DOI: 10.7910/dvn/kbyqq7
title: 3D Acoustic Numerical Breast Phantoms

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

Fu Li, Umberto Villa, Seonyeong Park, Mark A. Anastasio. &lt;em&gt;Three-dimensional stochastic numerical breast phantoms for enabling virtual imaging trials of ultrasound computed tomography&lt;/em&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 three-dimensional numerical breast phantoms (NBPs) for use in ultrasound computed tomography studies. The anatomical structures of these NBPs were obtained by use of tools from the &lt;em&gt;Virtual Imaging Clinical Trial for Regulatory Evaluation (VICTRE)&lt;/em&gt; 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;
&lt;br/&gt;
Four 3D NBPs are included in this dataset, one for each of the 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 3D maps of tissue labels, speed of sound, attenuation,
and density. Those data are saved as Matlab binary files (extension &lt;b&gt;.mat&lt;/b&gt;), which can be easily read using the &lt;b&gt;load&lt;/b&gt; function in MATLAB.&lt;br/&gt;
&lt;br/&gt;
The dataset comprises four sub-directories, one for each NBP. 
The files contained in each sub-directory are described below. Here, &lt;b&gt;{breast_id}&lt;/b&gt; is a 6 digit identifier for the NBP (corresponding to the random seed used to generate the anatomical structures) followed by a single character (denoting the breast composition type).&lt;br/&gt;
&lt;br/&gt;
&lt;ul&gt;
&lt;li&gt; &lt;b&gt;{breast_id}_label.mat:&lt;/b&gt; 3D anatomical structures map with a resolution of 0.1 mm. Each voxel indicates a type of tissue type and is stored as &lt;b&gt;unit8&lt;/b&gt; data type. The tissue types corresponding to each label are: &lt;br/&gt;
&lt;ul&gt;
&lt;li&gt; &lt;b&gt;0&lt;/b&gt;: Water;&lt;/li&gt;
&lt;li&gt; &lt;b&gt;1&lt;/b&gt;: Fat;&lt;/li&gt;
&lt;li&gt; &lt;b&gt;2&lt;/b&gt;: Skin;&lt;/li&gt;
&lt;li&gt; &lt;b&gt;29&lt;/b&gt;:Glandular;&lt;/li&gt;
&lt;li&gt; &lt;b&gt;88&lt;/b&gt;: Ligament;&lt;/li&gt;
&lt;li&gt; &lt;b&gt;200&lt;/b&gt;: Lesion.&lt;/li&gt;
&lt;/ul&gt;


&lt;/li&gt;

&lt;li&gt;&lt;b&gt;{breast_id}_info.mat:&lt;/b&gt; Information about NBP: random seed, number of voxels, voxel size (&lt;i&gt;mm&lt;/i&gt;), and breast type (A-D). &lt;br/&gt;
&lt;/li&gt;

&lt;li&gt;
&lt;b&gt;{breast_id}_sos.mat&lt;/b&gt; 3D speed of sound map (&lt;i&gt;mm/&#x03BC;s&lt;/i&gt;). Data is stored as &lt;b&gt;float32&lt;/b&gt; data type.&lt;br/&gt;
&lt;/li&gt;

&lt;li&gt;
&lt;b&gt;{breast_id}_aa.mat:&lt;/b&gt; 3D acoustic attenuation map (&lt;i&gt;Np/m/MHz&lt;sup&gt;y&lt;/sup&gt;&lt;/i&gt;). Data is stored as &lt;b&gt;float32&lt;/b&gt; data type.&lt;br/&gt;
&lt;/li&gt;

&lt;li&gt;
&lt;b&gt;{breast_id}_density.mat:&lt;/b&gt; 3D density map (&lt;i&gt;kg/mm&lt;sup&gt;3&lt;/sup&gt;&lt;/i&gt;). Data is stored as &lt;b&gt;float32&lt;/b&gt; data type.&lt;br/&gt;
&lt;/li&gt;
&lt;/ul&gt;
&lt;br/&gt;

An utility Matlab function (&lt;b&gt;gen_vtk.m&lt;/b&gt;) is also provided to convert our NBPs to vtk format for 3D visualization in Paraview.&lt;br/&gt;

&lt;!--
The size of four phantoms are:
&lt;br/&gt; 
544285982A: &lt;br/&gt; 
Nz = 784; Nx = 1040; Ny = 1090; [0.1mmx0.1mmx0.1mm]&lt;br/&gt; 
&lt;br/&gt; 
533476231B: &lt;br/&gt; 
Nz = 1056; Nx = 1108; Ny = 1166; [0.1mmx0.1mmx0.1mm]&lt;br/&gt; 
&lt;br/&gt; 
723077956C: &lt;br/&gt; 
Nz = 862; Nx = 1078; Ny = 1158; [0.1mmx0.1mmx0.1mm]&lt;br/&gt; 
&lt;br/&gt; 
715303298D: &lt;br/&gt; 
Nz = 690; Nx = 980; Ny = 1066; [0.1mmx0.1mmx0.1mm]&lt;br/&gt;
--&gt;

&lt;hr&gt;

&lt;b&gt; Warning: &lt;/b&gt; This is a large dataset. Please check out our &lt;a href="https://github.com/comp-imaging-sci/dataverse-pyclient"&gt; download script&lt;/a&gt; written in python.