@inproceedings{KaplanBuchmannProhaskaetal., author = {Kaplan, Bernhard and Buchmann, Jens and Prohaska, Steffen and Laufer, Jan}, title = {Monte-Carlo-based inversion scheme for 3D quantitative photoacoustic tomography}, series = {Proc. of SPIE, Photons Plus Ultrasound: Imaging and Sensing 2017}, volume = {10064}, booktitle = {Proc. of SPIE, Photons Plus Ultrasound: Imaging and Sensing 2017}, doi = {10.1117/12.2251945}, pages = {100645J -- 100645J-13}, abstract = {The goal of quantitative photoacoustic tomography (qPAT) is to recover maps of the chromophore distributions from multiwavelength images of the initial pressure. Model-based inversions that incorporate the physical processes underlying the photoacoustic (PA) signal generation represent a promising approach. Monte-Carlo models of the light transport are computationally expensive, but provide accurate fluence distributions predictions, especially in the ballistic and quasi-ballistic regimes. Here, we focus on the inverse problem of 3D qPAT of blood oxygenation and investigate the application of the Monte-Carlo method in a model-based inversion scheme. A forward model of the light transport based on the MCX simulator and acoustic propagation modeled by the k-Wave toolbox was used to generate a PA image data set acquired in a tissue phantom over a planar detection geometry. The combination of the optical and acoustic models is shown to account for limited-view artifacts. In addition, the errors in the fluence due to, for example, partial volume artifacts and absorbers immediately adjacent to the region of interest are investigated. To accomplish large-scale inversions in 3D, the number of degrees of freedom is reduced by applying image segmentation to the initial pressure distribution to extract a limited number of regions with homogeneous optical parameters. The absorber concentration in the tissue phantom was estimated using a coordinate descent parameter search based on the comparison between measured and modeled PA spectra. The estimated relative concentrations using this approach lie within 5 \% compared to the known concentrations. Finally, we discuss the feasibility of this approach to recover the blood oxygenation from experimental data.}, language = {en} } @inproceedings{BuchmannKaplanProhaskaetal., author = {Buchmann, Jens and Kaplan, Bernhard and Prohaska, Steffen and Laufer, Jan}, title = {Experimental validation of a Monte-Carlo-based inversion scheme for 3D quantitative photoacoustic tomography}, series = {Proc. of SPIE, Photons Plus Ultrasound: Imaging and Sensing}, volume = {10064}, booktitle = {Proc. of SPIE, Photons Plus Ultrasound: Imaging and Sensing}, doi = {10.1117/12.2252359}, pages = {1006416 -- 1006416-8}, abstract = {Quantitative photoacoustic tomography (qPAT) aims to extract physiological parameters, such as blood oxygen saturation (sO2), from measured multi-wavelength image data sets. The challenge of this approach lies in the inherently nonlinear fluence distribution in the tissue, which has to be accounted for by using an appropriate model, and the large scale of the inverse problem. In addition, the accuracy of experimental and scanner-specific parameters, such as the wavelength dependence of the incident fluence, the acoustic detector response, the beam profile and divergence, needs to be considered. This study aims at quantitative imaging of blood sO2, as it has been shown to be a more robust parameter compared to absolute concentrations. We propose a Monte-Carlo-based inversion scheme in conjunction with a reduction in the number of variables achieved using image segmentation. The inversion scheme is experimentally validated in tissue-mimicking phantoms consisting of polymer tubes suspended in a scattering liquid. The tubes were filled with chromophore solutions at different concentration ratios. 3-D multi-spectral image data sets were acquired using a Fabry-Perot based PA scanner. A quantitative comparison of the measured data with the output of the forward model is presented. Parameter estimates of chromophore concentration ratios were found to be within 5 \% of the true values.}, language = {en} } @article{BuchmannKaplanPowelletal., author = {Buchmann, Jens and Kaplan, Bernhard and Powell, Samuel and Prohaska, Steffen and Laufer, Jan}, title = {Quantitative PA tomography of high resolution 3-D images: experimental validation in tissue phantoms}, series = {Photoacoustics}, volume = {17}, journal = {Photoacoustics}, doi = {10.1016/j.pacs.2019.100157}, pages = {100157}, abstract = {Quantitative photoacoustic tomography aims recover the spatial distribution of absolute chromophore concentrations and their ratios from deep tissue, high-resolution images. In this study, a model-based inversion scheme based on a Monte-Carlo light transport model is experimentally validated on 3-D multispectral images of a tissue phantom acquired using an all-optical scanner with a planar detection geometry. A calibrated absorber allowed scaling of the measured data during the inversion, while an acoustic correction method was employed to compensate the effects of limited view detection. Chromophore- and fluence-dependent step sizes and Adam optimization were implemented to achieve rapid convergence. High resolution 3-D maps of absolute concentrations and their ratios were recovered with high accuracy. Potential applications of this method include quantitative functional and molecular photoacoustic tomography of deep tissue in preclinical and clinical studies.}, language = {en} } @article{BuchmannKaplanPowelletal., author = {Buchmann, Jens and Kaplan, Bernhard and Powell, Samuel and Prohaska, Steffen and Laufer, Jan}, title = {3D quantitative photoacoustic tomography using an adjoint radiance Monte Carlo model and gradient descent}, series = {Journal of Biomedical Optics}, volume = {24}, journal = {Journal of Biomedical Optics}, number = {6}, doi = {10.1117/1.JBO.24.6.066001}, pages = {066001}, abstract = {Quantitative photoacoustic tomography aims to recover maps of the local concentrations of tissue chromophores from multispectral images. While model-based inversion schemes are promising approaches, major challenges to their practical implementation include the unknown fluence distribution and the scale of the inverse problem. This paper describes an inversion scheme based on a radiance Monte Carlo model and an adjoint-assisted gradient optimization that incorporates fluence-dependent step sizes and adaptive moment estimation. The inversion is shown to recover absolute chromophore concentrations, blood oxygen saturation and the Gr{\"u}neisen parameter from in silico 3D phantom images for different radiance approximations. The scattering coefficient was assumed to be homogeneous and known a priori.}, language = {en} } @misc{BuchmannKaplanPowelletal., author = {Buchmann, Jens and Kaplan, Bernhard and Powell, Samuel and Prohaska, Steffen and Laufer, Jan}, title = {3D quantitative photoacoustic tomography using an adjoint radiance Monte Carlo model and gradient descent}, issn = {1438-0064}, doi = {10.1117/1.JBO.24.6.066001}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-72995}, abstract = {Quantitative photoacoustic tomography aims to recover maps of the local concentrations of tissue chromophores from multispectral images. While model-based inversion schemes are promising approaches, major challenges to their practical implementation include the unknown fluence distribution and the scale of the inverse problem. This paper describes an inversion scheme based on a radiance Monte Carlo model and an adjoint-assisted gradient optimization that incorporates fluence-dependent step sizes and adaptive moment estimation. The inversion is shown to recover absolute chromophore concentrations, blood oxygen saturation and the Gr{\"u}neisen parameter from in silico 3D phantom images for different radiance approximations. The scattering coefficient was assumed to be homogeneous and known a priori.}, language = {en} } @misc{BuchmannKaplanPowelletal., author = {Buchmann, Jens and Kaplan, Bernhard and Powell, Samuel and Prohaska, Steffen and Laufer, Jan}, title = {Quantitative PA tomography of high resolution 3-D images: experimental validation in tissue phantoms}, issn = {1438-0064}, doi = {10.1016/j.pacs.2019.100157}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-75416}, abstract = {Quantitative photoacoustic tomography aims recover the spatial distribution of absolute chromophore concentrations and their ratios from deep tissue, high-resolution images. In this study, a model-based inversion scheme based on a Monte-Carlo light transport model is experimentally validated on 3-D multispectral images of a tissue phantom acquired using an all-optical scanner with a planar detection geometry. A calibrated absorber allowed scaling of the measured data during the inversion, while an acoustic correction method was employed to compensate the effects of limited view detection. Chromophore- and fluence-dependent step sizes and Adam optimization were implemented to achieve rapid convergence. High resolution 3-D maps of absolute concentrations and their ratios were recovered with high accuracy. Potential applications of this method include quantitative functional and molecular photoacoustic tomography of deep tissue in preclinical and clinical studies.}, language = {en} } @misc{KaplanLauferProhaskaetal., author = {Kaplan, Bernhard and Laufer, Jan and Prohaska, Steffen and Buchmann, Jens}, title = {Monte-Carlo-based inversion scheme for 3D quantitative photoacoustic tomography}, issn = {1438-0064}, doi = {10.1117/12.2251945}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-62318}, abstract = {The goal of quantitative photoacoustic tomography (qPAT) is to recover maps of the chromophore distributions from multiwavelength images of the initial pressure. Model-based inversions that incorporate the physical processes underlying the photoacoustic (PA) signal generation represent a promising approach. Monte-Carlo models of the light transport are computationally expensive, but provide accurate fluence distributions predictions, especially in the ballistic and quasi-ballistic regimes. Here, we focus on the inverse problem of 3D qPAT of blood oxygenation and investigate the application of the Monte-Carlo method in a model-based inversion scheme. A forward model of the light transport based on the MCX simulator and acoustic propagation modeled by the k-Wave toolbox was used to generate a PA image data set acquired in a tissue phantom over a planar detection geometry. The combination of the optical and acoustic models is shown to account for limited-view artifacts. In addition, the errors in the fluence due to, for example, partial volume artifacts and absorbers immediately adjacent to the region of interest are investigated. To accomplish large-scale inversions in 3D, the number of degrees of freedom is reduced by applying image segmentation to the initial pressure distribution to extract a limited number of regions with homogeneous optical parameters. The absorber concentration in the tissue phantom was estimated using a coordinate descent parameter search based on the comparison between measured and modeled PA spectra. The estimated relative concentrations using this approach lie within 5 \% compared to the known concentrations. Finally, we discuss the feasibility of this approach to recover the blood oxygenation from experimental data.}, language = {en} }