DOI: 10.7910/dvn/8jvlae
title: 3D Numerical Breast Phantoms and Ring-Array USCT measurements (3 rings)
title: Replication data: A forward model incorporating elevation-focused transducer properties for 3D full-waveform inversion in ultrasound computed tomography

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

&lt;p&gt;
 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.
&lt;/p&gt;

 Two representative ACR BI-RADS breast composition types are selected:
 &lt;li&gt;&lt;strong&gt;B:&lt;/strong&gt; Scattered areas of fibroglandular density&lt;/li&gt;
 &lt;li&gt;&lt;strong&gt;C:&lt;/strong&gt; Heterogeneously dense breast&lt;/li&gt;
 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.
&lt;/p&gt;

&lt;hr&gt;

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

&lt;p&gt;&lt;strong&gt;B:/C:&lt;/strong&gt;&lt;/p&gt;
&lt;p&gt;
 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 
&lt;/p&gt;
&lt;ul&gt;
 &lt;li&gt;
 &lt;em&gt;phantom.mat&lt;/em&gt;: This .mat file contains three acoustic media:
 &lt;ul&gt;
 &lt;li&gt;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.&lt;/li&gt;
 &lt;li&gt;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.&lt;/li&gt;
 &lt;li&gt;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.&lt;/li&gt;
 
 &lt;/ul&gt;
 Note: These data are used to generate the corresponding acoustic media for each ring simulation by executing the Matlab script &lt;i&gt;generate_slab.m&lt;/i&gt;. See the description of &lt;i&gt;generate_slab.m&lt;/i&gt; for more details.
&lt;p&gt;
 
 &lt;/li&gt;
 &lt;li&gt;
 &lt;em&gt;data_ring_{i}.h5&lt;/em&gt;: 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. 
 &lt;/li&gt;
&lt;/ul&gt;




&lt;p&gt;&lt;strong&gt;imaging_system:&lt;/strong&gt;&lt;/p&gt;
&lt;ul&gt;
 &lt;li&gt;&lt;em&gt;source300.mat&lt;/em&gt;: Time profile of the excitation pulse. Comprises 300 time samples with a sampling frequency of 25MHz.&lt;/li&gt;
 &lt;li&gt;&lt;em&gt;receiver_locations_1024.mat&lt;/em&gt;: 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].&lt;/li&gt;
 &lt;li&gt;&lt;em&gt;emitter_locations_128.mat&lt;/em&gt;: 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].&lt;/li&gt;
 &lt;li&gt;&lt;em&gt;lens_thickness.mat&lt;/em&gt;: 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.

&lt;/ul&gt;



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

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 &lt;i&gt;i&lt;/i&gt; corresponds to the central z-slice of each computational domain. The positions of each ring-array thin-slab are illustrated in the following figure. 
&lt;br&gt;
&lt;img src="https://dataverse.harvard.edu/api/access/datafile/7351428
" alt="Illustration of thin-slab phantom locations" width="100%" height="15%"&gt;
&lt;br&gt;
This function will generate data files named &lt;i&gt;phantom_ring_{i}.mat&lt;/i&gt;, where i=-1, 0, 1. These correspond to the different ring-array simulation grids used to produce the shared three ring-array measurement data.
&lt;/ul&gt;

&lt;hr&gt;

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