 mm inclusion in an irregular object located in 64 mm phantom is recovered with 11% error when MR a priori information is used. ENU induced tumor model is used to test the performance of the system in vivo.

Fluorescence Imaging in Vivo: Raster Scanned Point-Source Imaging Provides More Accurate Quantification than Broad Beam Geometries

Two fluorescence imaging systems were compared for their ability to quantify mean fluorescence intensity from surface-weighted imaging of tissue. A broad beam CCD camera system was compared to a point sampling system that raster scans to create the image. The effects of absorption and scattering in the background tissue volume were shown to be similar in their effect upon the signal, but the effect of the three-dimensional shape of the tissue was shown to be a significant distortion upon the signal. Spherical phantoms with Intralipid and blood for absorber and scatterer were used with a fixed concentration of aluminum phthalocyanine fluorophore to illustrate that the mean intensity observed with the broad beam system increased with size, while the mean intensity observed with the raster scanned system was not as significantly affected. Similar results were observed in vivo with mice injected with the fluorophore and imaged multiple times to observe the pharmacokinetics of the drug. The fluorescence in the tumor observed with the broad beam system was higher than that observed with the raster scanned system. Based upon the phantom and animal observations in this study, it should be concluded that using broad beam fluorescence imaging systems to quantify fluorescence in vivo may be problematic when comparing tissues with different three dimensional characteristics. In particular, the ratio of fluorescence from tumor to normal tissue can yield inaccurate results when the tumor is large. However, similar measurements with a narrow beam system that is raster scanned to create the images are not as significantly affected by the three dimensional shape of the tissue. Raster scanned imaging appears to provide a more uniform and accurate way to quantify fluorescence signals from distributed tissues in vivo.

Method for estimating closed-form solutions of the light diffusion equation for turbid media of any boundary shape

This paper reports a method of estimating an approximate closed-form solution to the light diffusion equation for any type of geometry involving Dirichlet's boundary condition with known source location. It is based on estimating the optimum locations of multiple imaginary point sources to cancel the fluence at the extrapolated boundary by constrained optimization using a genetic algorithm. The mathematical derivation of the problem to approach the optimum solution for the direct-current type of diffuse optical systems is described in detail. Our method is first applied to slab geometry and compared with a truncated series solution. After that, it is applied to hemispherical geometry and compared with Monte Carlo simulation results. The method provides a fast and sufficiently accurate fluence distribution for optical reconstruction.

Analytical reconstruction of the bioluminescent source with priors

Bioluminescence imaging has been a popular tool in small animal imaging. During the last decade, the efforts have focused on the development of tomographic systems. However, due to the difficulties in the nature of inverse source problem, multi-modal systems have been the center of attention for the last couple of years. These systems provide complementary information such that the difficulties of the inverse source problem could be overcome using the a priori information obtained. Motivated by these advances in multi-modal systems, this work presents a novel analytical reconstruction of the bioluminescent source. It is shown that if source strength is known a priori then source position could be calculated or vice versa, if source location is known a priori, source strength could be calculated as well as the photon fluence rate. The determination of the source location can be achieved by another imaging system such as X-ray computed tomography. Therefore, in bioluminescence tomography together with an imaging system can be utilized as a multi-modal system. In this work, conventional finite element based simulations are also performed and the numerical results are compared with the analytical ones. It turns out to be that the analytical results are in a good accordance with the numerical results.

Incorporating MRI structural information into bioluminescence tomography: system, heterogeneous reconstruction and in vivo quantification

Combining two or more imaging modalities to provide complementary information has become commonplace in clinical practice and in preclinical and basic biomedical research. By incorporating the structural information provided by computed tomography (CT) or magnetic resonance imaging (MRI), the ill poseness nature of bioluminescence tomography (BLT) can be reduced significantly, thus improve the accuracies of reconstruction and in vivo quantification. In this paper, we present a small animal imaging system combining multi-view and multi-spectral BLT with MRI. The independent MRI-compatible optical device is placed at the end of the clinical MRI scanner. The small animal is transferred between the light tight chamber of the optical device and the animal coil of MRI via a guide rail during the experiment. After the optical imaging and MRI scanning procedures are finished, the optical images are mapped onto the MRI surface by interactive registration between boundary of optical images and silhouette of MRI. Then, incorporating the MRI structural information, a heterogeneous reconstruction algorithm based on finite element method (FEM) with L 1 normalization is used to reconstruct the position, power and region of the light source. In order to validate the feasibility of the system, we conducted experiments of nude mice model implanted with artificial light source and quantitative analysis of tumor inoculation model with MDA-231-GFP-luc. Preliminary results suggest the feasibility and effectiveness of the prototype system.

Fast segmentation and high-quality three-dimensional volume mesh creation from medical images for diffuse optical tomography

Multimodal approaches that combine near-infrared (NIR) and conventional imaging modalities have been shown to improve optical parameter estimation dramatically and thus represent a prevailing trend in NIR imaging. These approaches typically involve applying anatomical templates from magnetic resonance imaging/computed tomography/ultrasound images to guide the recovery of optical parameters. However, merging these data sets using current technology requires multiple software packages, substantial expertise, significant time-commitment, and often results in unacceptably poor mesh quality for optical image reconstruction, a reality that represents a significant roadblock for translational research of multimodal NIR imaging. This work addresses these challenges directly by introducing automated digital imaging and communications in medicine image stack segmentation and a new one-click three-dimensional mesh generator optimized for multimodal NIR imaging, and combining these capabilities into a single software package (available for free download) with a streamlined workflow. Image processing time and mesh quality benchmarks were examined for four common multimodal NIR use-cases (breast, brain, pancreas, and small animal) and were compared to a commercial image processing package. Applying these tools resulted in a fivefold decrease in image processing time and 62% improvement in minimum mesh quality, in the absence of extra mesh postprocessing. These capabilities represent a significant step toward enabling translational multimodal NIR research for both expert and nonexpert users in an open-source platform.

Use of optical imaging to progress novel therapeutics to the clinic

There is an undisputed need for employment and improvement of robust technology for real-time analyses of therapeutic delivery and responses in clinical translation of gene and cell therapies. Over the past decade, optical imaging has become the in vivo imaging modality of choice for many preclinical laboratories due to its efficiency, practicality and affordability, while more recently, the clinical potential for this technology is becoming apparent. This review provides an update on the current state of the art in in vivo optical imaging and discusses this rapidly improving technology in the context of it representing a translation enabler or indeed a future clinical imaging modality in its own right.

A near-infrared spectroscopy computational model for cerebral hemodynamics

Near infrared spectroscopy (NIRS) is a technique used to detect and measure changes in the concentrations of oxygenated hemoglobin, deoxygenated hemoglobin, and water in tissues based on the differential absorption, scattering, and refraction of the near infrared light. In this imaging technique, the optical properties of tissues are reconstructed from the measurements obtained from the sensors located on the boundary. A computational method for the rapid noninvasive detection ∕ quantification of cerebral hemorrhage is described using the above procedure. CFD Research Corporation's finite volume computational biology code was used to numerically mimic the NIRS procedure by (i) noninvasively 'numerically penetrating' the brain tissues and (ii) reconstructing the optical properties the presence of water, oxygenated, and deoxygenated blood. These numerical noninvasive measurements are then used to predict the extent and severity of the brain hemorrhage. The paper also discusses ideas to obtain the location and the severity of a localized injury. Two-dimensional and three-dimensional simulations are performed as a proof of concept for the numerical formulation being feasible for the above mentioned detection/quantification. The results demonstrate that this numerical NIRS formulation can be used as a noninvasive technique for both qualitative and quantitative evaluation of cerebral hemodynamics.

Near-infrared spectral tomography integrated with digital breast tomosynthesis: effects of tissue scattering on optical data acquisition design

PURPOSE

Design optimization and phantom validation of an integrated digital breast tomosynthesis (DBT) and near-infrared spectral tomography (NIRST) system targeting improvement in sensitivity and specificity of breast cancer detection is presented. Factors affecting instrumentation design include minimization of cost, complexity, and examination time while maintaining high fidelity NIRST measurements with sufficient information to recover accurate optical property maps.

METHODS

Reconstructed DBT slices from eight patients with abnormal mammograms provided anatomical information for the NIRST simulations. A limited frequency domain (FD) and extensive continuous wave (CW) NIRST system was modeled. The FD components provided tissue scattering estimations used in the reconstruction of the CW data. Scattering estimates were perturbed to study the effects on hemoglobin recovery. Breast mimicking agar phantoms with inclusions were imaged using the combined DBT∕NIRST system for comparison with simulation results.

RESULTS

Patient simulations derived from DBT images show successful reconstruction of both normal and malignant lesions in the breast. They also demonstrate the importance of accurately quantifying tissue scattering. Specifically, 20% errors in optical scattering resulted in 22.6% or 35.1% error in quantification of total hemoglobin concentrations, depending on whether scattering was over- or underestimated, respectively. Limited frequency-domain optical signal sampling provided two regions scattering estimates (for fat and fibroglandular tissues) that led to hemoglobin concentrations that reduced the error in the tumor region by 31% relative to when a single estimate of optical scattering was used throughout the breast volume of interest. Acquiring frequency-domain data with six wavelengths instead of three did not significantly improve the hemoglobin concentration estimates. Simulation results were confirmed through experiments in two-region breast mimicking gelatin phantoms.

CONCLUSIONS

Accurate characterization of scattering is necessary for quantification of hemoglobin. Based on this study, a system design is described to optimally combine breast tomosynthesis with NIRST.

Practical fully three-dimensional reconstruction algorithms for diffuse optical tomography

We have developed an efficient fully three-dimensional (3D) reconstruction algorithm for diffuse optical tomography (DOT). The 3D DOT, a severely ill-posed problem, is tackled through a pseudodynamic (PD) approach wherein an ordinary differential equation representing the evolution of the solution on pseudotime is integrated that bypasses an explicit inversion of the associated, ill-conditioned system matrix. One of the most computationally expensive parts of the iterative DOT algorithm, the reevaluation of the Jacobian in each of the iterations, is avoided by using the adjoint-Broyden update formula to provide low rank updates to the Jacobian. In addition, wherever feasible, we have also made the algorithm efficient by integrating along the quadratic path provided by the perturbation equation containing the Hessian. These algorithms are then proven by reconstruction, using simulated and experimental data and verifying the PD results with those from the popular Gauss-Newton scheme. The major findings of this work are as follows: (i) the PD reconstructions are comparatively artifact free, providing superior absorption coefficient maps in terms of quantitative accuracy and contrast recovery; (ii) the scaling of computation time with the dimension of the measurement set is much less steep with the Jacobian update formula in place than without it; and (iii) an increase in the data dimension, even though it renders the reconstruction problem less ill conditioned and thus provides relatively artifact-free reconstructions, does not necessarily provide better contrast property recovery. For the latter, one should also take care to uniformly distribute the measurement points, avoiding regions close to the source so that the relative strength of the derivatives for measurements away from the source does not become insignificant.

Improving the accuracy of the diffusion model in highly absorbing media

The diffusion approximation of the Boltzmann transport equation is most commonly used for describing the photon propagation in turbid media. It produces satisfactory results in weakly absorbing and highly scattering media, but the accuracy lessens with the decreasing albedo. In this paper, we presented a method to improve the accuracy of the diffusion model in strongly absorbing media by adjusting the optical parameters. Genetic algorithm-based optimization tool is used to find the optimal optical parameters. The diffusion model behaves more closely to the physical model with the actual optical parameters substituted by the optimized optical parameters. The effectiveness of the proposed technique was demonstrated by the numerical experiments using the Monte Carlo simulation data as measurements.

Differential evolution approach for regularized bioluminescence tomography

Bioluminescence tomography (BLT) is an inverse source problem that localizes and quantifies bioluminescent probe distribution in 3-D. The generic BLT model is ill-posed, leading to nonunique solutions and aberrant reconstruction in the presence of measurement noise and optical parameter mismatches. In this paper, we introduce the knowledge of the number of bioluminescence sources to stabilize the BLT problem. Based on this regularized BLT model, we develop a differential evolution-based reconstruction algorithm to determine the source locations and strengths accurately and reliably. Then, we evaluate this novel approach in numerical, phantom, and mouse studies.

Direct-current-based image reconstruction versus direct-current included or excluded frequency-domain reconstruction in diffuse optical tomography

We study the level of image artifacts in optical tomography associated with measurement uncertainty under three reconstruction configurations, namely, by using only direct-current (DC), DC-excluded frequency-domain, and DC-included frequency-domain data. Analytic and synthetic studies demonstrate that, at the same level of measurement uncertainty typical to optical tomography, the ratio of the standard deviation of mu(a) over mu(a) reconstructed by DC only is at least 1.4 times lower than that by frequency-domain methods. The ratio of standard deviations of D (or mu(s)') over D (or mu(s)') reconstructed by DC only are slightly lower than those by frequency-domain methods. Frequency-domain reconstruction including DC generally outperforms that excluding DC, but as the amount of measurements increases, the difference between the two diminishes. Under the condition of a priori structural information, the performances of three reconstruction configurations are seemingly equivalent.

Multistage inversion algorithm for biological tissue imaging

A new inversion method for diffuse optical tomography is proposed. This is a multistage algorithm, that uses a signal subspace-based method to simplify the inverse problem and proposes a guided iterative inversion process to improve the imaging. First, subspace-based analysis is used to determine the voxels that definitely belong to the background and exclude them from further consideration. Then, the pseudo-inverse technique is applied for reconstruction. In the final stage, the reconstruction is improved iteratively by finding and excluding more voxels belonging to background. The method reduces the ill-posedness of the image reconstruction problem iteratively such that good imaging results are obtained for multiple heterogeneities having complicated geometries even in the presence of 3% additive white noise.

The utility of a marched absorbing layer boundary condition in the finite element analysis of diffuse photon density wave propagation in tissues relevant to breast imaging

Here we introduce a marched absorbing layer boundary condition for the finite element analysis of diffuse photon density wave propagation in tissues. We investigated and optimized the parameters required to set up a marched absorbing layer boundary for diffuse photon density wave propagation in media with different absorption and scattering coefficients. Comparing with using a breast model connected to a large substrate and a Robin boundary condition, using a marched absorbing layer boundary condition to replace part of the large base reduced the time for forward modeling by about 30%.

Selection of optimal wavelengths for spectral reconstruction in diffuse optical tomography

Using lasers with different wavelengths in diffuse optical tomography (spectral DOT) has the advantage that the concentrations of chromophores can be reconstructed quantitatively. In continuous wave spectral DOT, it is furthermore possible to distinguish between scattering and absorption. The choice of the laser wavelengths has a strong impact on how well the scattering parameter and chromophore concentrations can be determined. Current methods to optimize the set of wavelengths disregard the sensitivity of the reconstruction result to uncertainties in the absorption spectra of the chromophores. But since available absorption spectra show significant deviations, it seems to be necessary to take this into account. The wavelength optimization approach presented here is an extension to a method of Corlu et al. The original method optimizes the wavelength sets such that scattering parameters and chromophore concentrations can be separated optimally. We introduce an additional criterion that evaluates the dependence of reconstructed chromophore concentrations on deviations of the extinction coefficients. The wavelength sets found by the new approach are different from those determined with the original method. Reconstructions of simulated data show the effect of using various absorption spectra for reconstruction with different wavelength sets and illustrate the advantages of the new wavelength sets.

Algebraic reconstruction techniques for spectral reconstruction in diffuse optical tomography

Reconstruction in diffuse optical tomography (DOT) necessitates solving the diffusion equation, which is nonlinear with respect to the parameters that have to be reconstructed. Currently applied solving methods are based on the linearization of the equation. For spectral three-dimensional reconstruction, the emerging equation system is too large for direct inversion, but the application of iterative methods is feasible. Computational effort and speed of convergence of these iterative methods are crucial since they determine the computation time of the reconstruction. In this paper, the iterative methods algebraic reconstruction technique (ART) and conjugated gradients (CGs) as well as a new modified ART method are investigated for spectral DOT reconstruction. The aim of the modified ART scheme is to speed up the convergence by considering the specific conditions of spectral reconstruction. As a result, it converges much faster to favorable results than conventional ART and CG methods.

Trans-rectal ultrasound-coupled near-infrared optical tomography of the prostate, part I: simulation

We investigate the feasibility of trans-rectal optical tomography of the prostate using an endo-rectal near-infrared (NIR) applicator that is to be integrated with a trans-rectal ultrasound (TRUS) probe. Integration with TRUS ensures accurate endo-rectal positioning of the NIR applicator and the utility of using TRUS spatial prior information to guide NIR image reconstruction. The prostate NIR image reconstruction is challenging even with the use of spatial prior owing to the anatomic complexity of the imaging domain. A hierarchical reconstruction algorithm is developed that implements cascaded initial-guesses for nested domains. This hierarchical image reconstruction method is then applied to evaluating a number of NIR applicator designs for integration with a sagittal TRUS transducer. A NIR applicator configuration feasible for instrumentation development is proposed that contains one linear array of optodes on each lateral side of the sagittal TRUS transducer. The performance of this NIR applicator is characterized for the recovery of single tumor mimicking lesion as well as dual targets in the prostate. The results suggest a strong feasibility of transrectal prostate imaging by use of the endo-rectal NIR/US probe.

Implementation of a computationally efficient least-squares algorithm for highly under-determined three-dimensional diffuse optical tomography problems

Three-dimensional (3D) diffuse optical tomography is known to be a nonlinear, ill-posed and sometimes under-determined problem, where regularization is added to the minimization to allow convergence to a unique solution. In this work, a generalized least-squares (GLS) minimization method was implemented, which employs weight matrices for both data-model misfit and optical properties to include their variances and covariances, using a computationally efficient scheme. This allows inversion of a matrix that is of a dimension dictated by the number of measurements, instead of by the number of imaging parameters. This increases the computation speed up to four times per iteration in most of the under-determined 3D imaging problems. An analytic derivation, using the Sherman-Morrison-Woodbury identity, is shown for this efficient alternative form and it is proven to be equivalent, not only analytically, but also numerically. Equivalent alternative forms for other minimization methods, like Levenberg-Marquardt (LM) and Tikhonov, are also derived. Three-dimensional reconstruction results indicate that the poor recovery of quantitatively accurate values in 3D optical images can also be a characteristic of the reconstruction algorithm, along with the target size. Interestingly, usage of GLS reconstruction methods reduces error in the periphery of the image, as expected, and improves by 20% the ability to quantify local interior regions in terms of the recovered optical contrast, as compared to LM methods. Characterization of detector photo-multiplier tubes noise has enabled the use of the GLS method for reconstructing experimental data and showed a promise for better quantification of target in 3D optical imaging. Use of these new alternative forms becomes effective when the ratio of the number of imaging property parameters exceeds the number of measurements by a factor greater than 2.

Tutorial on diffuse light transport

A tutorial introduction to diffuse light transport is presented. The basic analytic equations of time-resolved, steady-state and modulated light transport are introduced. The perturbation method for handling slight heterogeneities in optical properties is outlined. The treatment of boundary conditions such as an air/tissue surface is described. Finite mesh-based numerical methods are introduced to calculate the diffuse light field in complex tissues with arbitrary boundaries. Applications in tissue spectroscopy and imaging illustrate these theoretical and computational tools.

UV-induced modification of stress distribution in optical fibers and its contribution to Bragg grating birefringence

This paper discusses the importance of stress-induced contributions to the photo-induced birefringence observed in fiber Bragg gratings. Optical tomography measurements are performed in exposed and unexposed fibers to extract the stress profiles induced by UV-writing of fiber Bragg gratings for various exposure levels. A photoelastic analysis and a high-order isoparametric finite elements method are then used to calculate the birefringence caused by stress profile modifications. The results are compared to the birefringence directly measured by spectral analysis of a chirped fiber grating with multiple phase-shifts. We can therefore estimate the fraction of the photo-induced birefringence due to stress-induced anisotropy following UV exposure.

Calibration of the second-order nonlinear optical susceptibility of surface and bulk of glass

A two-beam second-harmonic generation technique is developed to calibrate the magnitude of the second-order nonlinear optical susceptibility components of surface and bulk (multipolar origin) of isotropic materials. The values obtained for fused silica calibrated against ChiXXX of crystalline quartz are chi parallel parallel perpendicular = 7.9(4), chi perpendicular parallel parallel (+)gamma = 3.8(4), parallel perpendicular perpendicular perpendicular(+)gamma = 59(4), and delta' = 7.8(4) in units of 10(-22) m(2)/V. Similar values are obtained for BK7 glass. An alternative way of calibration against ChiXYZ of quartz is demonstrated. The technique could also be extended to characterize the susceptibility tensor of crystals as a convenient alternative to the Maker-fringe technique.

Polarization dependence of non-linear gain compression factor in semiconductor optical amplifier

We investigate the power and the polarization dependence of the intraband dynamics in a bulk semiconductor optical amplifier using both a 2.5-ps pump-probe experimental set-up in contra-propagation and a theoretical model. Our model is based on the rate equations and takes into account the polarization dependence of the gain. By comparing experimental and computational results we are able to highlight the dependences of the intraband dynamics and to extract the non-linear gain compression factor as a function of both pulse energy and polarization of the injected pulses.

Simple and robust image-based autofocusing for digital microscopy

A simple image-based autofocusing scheme for digital microscopy is demonstrated that uses as few as two intermediate images to bring the sample into focus. The algorithm is adapted to a commercial inverted microscope and used to automate brightfield and fluorescence imaging of histopathology tissue sections.

Silicon cross-connect filters using microring resonator coupled multimode-interference-based waveguide crossings

We report silicon cross-connect filters using microring resonator coupled multimode-interference (MMI) based waveguide crossings. Our experiments reveal that the MMI-based cross-connect filters impose lower crosstalk at the crossing than the conventional cross-connect filters using plain crossings, while offering a nearly symmetric resonance line shape in the drop-port transmission. As a proof-of-concept for cross-connection applications, we demonstrate on a silicon-on-insulator substrate (i) a 4-channel 1 x 4 linear-cascaded MMI-based cross-connect filter, and (ii) a 2-channel 2 x 2 array-cascaded MMI-based cross-connect filter.

Blazed high-efficiency x-ray diffraction via transmission through arrays of nanometer-scale mirrors

Diffraction gratings are ubiquitous wavelength dispersive elements for photons as well as for subatomic particles, atoms, and large molecules. They serve as enabling devices for spectroscopy, microscopy, and interferometry in numerous applications across the physical sciences. Transmission gratings are required in applications that demand high alignment and figure error tolerances, low weight and size, or a straight-through zero-order beam. However, photons or particles are often strongly absorbed upon transmission, e.g., in the increasingly important extreme ultraviolet (EUV) and soft x-ray band, leading to low diffraction efficiency. We demonstrate the performance of a critical-angle transmission (CAT) grating in the EUV and soft x-ray band that for the first time combines the advantages of transmission gratings with the superior broadband efficiency of blazed reflection gratings via reflection from nanofabricated periodic arrays of atomically smooth nanometer-thin silicon mirrors at angles below the critical angle for total external reflection. The efficiency of the CAT grating design is not limited to photons, but also opens the door to new, sensitive, and compact experiments and applications in atom and neutron optics, as well as for the efficient diffraction of electrons, ions, or molecules.

Birefringence and optical power confinement in horizontal multi-slot waveguides made of Si and SiO2

Through simulations and measurements, we show that in multi-slot thin film waveguides, the TM polarized modes can be confined mostly in the low refractive index layers of the waveguide. The structure consisted of alternating layers of a-Si and SiO(2), in the thickness range between 3 and 40 nm, for which the slots were the SiO(2) layers. Simulations were performed using the transfer matrix method and experiments using the m-line technique at 1.55 mum. The dependence of the birefringence and of the power confinement in the slots was studied as a function of the waveguide thickness, the Si and SiO(2) layer thicknesses, and the SiO(2) / Si layer thickness ratio. We find a large birefringence-a refractive index difference between TE and TM modes-as large as 0.8. For TM polarized modes, up to ~ 85% of the total power in the fundamental mode can be confined in the slots.

High-power, femtosecond, thermal-lens-shaped Yb:KGW oscillator

Thermal lens shaping for astigmatism compensation is extended to a high-power, diode-pumped, Yb:KGW laser by employing a gain crystal geometry designed for efficient polarized pumping. The 63MHz oscillator is soliton mode-locked with the aid of a saturable Bragg reflector to yield 250fs (347fs) pulses at an output power of 3.5W (5W). Frequency doubling of the 250fs pulses with an intrinsic efficiency >60% provides 1.65W of average green power.

Interaction of transverse modes in a single-frequency few-mode fiber amplifier caused by local gain saturation

We report on the behavior of modal polarization states in a single-frequency, ytterbium-doped, few-mode fiber amplifier. Experimental data show that the polarization of the individual transverse modes depends on the pump power and that the modes tend towards orthogonally polarized states with increasing gain. The observations can be explained by local gain saturation that favors the amplification of differently polarized modes.

Measurement of internal tissue optical properties at ultraviolet and visible wavelengths: Development and implementation of a fiberoptic-based system

A novel, multi-wavelength, fiberoptic system was constructed, evaluated and implemented to determine internal tissue optical properties at ultraviolet A (UVA) and visible (VIS) wavelengths. Inverse modeling was performed with a neural network to estimate absorption and reduced scattering coefficients based on spatially-resolved reflectance distributions. The model was calibrated with simulated reflectance datasets generated using a condensed Monte Carlo approach with absorption coefficients up to 85 cm(-1) and reduced scattering coefficients up to 118 cm(-1). After theoretical and experimental evaluations of the system, optical properties of porcine bladder, colon, esophagus, oral mucosa, and liver were measured at 325, 375, 405, 445 and 532 nm. These data provide evidence that as wavelengths decrease into the UVA, the dominant tissue chromophore shifts from hemoglobin to structural proteins such as collagen. This system provides a high level of accuracy over a wide range of optical properties, and should be particularly useful for in situ characterization of highly attenuating biological tissues in the UVA-VIS.

Low jitter Q-switched fiber laser using optically driven surface-normal saturable absorber modulator

A technique for stabilizing the repetition frequency of a passively Q-switched laser is presented using an optically driven surface-normal semiconductor modulator. A method is capable of significant reduction of the timing jitter in a passively Q-switched laser by optical triggering the saturable absorber semiconductor reflector. The experimental demonstration using passively Q-switched ytterbium-doped fiber laser shows the jitter reduction by factor of 1.66??10(3) from 50 mus down to 30 ns.

Fluorescence tomography characterization for sub-surface imaging with protoporphyrin IX

Optical imaging of fluorescent objects embedded in a tissue simulating medium was characterized using non-contact based approaches to fluorescence remittance imaging (FRI) and sub-surface fluorescence diffuse optical tomography (FDOT). Using Protoporphyrin IX as a fluorescent agent, experiments were performed on tissue phantoms comprised of typical in-vivo tumor to normal tissue contrast ratios, ranging from 3.5:1 up to 10:1. It was found that tomographic imaging was able to recover interior inclusions with high contrast relative to the background; however, simple planar fluorescence imaging provided a superior contrast to noise ratio. Overall, FRI performed optimally when the object was located on or close to the surface and, perhaps most importantly, FDOT was able to recover specific depth information about the location of embedded regions. The results indicate that an optimal system for localizing embedded fluorescent regions should combine fluorescence reflectance imaging for high sensitivity and sub-surface tomography for depth detection, thereby allowing more accurate localization in all three directions within the tissue.

Aberration reduction and unique light focusing in a photonic crystal negative refractive lens

Light focusing characteristics of a negative refractive lens fabricated out of a silicon-on-insulator photonic crystal (PC) slab are investigated theoretically and experimentally. It focuses in the near infrared, but the focal spot is degraded by a lens aberration. To reduce the aberration, we designed a composite PC that gives rise to a narrower focal spot. In addition, two unique functions of this lens are demonstrated: refocusing outside of the PC and parallel focusing, enabling image transfer and real image formation, respectively. These results prove the feasibility of an in-plane free space optical network based on negative refraction.

The physics, biophysics and technology of photodynamic therapy

Photodynamic therapy (PDT) uses light-activated drugs to treat diseases ranging from cancer to age-related macular degeneration and antibiotic-resistant infections. This paper reviews the current status of PDT with an emphasis on the contributions of physics, biophysics and technology, and the challenges remaining in the optimization and adoption of this treatment modality. A theme of the review is the complexity of PDT dosimetry due to the dynamic nature of the three essential components -- light, photosensitizer and oxygen. Considerable progress has been made in understanding the problem and in developing instruments to measure all three, so that optimization of individual PDT treatments is becoming a feasible target. The final section of the review introduces some new frontiers of research including low dose rate (metronomic) PDT, two-photon PDT, activatable PDT molecular beacons and nanoparticle-based PDT.

Digital mouse phantom for optical imaging

We present a method for design and use of a digital mouse phantom for small animal optical imaging. We map the boundary of a mouse model from magnetic resonance imaging (MRI) data through image processing algorithms and discretize the geometry by a finite element (FE) descriptor. We use a validated FE implementation of the three-dimensional (3-D) diffusion equation to model transport of near infrared (NIR) light in the phantom with a mesh resolution optimized for representative tissue optical properties on a computing system with 8-GB RAM. Our simulations demonstrate that a section of the mouse near the light source is adequate for optical system design and that the variation of intensity of light on the boundary is well within typical noise levels for up to 20% variation in optical properties and nodes used to model the boundary of the phantom. We illustrate the use of the phantom in setting goals for specific binding of targeted exogenous fluorescent contrasts based on anatomical location by simulating a nearly tenfold change in the detectability of a 2-mm-deep target depending on its placement. The methodology described is sufficiently general and may be extended to generate digital phantoms for designing clinical optical imaging systems.

Receiver operating characteristic and location analysis of simulated near-infrared tomography images

Receiver operating characteristic (ROC) analysis was performed on simulated near-infrared tomography images, using both human observer and contrast-to-noise ratio (CNR) computational assessment, for application in breast cancer imaging. In the analysis, a nonparametric approach was applied for estimating the ROC curves. Human observer detection of objects had superior capability to localize the presence of heterogeneities when the objects were small with high contrast, with a minimum detectable threshold of CNR near 3.0 to 3.3 in the images. Human observers were able to detect heterogeneities in the images below a size limit of 4 mm, yet could not accurately find the location of these objects when they were below 10 mm diameter. For large objects, the lower limit of a detectable contrast limit was near 10% increase relative to the background. The results also indicate that iterations of the nonlinear reconstruction algorithm beyond 4 did not significantly improve the human detection ability, and degraded the overall localization ability for the objects in the image, predominantly by increasing the noise in the background. Interobserver variance performance in detecting objects in these images was low, suggesting that because of the low spatial resolution, detection tasks with NIR tomography is likely consistent between human observers.

Using a priori structural information from magnetic resonance imaging to investigate the feasibility of prostate diffuse optical tomography and spectroscopy: a simulation study

Implementation of diffuse optical tomography (DOT) for prostate cancer is challenging because the prostate is a deep-seated organ. We investigated whether diffuse optical tomography (DOT) and spectroscopy could be applied to monitor the physiology of prostate cancer using a small probe that could be placed endorectally. We manually segmented the prostate, the intraprostatic tumor, and the rectum using data from endorectal magnetic resonance imaging. These structures were reconstructed and meshed with tetrahedral finite elements in three dimensions. A 2 x 4 cm probe that has ten sources and 52 detectors were placed to face the anterior wall of the rectum in our simulation. Optical properties of the organs were obtained from the literature in the near infrared regime. Diffusion approximation was used to simulate photon migration with finite element method. Five wavelengths were used to simulate tissue absorption with realistic water, oxy- and deoxyhaemoglobin concentrations in the prostate. We combined a global search based on genetic algorithm with gradient-driven local search methods to fit the simulated data. Our results suggest that the optical properties and the concentrations of the chromophores of the prostate and the prostate cancer can be reliably recovered from the measurements using an endorectal probe. Prostate DOT is worth further investigation for clinical application.

Tomographic imaging of oxygen by phosphorescence lifetime

Imaging of oxygen in tissue in three dimensions can be accomplished by using the phosphorescence quenching method in combination with diffuse optical tomography. We experimentally demonstrate the feasibility of tomographic imaging of oxygen by phosphorescence lifetime. Hypoxic phantoms were immersed in a cylinder with scattering solution equilibrated with air. The phantoms and the medium inside the cylinder contained near-infrared phosphorescent probe(s). Phosphorescence at multiple boundary sites was registered in the time domain at different delays (t(d)) following the excitation pulse. The duration of the excitation pulse (t(p)) was regulated to optimize the contrast in the images. The reconstructed integral intensity images, corresponding to delays t(d), were fitted exponentially to give the phosphorescence lifetime image, which was converted into the three-dimensional image of oxygen concentrations in the volume. The time-independent diffusion equation and the finite element method were used to model the light transport in the medium. The inverse problem was solved by the recursive maximum entropy method. We provide what we believe to be the first example of oxygen imaging in three dimensions using long-lived phosphorescent probes and establish the potential of these probes for diffuse optical tomography.

Fluorescence-enhanced optical tomography of a large tissue phantom using point illumination geometries

We demonstrate fluorescence-enhanced optical imaging of single and multiple fluorescent targets within a large (approximately 1081 cm3) phantom using frequency-domain photon migration measurements of fluorescence collected at individual points in response to illumination of excitation light at individual points on the boundary. The tissue phantom was filled with a 1% lipid solution with and without 0.01 microM Indocyanine Green (ICG) and targets consisted of vials filled with the 1% lipid containing 1-2.5 microM ICG. Measurements were acquired using a modulated intensified CCD imaging system under different experimental conditions. For 3-D image reconstruction, the gradient-based penalty modified barrier function (PMBF) method with simple bounds constrained truncated Newton with trust region method (CONTN) was used. Targets of 0.5, 0.6, and 1.0 cm3 at depths of 1.4-2.8 cm from the phantom surface were tomographically reconstructed. This work demonstrates the practicality of fluorescence-enhanced tomography in clinically relevant volumes.

Optical imaging of breast tumor through temporal log-slope difference mappings

A novel optical temporal log-slope difference mapping approach is proposed for cancerous breast tumor detection. In this method, target tissues are illuminated by near-infrared (700-1000 nm) ultrashort laser pulses from various surface source points, and backscattered time-resolved light signals are collected at the same surface points. By analyzing the log-slopes of decaying signals over all points on the source-detection grid, a log-slope distribution on the surface is obtained. After administration of absorption contrast agents, the presence of cancerous tumors increases the decaying steepness of the transient signals. The mapping of log-slope difference between native tissue and absorption-enhanced cancerous tissue indicates the location and projection of tumors on the detection surface. In this paper, we examine this method in the detection of breast tumors in two model tissue phantoms through computer simulation. The first model has a spherical tumor of 6mm in diameter embedded at the tissue center. The second model is a large tissue phantom embedded with a non-centered spherical tumor 8mm in diameter. Monte Carlo methods were employed to simulate the light transport and signal measurement. It is shown that the tumor in both the tissue models will be accurately projected on the detection surface by the proposed log-slope difference mapping method. The image processing is very fast and does not require any inverse optimization in image reconstruction.

Combining near-infrared tomography and magnetic resonance imaging to study in vivo breast tissue: implementation of a Laplacian-type regularization to incorporate magnetic resonance structure

An imaging system that simultaneously performs near infrared (NIR) tomography and magnetic resonance imaging (MRI) is used to study breast tissue phantoms and a healthy woman in vivo. An NIR image reconstruction that exploits the combined data set is presented that implements the MR structure as a soft-constraint in the NIR property estimation. The algorithm incorporates the MR spatially segmented regions into a regularization matrix that links locations with similar MR properties, and applies a Laplacian-type filter to minimize variation within each region. When prior knowledge of the structure of phantoms is used to guide NIR property estimation, root mean square (rms) image error decreases from 26 to 58%. For a representative in vivo case, images of hemoglobin concentration, oxygen saturation, water fraction, scattering power, and scattering amplitude are derived and the properties of adipose and fibroglandular breast tissue types, identified from MRI, are quantified. Fibroglandular tissue is observed to have more than four times as much water content as adipose tissue, almost twice as much blood volume, and slightly reduced oxygen saturation. This approach is expected to improve recovery of abnormalities within the breast, as the inclusion of structural information increases the accuracy of recovery of embedded heterogeneities, at least in phantom studies.

Recent advances in diffuse optical imaging

We review the current state-of-the-art of diffuse optical imaging, which is an emerging technique for functional imaging of biological tissue. It involves generating images using measurements of visible or near-infrared light scattered across large (greater than several centimetres) thicknesses of tissue. We discuss recent advances in experimental methods and instrumentation, and examine new theoretical techniques applied to modelling and image reconstruction. We review recent work on in vivo applications including imaging the breast and brain, and examine future challenges.

Tomographic fluorescence imaging in tissue phantoms: a novel reconstruction algorithm and imaging geometry

A novel image reconstruction algorithm has been developed and demonstrated for fluorescence-enhanced frequency-domain photon migration (FDPM) tomography from measurements of area illumination with modulated excitation light and area collection of emitted fluorescence light using a gain modulated image-intensified charge-coupled device (ICCD) camera. The image reconstruction problem was formulated as a nonlinear least-squares-type simple bounds constrained optimization problem based upon the penalty/modified barrier function (PMBF) method and the coupled diffusion equations. The simple bounds constraints are included in the objective function of the PMBF method and the gradient-based truncated Newton method with trust region is used to minimize the function for the large-scale problem (39919 unknowns, 2973 measurements). Three-dimensional (3-D) images of fluorescence absorption coefficients were reconstructed using the algorithm from experimental reflectance measurements under conditions of perfect and imperfect distribution of fluorophore within a single target. To our knowledge, this is the first time that targets have been reconstructed in three-dimensions from reflectance measurements with a clinically relevant phantom.

Lighting up tumors with receptor-specific optical molecular probes

Accurate and rapid detection of tumors is of great importance for interrogating the molecular basis of cancer pathogenesis, preventing the onset of complications, and implementing a tailored therapeutic regimen. In this era of molecular medicine, molecular probes that respond to, or target molecular processes are indispensable. Although numerous imaging modalities have been developed for visualizing pathologic conditions, the high sensitivity and relatively innocuous low energy radiation of optical imaging method makes it attractive for molecular imaging. While many human diseases have been studied successfully by using intrinsic optical properties of normal and pathologic tissues, molecular imaging of the expression of aberrant genes, proteins, and other pathophysiologic processes would be enhanced by the use of highly specific exogenous molecular beacons. This review focuses on the development of receptor-specific molecular probes for optical imaging of tumors. Particularly, bioconjugates of probes that absorb and fluoresce in the near infrared wavelengths between 750 and 900 nm will be reviewed.

Characterization of hemoglobin, water, and NIR scattering in breast tissue: analysis of intersubject variability and menstrual cycle changes

Near-infrared imaging was used to quantify typical values of hemoglobin concentration, oxygen saturation, water fraction, scattering power, and scattering amplitude within the breast tissue of volunteer subjects. A systematic study of the menstrual variations in these parameters was carried out by measuring a group of seven premenopausal normal women (aged 41 to 47 years) in the follicular (days 7 to 14 of the cycle) and secretory phases (days 21 to 28) of the cycle, for two complete menstrual cycles. An average increase in hemoglobin concentration of 2.6 microM or 13% of the background breast values was observed in the secretory phase relative to the follicular phase (p<0.0001), but no other average near-infrared parameter changes were significant. While repeatable and systematic changes were observed in all parameters for individual subjects, large intersubject variations were present in all parameters. In a survey of thirty-nine normal subjects, the total hemoglobin varied from 9 to 45 microM, with a systematic correlation observed between total hemoglobin concentration and breast radiographic density. Scattering power and scattering amplitude were also correlated with radiographic density, but oxygen saturation and water fraction were not. Images of breast lesions indicate that total hemoglobin-based contrast can be up to 200% relative to the background in the same breast. Yet, since the background hemoglobin values vary considerably among breasts, the maximum hemoglobin concentrations observed in cancer tumors may vary considerably as well. In light of these observations, it may be important to use hemoglobin contrast values relative to the background for a given breast, rather than absolute hemoglobin contrast when trying to compare the features of breast lesions among subjects.

Breast deformation modelling for image reconstruction in near infrared optical tomography

Near infrared tomography (NIR) is a novel imaging technique that can be used to reconstruct tissue optical properties from measurements of light propagation through tissue. More specifically NIR measurements over a range of wavelengths can be used to obtain internal images of physiologic parameters and these images can be used to detect and characterize breast tumour. To obtain good NIR measurements, it is essential to have good contact between the optical fibres and the breast which in-turn results in the deformation of the breast due to the soft plasticity of the tissue. In this work, a tissue deformation model of the female breast is presented that will account for the altered shape of the breast during clinical NIR measurements. Using a deformed model of a breast, simulated NIR data were generated and used to reconstruct images of tissue absorption and reduced scatter using several assumptions about the imaging domain. Using either a circular or irregular 2D geometry for image reconstruction produces good localization of the absorbing anomaly, but it leads to degradation of the image quality. By modifying the assumptions about the imaging domain to a 3D conical model, with the correct diameter at the plane of NIR measurement, significantly improves the quality of reconstructed images and helps reduce image artefacts. Finally, assuming a non-deformed breast shape for image reconstruction is shown to lead to poor quality images since the geometry of the breast is greatly altered, whereas using the correct deformed geometry produces the best images.

Fluorescence-enhanced optical tomography using referenced measurements of heterogeneous media

A three-dimensional image reconstruction for fluorescence-enhanced frequency-domain photon migration (FDPM) measurements in turbid media is developed and investigated for three different simulated measurement types: 1) absolute emission measurement, or emission measurements of phase and amplitude attenuation made for a given incident point source of excitation light; 2) referenced emission measurements made relative to an excitation measurement conducted at a single reference point away from the incident source; and 3) referenced emission measurements made relative to the excitation measurement conducted at identical points of detection. The image reconstruction algorithm employs a gradient-based constrained truncated Newton (CONTN) method which implements a bounding parameter, which can be used to govern the level of contrast used to discriminate tissue volumes from heterogeneous background tissues. Reverse differentiation technique is used to calculate the gradients. Using simulated data with superimposed noise to achieve a signal-to-noise ratio of 55 and 35 dB to mimic experimental excitation and emission FDPM measurements, respectively, we show the robustness of emission measurements referenced to excitation light. We investigate the performance of algorithm CONTN using these measurement techniques and show that the absorption coefficients due to fluorophore are reconstructed by CONTN accurately and efficiently. Furthermore, we demonstrate the performance of the bounding parameter for rejection of background artifacts owing to background tissue heterogeneity.

Three-dimensional optical tomography: resolution in small-object imaging

Near-infrared (NIR) optical tomography provide estimates of the internal distribution of optical absorption and transport scattering from boundary measurement of light propagation within biological tissue. Although this is a truly three-dimensional (3D) imaging problem, most research to date has concentrated on two-dimensional modeling and image reconstruction. More recently, 3D imaging algorithms are demonstrating better estimation of the light propagation within the imaging region and are providing the basis of more accurate image construction algorithms. As 3D methods emerge, it will become increasingly important to evaluate their resolution, contrast, and localization of optical property heterogeneity. We present a concise study of 3D reconstructed resolution of a small, low-contrast, absorbing and scattering anomaly as it is placed in different locations within a cylindrical phantom. The object is an 8-mm-diameter cylinder, which represents a typical small target that needs to be resolved in NIR mammographic imaging. The best resolution and contrast is observed when the object is located near the periphery of the imaging region (12-22 mm from the edge) and is also positioned within the multiple measurement planes, with the most accurate results seen for the scatter image when the anomaly is at 17 mm from the edge. Furthermore, the accuracy of quantitative imaging is increased to almost 100% of the target values when a priori information regarding the internal structure of imaging domain is utilized.