j-Wave: An open-source differentiable wave simulator

Stanziola, Antonio; Arridge, Simon R.; Cox, Ben T.; Treeby, Bradley E.

doi:10.1016/j.softx.2023.101338

Cited by 10 publications

(7 citation statements)

References 43 publications

(61 reference statements)

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“…To determine the impact of acoustic modeling, we ran the forward acoustic model in j-Wave 45 to calculate the pressure time series detected by the ultrasound transducer array for the initial pressure distributions. Simulations were run in three dimensions, with a grid size of 240 μm, and a speed of sound of 1500 m s−1.…”

Section: Methodsmentioning

confidence: 99%

Effects of skin tone on photoacoustic imaging and oximetry

Else,

Hacker,

Gröhl

et al. 2023

J. Biomed. Opt.

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. Significance Photoacoustic imaging (PAI) provides contrast based on the concentration of optical absorbers in tissue, enabling the assessment of functional physiological parameters such as blood oxygen saturation ( ). Recent evidence suggests that variation in melanin levels in the epidermis leads to measurement biases in optical technologies, which could potentially limit the application of these biomarkers in diverse populations. Aim To examine the effects of skin melanin pigmentation on PAI and oximetry. Approach We evaluated the effects of skin tone in PAI using a computational skin model, two-layer melanin-containing tissue-mimicking phantoms, and mice of a consistent genetic background with varying pigmentations. The computational skin model was validated by simulating the diffuse reflectance spectrum using the adding-doubling method, allowing us to assign our simulation parameters to approximate Fitzpatrick skin types. Monte Carlo simulations and acoustic simulations were run to obtain idealized photoacoustic images of our skin model. Photoacoustic images of the phantoms and mice were acquired using a commercial instrument. Reconstructed images were processed with linear spectral unmixing to estimate blood oxygenation. Linear unmixing results were compared with a learned unmixing approach based on gradient-boosted regression. Results Our computational skin model was consistent with representative literature for in vivo skin reflectance measurements. We observed consistent spectral coloring effects across all model systems, with an overestimation of and more image artifacts observed with increasing melanin concentration. The learned unmixing approach reduced the measurement bias, but predictions made at lower blood still suffered from a skin tone-dependent effect. Conclusion PAI demonstrates measurement bias, including an overestimation of blood , in higher Fitzpatrick skin types. Future research should aim to characterize this effect in humans to ensure equitable application of the technology.

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Section: Methodsmentioning

confidence: 99%

Effects of skin tone on photoacoustic imaging and oximetry

Else,

Hacker,

Gröhl

et al. 2023

J. Biomed. Opt.

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“…Solvers for the two governing equations given in Section 2.1 are constructed using JaxDF [22]. This is a discretization framework that decouples the mathematical definition of the problem from the underlying discretization.…”

Section: Methodsmentioning

confidence: 99%

“…Here we present j-Wave: a customizable Python simulator, written on top of the JAX library [12] and the discretization framework JaxDF [22], for fast, parallelizable, and differentiable acoustic simulations. j-Wave solves both time-varying and timeharmonic forms of the wave equation with support for multiple discretizations, including finite differences and Fourier spectral methods, in 1D, 2D and 3D.…”

Section: Aimmentioning

confidence: 99%

J-Wave: An Open-Source Differentiable Wave Simulator

et al. 2022

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“…It tests only the extremes of the HU-ρ functions within the ±1 STD ROI range. Fully sampling the HU-ρ distribution requires a Monte Carlo approach (Stanziola et al 2023b) or linear uncertainty propagation with a differentiable simulator (Stanziola et al 2023a(Stanziola et al , 2023b, which was beyond the scope of this work.…”

Section: Uncertaintymentioning

confidence: 99%

Strategies and safety simulations for ultrasonic cervical spinal cord neuromodulation

Xu,

Bestmann,

Treeby

et al. 2024

Phys. Med. Biol.

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Focused ultrasound spinal cord neuromodulation studies have demonstrated the capacity for neuromodulation of the spinal cord in small animals. The safe and efficacious translation of these approaches to human scale requires an understanding of ultrasound propagation and heat deposition within the human spine. To address this, combined acoustic and thermal modelling was used to assess the pressure and heat distributions produced by a 500 kHz source focused to the C5/C6 level of the cervical spine via two approaches a) the posterior acoustic window between vertebral posterior arches, or b) the lateral intervertebral foramen from which the C6 spinal nerve exits. Pulse trains of 150 0.1 s pulses with a pulse repetition frequency of 0.33 Hz and free-field spatial peak pulse-averaged intensity of 10 W/cm2 were simulated for the CT volumes of four subjects and for ±10 mm translational and ±10° rotational source positioning errors. Target pressures ranged between 20% and 70% of free-field spatial peak pressures with the posterior approach, and 20% and 100% with the lateral approach. When the source was optimally positioned with the posterior approach, peak spine heating values were below 1°C, but source mis-positioning resulted in bone heating up to 4°C. Heating with the lateral approach did not exceed 2°C within the mispositioning range. There were substantial inter-subject differences in target pressures and peak heating values. Target pressure varied three to four-fold between subjects, depending on approach, while peak heating varied approximately two-fold between subjects. This results in a nearly ten-fold range in the target pressure achieved per degree of maximum heating between subjects. This study highlights the importance of developing trans-spine ultrasound simulation software for the assurance of subject-specific safety and efficacy of focused ultrasound spinal cord therapies.

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j-Wave: An open-source differentiable wave simulator

Cited by 10 publications

References 43 publications

Effects of skin tone on photoacoustic imaging and oximetry

Effects of skin tone on photoacoustic imaging and oximetry

J-Wave: An Open-Source Differentiable Wave Simulator

Strategies and safety simulations for ultrasonic cervical spinal cord neuromodulation

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