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DigiBreast - A Complex Digital Breast Phantom with Clinically-Derived Tissue Compositions

  • Release date: work-in-progress
  • Created by: Bin Deng <bdeng1 at nmr.mgh.harvard.edu>, Qianqian Fang <fangq at nmr.mgh.harvard.edu>
  • License: The DigiBreast phantom main and source data are in the public domain; the MATLAB scripts are covered under the BSD license. Please refer to the LICENSE_BSD.txt for proper use and redistribution of the contents.

1. Download
2. Introduction
3. What's in the package
3.1. Folder Structure
3.2. DigiBreast Data
3.3. DigiBreast Source Data
3.4. Script
4. Tissue optical properties
5. Footnote
6. Reference

1. Download

Coming soon…

2. Introduction

3. What's in the package

3.1. Folder Structure

The DigiBreast package is comprised of the "data" folder and the "script" folder, together with related documentation. The package folder/file structure is explained below. 

DigiBreast
├── AUTHORS.txt                      # Acknowledgement of contributions
├── README.txt                       # This file
├── data                             # DigiBreast data in MATLAB .mat format
│   └── DigiBreast.mat                 # DigiBreast main data
│   └── DigiBreast_source.mat          # DigiBreast source data
├── script                           # All related MATLAB scripts
│   ├── digibreast_meshrefine.m        # Creating the refined meshes at a given ROI
│   ├── digibreast_savejson.m          # Saving DigiBreast data in JSON and UBJSON
│   ├── digibreast_priors.m            # Creating tissue compositional maps
│   ├── digibreast_lesionprofile.m     # Creating a Gaussian-spherical tumor prior
│   └── digibreast_tablelookup.m       # Utility to lookup the optical properties
└── LICENSE_BSD.txt                  # License file

3.2. DigiBreast Data

DigiBreast.mat is a MAT-file that contains all essential components of the digital breast phantom used in the simulation study as presented in Deng2015 paper, including variables ForwardMesh, ReconMesh, LesionCentroids, and OpticalProperties.

ForwardMesh
a 1x1 structure contains three fields, namely "node","elem",and "glandularity".

  • ForwardMesh.node:
  • ForwardMesh.elem:
  • ForwardMesh.glandularity:
    • ForwardMesh.glandularity.truth:
    • ForwardMesh.glandularity.empirical:
    • ForwardMesh.glandularity.dualgaussian:
    • ForwardMesh.glandularity.thresholdp2:
    • ForwardMesh.glandularity.threshold2:

ReconMesh
a 1x1 structure contains two fields, namely "node" and "elem".
  • ReconMesh.node:
  • ReconMesh.elem:

LesionCentroids
a 1x1 structure with two fields, "adipose" and "fibroglandular", containing the [x,y,z] lesion centroids (in mm) of the two simulated lesion locations (as used in the Deng2015 paper) within either adipose or fibroglandular tissue vicinity.

OpticalProperties

3.3. DigiBreast Source Data

DigiBreast_source.mat is a MAT-file that contains all essential components of the digital breast phantom, including variables Mammogram, Glandularity_Truth, Thickness, and CoordinateMap.

Mammogram
Generate the Gaussian sphere lesion profile at defined centroid.

Glandularity_Truth
Refine the input mesh within a spherical region centered at centroid.

Thickness
Generate tissue compositional priors for the DigiBreast phantom.

CoordinateMap
Export DigiBreast mesh data into JSON and UBJSON files.

3.4. Script

digibreast_lesionprofile.m
Generate the Gaussian sphere lesion profile at defined centroid.

digibreast_meshrefine.m
Refine the input mesh within a spherical region centered at centroid.

digibreast_priors.m
Generate tissue compositional priors for the DigiBreast phantom.

digibreast_savejson.m
Export DigiBreast mesh data into JSON and UBJSON files.

digibreast_tablelookup.m
Search optical properties from the OpticalProperties table by tissue and property names.

4. Tissue optical properties

With the provided fibroglandular tissue volume fraction map, users can freely build your own breast phantom by multiplying the optical properties of fibroglandular, adipose, and cancerous tissues to the volume fractions at each pixel/node.

Tissue type HbO (μM) HbR (μM) μs’ (mm−1)
at 690 nm at 830 nm
Adipose 13.84 4.81 0.851 0.713
Fibroglandular 18.96 6.47 0.925 0.775
Malignant 20.60 6.72 0.957 0.801

5. Footnote

The DigiBreast phantom main and source data is in the public domain. The MATLAB scripts under the "script" sub-folder have a BSD license. See LICENSE_BSD.txt for details.

Some of the scripts included in this package requires the installation of the "

If you use this DigiBreast phantom main or source data in your publication, please cite the phantom version number (currently Version_1) to avoid conflict to any further updates of this mesh. We are also appreciated if you can cite the Deng2015 paper below.

6. Reference

[Deng2015] B. Deng, D. H. Brooks, D. A. Boas, M. Lundqvist, and Q. Fang, "Characterization of structural-prior guided optical tomography using realistic breast models derived from dual-energy x-ray mammography," Biomedical Optics Express 6(7): 2366-79 (2015). doi: 10.1364/BOE.6.002366

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