DOI: 10.7910/dvn/cufvke
title: 2D Acoustic Numerical Breast Phantoms and USCT Measurement Data

description: Companion dataset of the manuscript:&lt;br&gt;

Fu Li, Umberto Villa, Seonyeong Park, Mark A. Anastasio. &lt;emph&gt;Three-dimensional stochastic numerical breast phantoms for enabling virtual imaging trials of ultrasound computed tomography&lt;/emph&gt;. Arxiv preprint &lt;a href="https://arxiv.org/abs/2106.02744"&gt;2106.02744&lt;/a&gt; (2021)

&lt;hr&gt;

This dataset includes a collection of 52 two-dimensional slices of numerical breast phantoms (NBPs) and corresponding ultrasound computed tomography (USCT) simulated measurement data. The anatomical structures of these NBPs were obtained by use of tools from the Virtual Imaging Clinical Trial for Regulatory Evaluation (VICTRE) project. More details on the modification and extension of the VICTRE NBPs for use in USCT studies can be found in the accompanying paper. &lt;br&gt;

The NBPs included in this dataset are representative of four ACR BI-RADS breast composition types:
&lt;ul&gt;
&lt;li&gt; &lt;strong&gt;A&lt;/strong&gt;. The breast is almost entirely fatty&lt;/li&gt;
&lt;li&gt; &lt;strong&gt;B&lt;/strong&gt;. There are scattered areas of fibroglandular density&lt;/li&gt;
&lt;li&gt; &lt;strong&gt;C&lt;/strong&gt;. The breasts is heterogeneously dense&lt;/li&gt;
&lt;li&gt; &lt;strong&gt;D&lt;/strong&gt;. The breast is extremely dense&lt;/li&gt;
&lt;/ul&gt;

Each NBP contains 2D maps of tissue labels, speed of sound, acoustic attenuation, density. A low-resolution speed-of-sound map is also provided to reproduce the FWI reconstruction results presented in the accompanying paper.&lt;br&gt;

Corresponding USCT measurement data were simulated by modeling 2D wave propagation in lossy heterogeneous media using a time explicit pseudospectral wave propagation solver. &lt;br&gt;

The dataset consists of three folders:
&lt;ul&gt;
&lt;li&gt; The &lt;b&gt;2d_slices&lt;/b&gt; folder contains the 52 slices extracted from 3D NBPs.&lt;/li&gt;
&lt;li&gt; The &lt;b&gt;measurements&lt;/b&gt; folder contains simulated measurement data corresponding to each slice.&lt;/li&gt;
&lt;li&gt;The &lt;b&gt;imaging_system&lt;/b&gt; folder contains information about the 2D imaging system (excitation source, transducer coordinates)&lt;/li&gt;
&lt;/ul&gt;

In addition, the following helper Matlab scripts are included:
&lt;ul&gt;
&lt;li&gt;&lt;b&gt;read_data.m&lt;/b&gt;: Helper function to load and visualize the excitation source and transducer locations.&lt;/li&gt;
&lt;li&gt;&lt;b&gt;read_waveform_data.m&lt;/b&gt;: Helper function to read the .h5 files containing the measurement data.&lt;/li&gt;
&lt;/ul&gt;
&lt;hr&gt;
Each slice is saved as a binary MATLAB file (&lt;b&gt;.mat&lt;/b&gt;) and contains the following variables
&lt;ul&gt;
&lt;li&gt; &lt;b&gt;label&lt;/b&gt;: tissue label map with [2560,2560] pixels and 0.1mm pixel size. Tissue types are denoted using the following labels: water (0), fat (1), skin (2), glandular (29), ligament (88), lesion (200).&lt;/li&gt;
&lt;li&gt; &lt;b&gt;sos&lt;/b&gt;: speed of sound map (&lt;i&gt;mm/&mu;s&lt;/i&gt;) with [2560,2560] pixels and 0.1 mm pixel size. Data is stored as data type float32.&lt;/li&gt;
&lt;li&gt; &lt;b&gt;aa&lt;/b&gt;: acoustic attenuation map (&lt;i&gt;Np/m/MHz&lt;sup&gt;y&lt;/sup&gt;&lt;/i&gt;) with [2560,2560] pixels and 0.1mm pixel size. Data is stored as data type float32.&lt;/li&gt;
&lt;li&gt; &lt;b&gt;density&lt;/b&gt;: density map (kg/mm&lt;sup&gt;3&lt;/sup&gt;) with [2560,2560] pixels and 0.1 mm pixel size. Data is stored as data type float32.&lt;/li&gt;
&lt;li&gt;&lt;b&gt;sos_ini&lt;/b&gt;: low resolution speed of sound map (&lt;i&gt;mm/&mu;s&lt;/i&gt;) with [1280,1280] pixels and 0.2mm pixel size. Data is stored as data type float32. This is the initial guess used in the speed of sound reconstructions in our paper.&lt;/li&gt;
&lt;li&gt; &lt;b&gt;y&lt;/b&gt;: attenuation exponent used for simulation.&lt;/li&gt;
&lt;li&gt; &lt;b&gt;seed:&lt;/b&gt; phantom id
&lt;li&gt; &lt;b&gt;type&lt;/b&gt;: breast composition type (A-D)&lt;/li&gt;
&lt;/ul&gt;
&lt;hr&gt;
The simulated measurement data is saved in hdf5 format. Measurement data corresponding the &lt;i&gt;i&lt;/i&gt;-th emitting transducer is stored with hdf5 key equal to the transducer index as a two-dimensional array of size [1024,4250]. Here, the rows represent the receiver index, and the columns the time sample. The sampling frequency is 25MHZ. Because of file size limitations, measurement data for each slice has been divided into 8 chunks, containing data from 128 receivers each. 
&lt;hr&gt;
The &lt;b&gt;imaging_system&lt;/b&gt; folder contains information regarding the 2D imaging system.
&lt;ul&gt;
&lt;li&gt;&lt;b&gt;source300.mat&lt;/b&gt; describes the time profile of the exitation pulse. It consists of 300 time samples at a sampling frequency of 25Mhz.&lt;/li&gt;
&lt;li&gt;&lt;b&gt;locations1024.mat&lt;/b&gt; provide the &lt;i&gt;xy&lt;/i&gt; coordinates (&lt;i&gt;mm&lt;/i&gt;)of the location of each transducer Data type is float32. Array size is [2x1024]. &lt;/li&gt;
&lt;/ul&gt;
&lt;hr&gt;
&lt;b&gt; Warning: &lt;/b&gt; This is a very large dataset (~1TB). Please check out our &lt;a href="https://github.com/comp-imaging-sci/dataverse-pyclient"&gt; download script&lt;/a&gt; written in python.
description: Computational resources for the generation of this dataset were granted to the authors by the Blue Waters sustained-petascale computing project, which is supported by the National Science Foundation (awards OCI-0725070 and ACI-1238993) the State of Illinois, and as of December 2019, the National Geospatial-Intelligence Agency. Blue Waters is a joint effort of the University of Illinois at Urbana-Champaign and its National Center for Supercomputing Applications.