3D Numerical Breast Phantoms and Ring-Array USCT measurements (3 rings)

<h3>Dataset Summary</h3>
<p>
This is the companion dataset for the manuscript by Fu Li, Umberto Villa, Neb Duric, and Mark A. Anastasio titled
<em>"A forward model incorporating elevation-focused transducer properties for 3D full-waveform inversion in ultrasound computed tomography"</em>. IEEE UFFC,
<a href="https://doi.org/10.1109/TUFFC.2023.3313549" target="_blank"> link</a> (2023).
</p>

<p>
The dataset comprises two types of thin-slab 3D numerical breast phantoms (NBPs) and their corresponding ring-array ultrasound computed tomography (USCT) simulated measurement data.
</p>

Two representative ACR BI-RADS breast composition types are selected:
<li><strong>B:</strong> Scattered areas of fibroglandular density</li>
<li><strong>C:</strong> Heterogeneously dense breast</li>
Each NBP contains maps of acoustic properties (speed of sound, acoustic attenuation, and density). The corresponding ring-array USCT measurement data were simulated using the elevation-focused transducer described in the accompanying paper. Wave propagation simulations were conducted in lossy heterogeneous media using k-wave.
</p>

<hr>

<h3>Dataset Structure</h3>
<p>The dataset is organized into three folders:</p>
<ul>
<li>Dataset folder for phantom type <strong>B</strong></li>
<li>Dataset folder for phantom type <strong>C</strong></li>
<li>The <strong>imaging_system</strong> folder, which contains details about the 3D imaging system, including the excitation source, transducer coordinates, and lens thickness.</li>
</ul>

<p><strong>B:/C:</strong></p>
<p>
This dataset folder houses three sets of ring-array data, corresponding to acquisitions at three distinct elevation locations. As described in the manuscript, these locations are: ring -1 at z=-1.8mm, ring 0 at z=0mm, and ring 1 at z=1.8mm. The employed NBP and the associated simulated measurement data for each ring are provided.
Specifically, the data files include
</p>
<ul>
<li>
<em>phantom.mat</em>: This .mat file contains three acoustic media:
<ul>
<li>sos: Speed of sound map (m/s) with dimensions [1280,1280,194] (x-,y-,z-direction) and a 0.2 mm pixel size. Data type is float32.</li>
<li>aa: Acoustic attenuation map (Np/m/MHz) with dimensions [1280,1280,194] (x-,y-,z-direction) and a 0.2 mm pixel size. Data type is float32.</li>
<li>density: Density map (kg/mm³) with dimensions [1280,1280,194] (x-,y-,z-direction) and a 0.2 mm pixel size. Data type is float32.</li>

</ul>
Note: These data are used to generate the corresponding acoustic media for each ring simulation by executing the Matlab script <i>generate_slab.m</i>. See the description of <i>generate_slab.m</i> for more details.
<p>

</li>
<li>
<em>data_ring_{i}.h5</em>: Measurement data of the i-th ring (for i = -1, 0, 1) . Measurement is stored with an hdf5 key that matches the transducer index. This is a two-dimensional array of size [1024,4200], where rows denote the receiver index and columns indicate the time sample. The sampling frequency is 25MHz.
</li>
</ul>

<p><strong>imaging_system:</strong></p>
<ul>
<li><em>source300.mat</em>: Time profile of the excitation pulse. Comprises 300 time samples with a sampling frequency of 25MHz.</li>
<li><em>receiver_locations_1024.mat</em>: XY coordinates (in mm) of the location for each receiver transducer in the imaging plane. Data type is float32 with an array size of [2x1024].</li>
<li><em>emitter_locations_128.mat</em>: XY coordinates (in mm) of the location for each emitter transducer in the imaging plane. Data type is float32 with an array size of [2x128].</li>
<li><em>lens_thickness.mat</em>: The thickness (in mm) of the lens model with size [1x90]. Each element denotes the thickness of each segment (voxel) of the line aperture, from top to bottom.

</ul>

<p>Additionally, the dataset includes helper MATLAB scripts:</p>
<ul>
<li><i>read_data.m</i>: A function to aid in loading and visualizing the excitation source, transducer locations, and hdf5 measurement data files.</li>
<li><i>generate_slab.m</i>: A script to extract thin-slab from <i>phantom.mat</i>, the extracted medium is the used as computational domain for each ring-array simulation (for ring -1,0,1).</li>

Specifically, acoustic media were extracted from the shared phantom at different elevation locations. Two adjacent slabs are shifted vertically by 1.8 mm. The imaging plane for ring <i>i</i> corresponds to the central z-slice of each computational domain. The positions of each ring-array thin-slab are illustrated in the following figure.
<br>
<img src="https://dataverse.harvard.edu/api/access/datafile/7351428
" alt="Illustration of thin-slab phantom locations" width="100%" height="15%">
<br>
This function will generate data files named <i>phantom_ring_{i}.mat</i>, where i=-1, 0, 1. These correspond to the different ring-array simulation grids used to produce the shared three ring-array measurement data.
</ul>

<hr>

<p>
For more details on the NBP generation, please refer to <a href="https://doi.org/10.1109/TUFFC.2021.3112544" target="_blank">li2021uffc</a> (2021). The anatomical structures of these NBPs were derived using tools from the Virtual Imaging Clinical Trial for Regulatory Evaluation (VICTRE) project.
</p>