Mocarts: a lightweight radiation transport simulator for easy handling of complex sensing geometries

In functional neuroimaging (fNIRS), elaborated sensing geometries pairing multiple light sources and detectors arranged over the tissue surface are needed. A variety of software tools for probing forward models of radiation transport in tissue exist, but their handling of sensing geometries and specification of complex tissue architectures is, most times, cumbersome. In this work, we introduce a lightweight simulator, Monte Carlo Radiation Transport Simulator (MOCARTS) that attends these demands for simplifying specification of tissue architectures and complex sensing geometries. An object-oriented architecture facilitates such goal. The simulator core is evolved from the Monte Carlo Multi-Layer (mcml) tool but extended to support multi-channel simulations. Verification against mcml yields negligible error (RMSE~4-10e-9) over a photon trajectory. Full simulations show concurrent validity of the proposed tool. Finally, the ability of the new software to simulate multi-channel sensing geometries and to define biological tissue models in an intuitive nested-hierarchy way are exemplified

Highly parallel Monte-Carlo simulations of the acousto-optic effect in heterogeneous turbid media

The development of a highly parallel simulation of the acousto-optic effect is detailed. The simulation supports optically heterogeneous simulation domains under insonification by arbitrary monochromatic ultrasound fields. An adjoint method for acousto-optics is proposed to permit point-source/point-detector simulations. The flexibility and efficiency of this simulation code is demonstrated in the development of spatial absorption sensitivity maps which are in broad agreement with current experimental investigations. The simulation code has the potential to provide guidance in the feasibility and optimization of future studies of the acousto-optic technique, and its speed may permit its use as part of an iterative inversion model

Optical spectroscopy of turbid media: time-domain measurements and accelerated Monte Carlo modelling

Optical spectroscopy is a versatile and powerful tool to probe translucent materials. In this work, the focus is on characterization of strongly scattering (turbid) materials by means of time-of-flight spectroscopy (TOFS). Instrumentation and modelling aspects of TOFS were investigated and improved, enabling significantly more accurate spectroscopic measurements. It was shown that the commonly used diffusion theory fails to accurately describe time-domain light propagation in e.g. tissue. A fully scalable Monte Carlo (MC) scheme (WMC) was developed, enabling MC to replace diffusion models in TOFS data evaluation. Consequently, the accuracy and capabilities of TOFS were significantly improved. Graphics processing units (GPUs) were introduced for acceleration of MC simulations in general, resulting in three orders of magnitude speedup. It was shown that proper utilization of the capabilities of modern GPUs allow similar performance, even for more complex problems. TOFS in combination with WMC was used in in vivo interstitial spectroscopy of the human prostate, demonstrating the need for better modelling in many clinical applications. To aid future interstitial in vivo measurements, a single-fibre TOFS system was developed and demonstrated in phantom experiments. Turning to investigations of pharmaceutical samples, a time-of-flight spectrometer, covering the 650-1400 nm spectral range, was developed, enabling TOFS for vibrational spectroscopy of solids. In spatially resolved TOFS measurements, compaction induced anisotropic light diffusion was observed. This is of great importance for the application of model-based optical spectroscopic tech- niques and may, in addition, provide important information about the sample microstructure. Furthermore, TOFS was used together with laser-based gas sensing to probe porous solids. Although a need for better models was revealed, excellent correlation between optical and actual porosity was demonstrated

Propagation of coherent polarized light in turbid highly scattering medium

Within the framework of further development of unified Monte Carlo code for the needs of biomedical optics and biophotonics, we present an approach for modeling of coherent polarized light propagation in highly scattering turbid media, such as biological tissues. The temporal coherence of light, linear and circular polarization, interference, and the helicity flip of circularly polarized light due to reflection at the medium boundary and/ or backscattering events are taken into account. To achieve higher accuracy in the results and to speed up the modeling, the implementation of the code utilizes parallel computing on NVIDIA graphics processing units using Compute Unified Device Architecture. The results of the simulation of coherent linearly and circularly polarized light are presented in comparison with the results of known theoretical studies and the results of alternative modelings

Simulation study on acousto-optics sensing of focused ultrasound

Abstract. The acousto-optics (AO) technique can provide a good contrast with high penetration depth (up to 5 cm) and can be potentially utilized in real time monitoring of the focused ultrasound (FUS) therapies. This work presents the AO simulation study on the interaction of light and FUS in the single-layer brain (SLB) medium and four-layer brain (FLB) medium. FUS pressure distribution at 0.5 MHz and 0.9 MHz frequency was simulated on k-Wave toolbox and the AO Monte Carlo (MC) algorithm was developed on MATLAB to simulate the AO effect in both mediums. The result for the SLB for both ultrasound (US) frequencies suggests that the modulation depth (MD) is high in the region of US focus with a magnitude of 2%-3% and <1% at 0.5 MHz and 0.9 MHz, respectively. Moreover, the MD decreases to 5 orders of magnitude at the source region. In the FLB, the MD decreased to 4–4.5 orders at the source and was present in the skull and US focus region with a magnitude of <1% at both US frequencies. These results suggest that AO can be utilized in sensing FUS effects on brain tissue and the AO signal-to-noise ratio (SNR) depends not only on the MD but also on the level of light intensity interacting with the US pressure

A modeling-based assessment of acousto-optic sensing for monitoring high-intensity focused ultrasound lesion formation

Real-time acousto-optic (AO) sensing - a dual-wave modality that combines ultrasound with diffuse light to probe the optical properties of turbid media - has been demonstrated to non-invasively detect changes in ex vivo tissue optical properties during high-intensity focused ultrasound (HIFU) exposure. The AO signal indicates the onset of lesion formation and predicts resulting lesion volumes. Although proof-of-concept experiments have been successful, many of the underlying parameters and mechanisms affecting thermally induced optical property changes and the AO detectability of HIFU lesion formation are not well understood. In thesis, a numerical simulation was developed to model the AO sensing process and capture the relevant acoustic, thermal, and optical transport processes. The simulation required data that described how optical properties changed with heating. Experiments were carried out where excised chicken breast was exposed to thermal bath heating and changes in the optical absorption and scattering spectra (500 nm - 1100 nm) were measured using a scanning spectrophotometer and an integrating sphere assembly. Results showed that the standard thermal dose model currently used for guiding HIFU treatments needs to be adjusted to describe thermally induced optical property changes. To model the entire AO process, coupled models were used for ultrasound propagation, tissue heating, and diffusive light transport. The angular spectrum method was used to model the acoustic field from the HIFU source. Spatial-temporal temperature elevations induced by the absorption of ultrasound were modeled using a finite-difference time-domain solution to the Pennes bioheat equation. The thermal dose model was then used to determine optical properties based on the temperature history. The diffuse optical field in the tissue was then calculated using a GPU-accelerated Monte Carlo algorithm, which accounted for light-sound interactions and AO signal detection. The simulation was used to determine the optimal design for an AO guided HIFU system by evaluating the robustness of the systems signal to changes in tissue thickness, lesion optical contrast, and lesion location. It was determined that AO sensing is a clinically viable technique for guiding the ablation of large volumes and that real-time sensing may be feasible in the breast and prostate

Aerospace medicine and biology: A continuing bibliography with indexes (supplement 355)

This bibliography lists 147 reports, articles and other documents introduced into the NASA Scientific and Technical Information System during October, 1991. Subject coverage includes: aerospace medicine and psychology, life support systems and controlled environments, safety equipment, exobiology and extraterrestrial life, and flight crew behavior and performance

Design and development of optical reflectance spectroscopy and optical coherence tomography catheters for myocardial tissue characterization

Catheter ablation therapy attempts to restore sinus rhythm in arrhythmia patients by producing site-specific tissue modification along regions which cause abnormal electrical activity. This treatment, though widely used, often requires repeat procedures to observe long-term therapeutic benefits. This limitation is driven in part by challenges faced by conventional schemes in validating lesion adequacy at the time of the procedure. Optical techniques are well-suited for the interrogation and characterization of biological tissues. In particular, optical coherence tomography (OCT) relies on coherence gating of singly-scattered light to enable high-resolution structural imaging for tissue diagnostics and procedural guidance. Alternatively, optical reflectance spectroscopy (ORS) is a point measurement technique which makes use of incoherent, multiply-scattered light to probe tissue volumes and derive important data from its optical signature. ORS relies on the fact that light-tissue interactions are regulated by absorption and scattering, which directly relate to the intrinsic tissue biochemistry and cellular organization. In this thesis, we explore the integration of these modalities into ablation catheters for obtaining procedural metrics which could be utilized to guide catheter ablation therapy. We first present the development of an accelerated computational light transport model and its application for guiding ORS catheter design. A custom ORS-integrated ablation catheter is then implemented and tested within porcine specimens in vitro. A model is proposed for real-time estimation of lesion size based on changes in spectral morphology acquired during ablation. We then fabricated custom integrated OCT M-mode RF catheters and present a model for detecting contact status based on deep convolutional neural networks trained on endomyocardial images. Additionally, we demonstrate for the first time, tracking of RF-induced lesion formation employing OCT Doppler micro-velocimetry; this response is shown to be commensurate with the degree of treatment. We further demonstrate for the first time spectroscopic tracking of kinetics related to the heme oxidation cascade during thermal treatment, which are linked to tissue denaturation. The pairing of these modalities into a single RF catheter was also validated for guiding lesion delivery in vitro and within live pigs. Finally, we conclude with a proof-of-concept demonstration of ORS as a mapping tool to guide epicardial ablation in human donor hearts. These results showcase the vast potential of ORS and OCT empowered RF catheters for aiding intraprocedural guidance of catheter ablation procedures which could be utilized alongside current practices