DOI: 10.25452/figshare.plus.28291988
title: Pulse-Echo Ultrasound Sound Speed Phantom and Meat Aberrating Layer Acquisitions

description: This dataset contains Verasonics Vantage 256 (Verasonics Inc., Kirkland, WA, USA) research scanner acquisitions of agar-propanol phantoms and an ATS 549 phantom with known measured sound speeds. Most of the acquisitions contain a meat aberrating layer above the phantom. We encourage use of this data to validate new techniques, including, but not limited to, sound speed estimators, aberration correction methods, and beamforming algorithms. If using this dataset, please cite the following paper:R. Ali <i>et al</i>., "Local Sound Speed Estimation for Pulse-Echo Ultrasound in Layered Media," in <i>IEEE Transactions on Ultrasonics, Ferroelectrics, and Frequency Control</i>, vol. 69, no. 2, pp. 500-511, Feb. 2022, doi: 10.1109/TUFFC.2021.3124479.Data OrganizationIn the <code>SoSExperiments_curated</code> folder, the data folders are organized by date, followed by transducer name, and subfolder(s) with the imaged medium setup.<code>august13_2020</code> - contains data taken using C5-2v, L12-3v, and L12-5 50mm transducers on an ATS 549 phantom and agar-propanol phantoms with and without meat layers above the phantoms. The folder names indicate the transducer, phantom, and medium configuration used for scanning.<code>June09_2020</code> - contains more agar-propanol phantom acquisition data taken with C5-2v, L12-3v, and L12-5 50mm transducers with meat layers. The folder names indicate the transducer, meat type used for the aberrating layer, and the phantom number.The <code>processing</code> folder contains code related to data loading or image reconstruction. To load in the data and relevant probe and sequence information, run <code>mainLoader.m</code>. To beamform images, <code>sos_experiments.m</code> has example code and instructions.All Verasonics data in .mat files contains Verasonics MATLAB structs (P, RcvData, Receive, Resource, TW, TX, Trans) that provide detailed information about the acquisition and transducer used.Phantom Data DetailsThe phantoms imaged in this portion of the dataset include the ATS 549 phantom, which is composed of a urethane-rubber-based mixture with a nominal sound speed of 1450 m/s, and six homogeneous phantoms made of agarose gelatin and speckle-generating 2% graphite powder, with sound speed variations induced by varying the n-propanol concentration of the phantom to be 0%, 5%, 10%, 15%, and 20% for phantoms 1 - 5 respectively. Some settling was observed for phantoms 4 and 5, leading to slight inhomogeneity. Full synthetic aperture (FSA), Hadamard, and multifocal transmit sequences were used with L12-3v, L12-5, and C5-2v transducers for acquisitions of the phantoms by themselves and with a 10-15 mm thick porcine (pork) or galline (chicken) meat layer above them to induce aberration. The ground truth sound speed measurements for the phantoms and meat layers were made with a similar setup as the murine liver data: a pulsar-receiver was used to drive a piston transducer, and time delays were measured using an oscilloscope to calculate the sound speed.Verasonics Capture DetailsFor the C5-2v data, the transmit pulse center frequency was 4.0 MHz. The FSA data included 128 transmits using each individual element to transmit and all elements to receive per transmit event. The Hadamard-encoded sequence used a Hadamard matrix to determine the pulse polarity for each of the transmits with all elements on for transmit and receive. The multifocal transmit used a walking aperture with two focal depths (radii) at approximately 23.1 mm and 46.2 mm, for a total of 128 * 2 transmit events.For the L12-3v data, the transmit pulse center frequency was 5.95 MHz. The FSA sequence used 192 unique transmit events using each individual element and the two entire receive subapertures at both ends of the array, resulting in a total of 192 * 2 transmit events. The Hadamard-encoded sequence used a total of 2 * 96 * 2 * 2 transmit events to transmit a Hadamard sequence over 192 elements, using a positive and negative pulse; two subapertures on both sides of the aperture, apodized to 96 elements to avoid overlaps; and the two subapertures on both ends of the aperture for receiving across all elements. The multifocal sequence used a walking aperture focused transmit sequence with three focal depths at approximately 23.1, 38.5, and 53.9 mm, for a total of 192 * 3 * 2 transmit events for the two receive subapertures needed to cover the entire transducer array and three focal depths.For the L12-5 data, the transmit pulse center frequency was 7.4 MHz. The FSA sequence included 256 unique transmit events using each individual element on the aperture and using the two complete subapertures on both ends of the transducer to receive in separate events to cover the entire array, for a total of 256 * 2 transmit events. The Hadamard-encoded sequence used a total of 2 * 128 * 2 * 2 transmit events to cover a 256-element Hadamard encoding by using 2 pulses for the positive and negative waveforms and two transmit and two receive subapertures at both ends of the transducer to cover the entire array. The multifocal transmit used a walking aperture focused transmit sequence with two focal depths at approximately 16.4 mm and 30.8 mm, for a total of 256 * 2 * 2 transmit events for the two receive subapertures needed to cover the entire transducer array and two focal depths.Phantom sound speed (SoS) informationAugust 13, 2020 data:<br>Phantom 4: 15% n-propanol, SoS = 1550.5 ± 3.8 m/s (at ~20.5°C)<br>Phantom 5: 20% n-propanol, SoS = 1590.4 ± 2.0 m/s (at ~20.5°C)<br>Chicken: SoS = 1568.5 ± 19.6 m/s (at ~20.5°C)<br>Pork: SoS = 1567.7 ± 3.6 m/s (at ~20.5°C)<br><br>Comments: A higher than usual temperature variation was observed in the building, additional SoS error due to uncertainty in temperature measurement (±1.5°C) is 0.3% (~ ±4.7 m/s). For example, a "final" SoS value for phantom 5 would be 1590.4 ± 6.7 m/s. || The top side of the phantom is indicated by a strong reflector placed in the proximity of the phantom which can be seen after reconstructing the B-mode image.<br>June 9, 2020 data<br>Phantom 1: 0% n-propanol, SoS = 1489.7 ± 1.2 m/s (at ~21°C)<br>Phantom 2: 5% n-propanol, SoS = 1516.2 ± 0.9 m/s (at ~21°C)<br>Phantom 3: 10% n-propanol, SoS = 1539.7 ± 0.7 m/s (at ~21°C)<br>Phantom 5: 20% n-propanol, SoS = 1585.9 ± 2.2 m/s (at ~21°C)<br>Chicken: SoS = 1575.3 ± 1.1 m/s (at ~21°C)<br>Pork: SoS = 1560.7 ± 1.0 m/s (at ~21°C)<br><br>Comments: Temperature measurements were confirmed, additional SoS error due to uncertainty in temperature measurement (±0.5°C) is ~1.5 m/s.<b>Publications Featuring this Data (Non-Exhaustive)</b>Manuscripts:R. Ali, T. Brevett, D. Hyun, L. L. Brickson and J. J. Dahl, "Distributed Aberration Correction Techniques Based on Tomographic Sound Speed Estimates," in IEEE Transactions on Ultrasonics, Ferroelectrics, and Frequency Control, vol. 69, no. 5, pp. 1714-1726, May 2022, doi: 10.1109/TUFFC.2022.3162836.R. Ali et al., "Sound Speed Estimation for Distributed Aberration Correction in Laterally Varying Media," in IEEE Transactions on Computational Imaging, vol. 9, pp. 367-382, 2023, doi: 10.1109/TCI.2023.3261507.Conference Proceedings:R. Ali, D. Hyun and J. J. Dahl, "Application of Common Midpoint Gathers to Medical Pulse-Echo Ultrasound for Optimal Coherence and Improved Sound Speed Estimation in Layered Media," 2020 IEEE International Ultrasonics Symposium (IUS), Las Vegas, NV, USA, 2020, pp. 1-4, doi: 10.1109/IUS46767.2020.9251370.S. J. Sanabria, T. Brevett, R. Ali, A. Telichko and J. Dahl, "Direct Speed of Sound Reconstruction from Full-Synthetic Aperture Data with Dual Regularization," 2022 IEEE International Ultrasonics Symposium (IUS), Venice, Italy, 2022, pp. 1-4, doi: 10.1109/IUS54386.2022.9958718.S. J. Sanabria, T. Brevett, A. Telichko and J. Dahl, "Speed of Sound Imaging with Curvilinear Probes from Full-Synthetic Aperture Data," 2022 IEEE International Ultrasonics Symposium (IUS), Venice, Italy, 2022, pp. 1-4, doi: 10.1109/IUS54386.2022.9957632.S. J. Sanabria, S. Munot, T. Brevett, A. Telichko and J. Dahl, "Pulse-Echo Ultrasound Computed Tomography of Frequency-Dependent Acoustic Attenuation," 2023 IEEE International Ultrasonics Symposium (IUS), Montreal, QC, Canada, 2023, pp. 1-4, doi: 10.1109/IUS51837.2023.10307604.S. J. Sanabria, S. Munot, T. Brevett, A. Telichko and J. Dahl, "Speed-of-Sound Dispersion Estimation from Pulse-Echo Data," 2023 IEEE International Ultrasonics Symposium (IUS), Montreal, QC, Canada, 2023, pp. 1-4, doi: 10.1109/IUS51837.2023.10306727.T. Brevett, S. Sanabria and J. J. Dahl, "A Comparison of Global and Local Sound Speed Estimation for Aberration Correction in Abdominal Models," 2023 IEEE International Ultrasonics Symposium (IUS), Montreal, QC, Canada, 2023, pp. 1-4, doi: 10.1109/IUS51837.2023.10307733.