@article{karbalaeisadegh_yao_zhu_grimal_muller_2023, title={Ultrasound Characterization of Cortical Bone Using Shannon Entropy}, volume={49}, ISSN={["1879-291X"]}, DOI={10.1016/j.ultrasmedbio.2023.04.006}, abstractNote={Ultrasound backscattered signals encompass information on the microstructure of heterogeneous media such as cortical bone, in which pores act as scatterers and result in the scattering and multiple scattering of ultrasound waves. The objective of this study was to investigate whether Shannon entropy can be exploited to characterize cortical porosity.In the study described here, to demonstrate proof of concept, Shannon entropy was used as a quantitative ultrasound parameter to experimentally evaluate microstructural changes in samples with controlled scatterer concentrations made of a highly absorbing polydimethylsiloxane matrix (PDMS). Similar assessment was then performed using numerical simulations on cortical bone structures with varying average pore diameter (Ct.Po.Dm.), density (Ct.Po.Dn.) and porosity (Ct.Po.).The results suggest that an increase in pore diameter and porosity lead to an increase in entropy, indicating increased levels of randomness in the signals as a result of increased scattering. The entropy-versus-scatterer volume fraction in PDMS samples indicates an initial increasing trend that slows down as the scatterer concentration increases. High levels of attenuation cause the signal amplitudes and corresponding entropy values to decrease drastically. The same trend is observed when porosity of the bone samples is increased above 15%.Sensitivity of entropy to microstructural changes in highly scattering and absorbing media can potentially be exploited to diagnose and monitor osteoporosis.}, number={8}, journal={ULTRASOUND IN MEDICINE AND BIOLOGY}, author={Karbalaeisadegh, Yasamin and Yao, Shanshan and Zhu, Yong and Grimal, Quentin and Muller, Marie}, year={2023}, month={Aug}, pages={1824–1829} }
 @article{yousefian_karbalaeisadegh_mueller_2021, title={Frequency-dependent analysis of ultrasound apparent absorption coefficient in multiple scattering porous media: application to cortical bone}, volume={66}, ISSN={["1361-6560"]}, DOI={10.1088/1361-6560/abb934}, abstractNote={Abstract}, number={3}, journal={PHYSICS IN MEDICINE AND BIOLOGY}, author={Yousefian, Omid and Karbalaeisadegh, Yasamin and Mueller, Marie}, year={2021}, month={Feb} }
 @article{lye_roshankhah_karbalaeisadegh_montgomery_egan_muller_mamou_2021, title={In vivo assessment of pulmonary fibrosis and edema in rodents using the backscatter coefficient and envelope statisticsa)}, volume={150}, ISSN={["1520-8524"]}, DOI={10.1121/10.0005481}, abstractNote={Quantitative ultrasound methods based on the backscatter coefficient (BSC) and envelope statistics have been used to quantify disease in a wide variety of tissues, such as prostate, lymph nodes, breast, and thyroid. However, to date, these methods have not been investigated in the lung. In this study, lung properties were quantified by BSC and envelope statistical parameters in normal, fibrotic, and edematous rat lungs in vivo. The average and standard deviation of each parameter were calculated for each lung as well as the evolution of each parameter with acoustic propagation time within the lung. The transport mean free path and backscattered frequency shift, two parameters that have been successfully used to assess pulmonary fibrosis and edema in prior work, were evaluated in combination with the BSC and envelope statistical parameters. Multiple BSC and envelope statistical parameters were found to provide contrast between control and diseased lungs. BSC and envelope statistical parameters were also significantly correlated with fibrosis severity using the modified Ashcroft fibrosis score as the histological gold standard. These results demonstrate the potential for BSC and envelope statistical parameters to improve the diagnosis of pulmonary fibrosis and edema as well as monitor pulmonary fibrosis.}, number={1}, journal={JOURNAL OF THE ACOUSTICAL SOCIETY OF AMERICA}, author={Lye, Theresa H. and Roshankhah, Roshan and Karbalaeisadegh, Yasamin and Montgomery, Stephanie A. and Egan, Thomas M. and Muller, Marie and Mamou, Jonathan}, year={2021}, month={Jul}, pages={183–192} }
 @article{mohanty_karbalaeisadegh_blackwell_ali_masuodi_egan_muller_2020, title={In Vivo Assessment of Pulmonary Fibrosis and Pulmonary Edema in Rodents Using Ultrasound Multiple Scattering}, volume={67}, ISSN={["1525-8955"]}, DOI={10.1109/TUFFC.2020.3023611}, abstractNote={Idiopathic pulmonary fibrosis (IPF) affects 200 000 patients in the United States of America. IPF is responsible for changes in the micro-architecture of the lung parenchyma, such as thickening of the alveolar walls, which reduces compliance and elasticity. In this study, we verify the hypothesis that changes in the microarchitecture of the lung parenchyma can be characterized by exploiting multiple scattering of ultrasound waves by the alveolar structure. Ultrasound propagation in a highly scattering regime follows a diffusion process, which can be characterized using the diffusion constant. We hypothesize that in a fibrotic lung, the thickening of the alveolar wall reduces the amount of air (compared with a healthy lung), thereby minimizing the scattering events. Pulmonary fibrosis is created in Sprague–Dawley rats by instilling bleomycin into the airway. The rats are studied within 3 weeks after bleomycin administration. Using a 128-element linear array transducer operating at 7.8 MHz, in vivo experimental data are obtained from Sprague–Dawley rats and the transport mean free path (L*) and backscatter frequency shift (BFS) are evaluated. Significant differences ( ${p}< 0.05$ ) in the L* values between control and fibrotic rats and in the BFS values between fibrotic and edematous rats showcase the potential of these parameters for diagnosis and monitoring of IPF.}, number={11}, journal={IEEE TRANSACTIONS ON ULTRASONICS FERROELECTRICS AND FREQUENCY CONTROL}, author={Mohanty, Kaustav and Karbalaeisadegh, Yasamin and Blackwell, John William and Ali, Mir Hasnain and Masuodi, Behrooz and Egan, Thomas and Muller, Marie}, year={2020}, month={Nov}, pages={2274–2280} }
 @article{karbalaeisadegh_yousefian_iori_raum_muller_2019, title={Acoustic diffusion constant of cortical bone: Numerical simulation study of the effect of pore size and pore density on multiple scattering}, volume={146}, ISSN={["1520-8524"]}, DOI={10.1121/1.5121010}, abstractNote={While osteoporosis assessment has long focused on the characterization of trabecular bone, the cortical bone micro-structure also provides relevant information on bone strength. This numerical study takes advantage of ultrasound multiple scattering in cortical bone to investigate the effect of pore size and pore density on the acoustic diffusion constant. Finite-difference time-domain simulations were conducted in cortical microstructures that were derived from acoustic microscopy images of human proximal femur cross sections and modified by controlling the density (Ct.Po.Dn) ∈[5−25] pore/mm2 and size (Ct.Po.Dm) ∈[30−100] μm of the pores. Gaussian pulses were transmitted through the medium and the backscattered signals were recorded to obtain the backscattered intensity. The incoherent contribution of the backscattered intensity was extracted to give access to the diffusion constant D. At 8 MHz, significant differences in the diffusion constant were observed in media with different porous micro-architectures. The diffusion constant was monotonously influenced by either pore diameter or pore density. An increase in pore size and pore density resulted in a decrease in the diffusion constant (D =285.9Ct.Po.Dm−1.49, R2=0.989 , p=4.96×10−5,RMSE=0.06; D=6.91Ct.Po.Dn−1.01, R2=0.94, p=2.8×10−3 , RMSE=0.09), suggesting the potential of the proposed technique for the characterization of the cortical microarchitecture.}, number={2}, journal={JOURNAL OF THE ACOUSTICAL SOCIETY OF AMERICA}, author={Karbalaeisadegh, Yasamin and Yousefian, Omid and Iori, Gianluca and Raum, Kay and Muller, Marie}, year={2019}, month={Aug}, pages={1015–1023} }
 @article{mohanty_yousefian_karbalaeisadegh_ulrich_grimal_muller_2019, title={Artificial neural network to estimate micro-architectural properties of cortical bone using ultrasonic attenuation: A 2-D numerical study}, volume={114}, ISBN={1879-0534}, DOI={10.1016/j.compbiomed.2019.103457}, abstractNote={The goal of this study is to estimate micro-architectural parameters of cortical porosity such as pore diameter (φ), pore density (ρ) and porosity (ν) of cortical bone from ultrasound frequency dependent attenuation using an artificial neural network (ANN). First, heterogeneous structures with controlled pore diameters and pore densities (mono-disperse) were generated, to mimic simplified structure of cortical bone. Then, more realistic structures were obtained from high resolution CT scans of human cortical bone. 2-D finite-difference time-domain simulations were conducted to calculate the frequency-dependent attenuation in the 1-8 MHz range. An ANN was then trained with the ultrasonic attenuation at different frequencies as the input feature vectors while the output was set as the micro-architectural parameters (pore diameter, pore density and porosity). The ANN is composed of three fully connected dense layers with 24, 12 and 6 neurons, connected to the output layer. The dataset was trained over 6000 epochs with a batch size of 16. The trained ANN exhibits the ability to predict the micro-architectural parameters with high accuracy and low losses. ANN approaches could potentially be used as a tool to help inform physics-based modelling of ultrasound propagation in complex media such as cortical bone. This will lead to the solution of inverse-problems to retrieve bone micro-architectural parameters from ultrasound measurements for the non-invasive diagnosis and monitoring osteoporosis.}, journal={COMPUTERS IN BIOLOGY AND MEDICINE}, author={Mohanty, Kaustav and Yousefian, Omid and Karbalaeisadegh, Yasamin and Ulrich, Micah and Grimal, Quentin and Muller, Marie}, year={2019}, month={Nov} }
 @article{yousefian_karbalaeisadegh_muller_2019, title={Modeling ultrasound attenuation in porous structures with mono-disperse random pore distributions using the independent scattering approximation: a 2D simulation study}, volume={64}, ISSN={["1361-6560"]}, DOI={10.1088/1361-6560/ab2a32}, abstractNote={The validity of the independent scattering approximation (ISA) to predict the frequency dependent attenuation in 2D models of simplified structures of cortical bone is studied. Attenuation of plane waves at central frequencies ranging from 1 to 8 MHz propagating in structures with mono-disperse random pore distributions with pore diameter and pore density in the range of those of cortical bone are evaluated by finite difference time domain numerical simulations. An approach to assess the multiple scattering of waves in random media is discussed to determine the pore diameter ranges at which the ISA is applicable. A modified version of the ISA is proposed to more accurately predict the attenuation in porosity ranges where it would traditionally fail. The results show that the modified ISA can model the frequency-dependent attenuation of ultrasonic wave with pore diameter and density ranges comparable to those of cortical bone.}, number={15}, journal={PHYSICS IN MEDICINE AND BIOLOGY}, author={Yousefian, Omid and Karbalaeisadegh, Yasamin and Muller, Marie}, year={2019}, month={Aug} }
 @article{mohanty_yousefian_karbalaeisadegh_ulrich_muller_2019, title={Predicting Structural Properties of Cortical Bone by Combining Ultrasonic Attenuation and an Artificial Neural Network (ANN): 2-D FDTD Study}, volume={11662}, ISBN={["978-3-030-27201-2"]}, ISSN={["1611-3349"]}, DOI={10.1007/978-3-030-27202-9_37}, abstractNote={The goal of this paper is to predict the micro-architectural parameters of cortical bone such as pore diameter (ϕ) and porosity (ν) from ultrasound attenuation measurements using an artificial neural network (ANN). Slices from a 3-D CT scan of human femur are obtained. The micro-architectural parameters of porosity such as average pore size and porosity are calculated using image processing. When ultrasound waves propagate in porous structures, attenuation is observed due to scattering. Two-dimensional finite-difference time-domain simulations are carried out to obtain frequency dependent attenuation in those 2D structures. An artificial neural network (ANN) is then trained with the input feature vector as the frequency dependent attenuation and output as pore diameter (ϕ) and porosity (ν). The ANN is composed of one input layer, 3 hidden layers and one output layer, all of which are fully connected. 340 attenuation data sets were acquired and trained over 2000 epochs with a batch size of 32. Data was split into train, validation and test. It was observed that the ANN predicted the micro-architectural parameters of the cortical bone with high accuracies and low losses with a minimum R2 (goodness of fit) value of 0.95. ANN approaches could potentially help inform the solution of inverse-problems to retrieve bone porosity from ultrasound measurements. Ultimately, those inverse-problems could be used for the non-invasive diagnosis and monitoring of osteoporosis.}, journal={IMAGE ANALYSIS AND RECOGNITION, ICIAR 2019, PT I}, author={Mohanty, Kaustav and Yousefian, Omid and Karbalaeisadegh, Yasamin and Ulrich, Micah and Muller, Marie}, year={2019}, pages={407–417} }
 @article{yousefian_white_karbalaeisadegh_banks_muller_2018, title={The effect of pore size and density on ultrasonic attenuation in porous structures with mono-disperse random pore distribution: A two-dimensional in-silico study}, volume={144}, ISSN={["1520-8524"]}, DOI={10.1121/1.5049782}, abstractNote={This work proposes a power law model to describe the attenuation of ultrasonic waves in non-absorbing heterogeneous media with randomly distributed scatterers, mimicking a simplified structure of cortical bone. This paper models the propagation in heterogeneous structures with controlled porosity using a two-dimensional finite-difference time domain numerical simulation in order to measure the frequency dependent attenuation. The paper then fits a phenomenological model to the simulated frequency dependent attenuation by optimizing parameters under an ordinary least squares framework. Local sensitivity analysis is then performed on the resulting parameter estimates in order to determine to which estimates the model is most sensitive. This paper finds that the sensitivity of the model to various parameter estimates depends on the micro-architectural parameters, pore diameter (ϕ) and pore density (ρ). In order to get a sense for how confidently model parameters are able to be estimated, 95% confidence intervals for these estimates are calculated. In doing so, the ability to estimate model-sensitive parameters with a high degree of confidence is established. In the future, being able to accurately estimate model parameters from which micro-architectural ones could be inferred will allow pore density and diameter to be estimated via an inverse problem given real or simulated ultrasonic data to be determined.}, number={2}, journal={JOURNAL OF THE ACOUSTICAL SOCIETY OF AMERICA}, author={Yousefian, Omid and White, R. D. and Karbalaeisadegh, Yasamin and Banks, H. T. and Muller, Marie}, year={2018}, month={Aug}, pages={709–719} }