Showing revision 3.1

DigiBreast

Version 1

  • Release Date: 06/20/2015
  • Created by: Bin Deng <bdeng1 at nmr.mgh.harvard.edu>, Qianqian Fang <fangq at nmr.mgh.harvard.edu>
  • License: This realistic digital breast phantom is released under 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. Data -- DigiBreast.mat
3.3. 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 license, authors and instruction documents.
DigiBreast
├── AUTHORS.txt
├── README.txt
├── data
│   └── DigiBreast.mat
├── script
│   ├── digibreast_lesionprofile.m
│   ├── digibreast_meshrefine.m
│   ├── digibreast_priors.m
│   ├── digibreast_savejson.m
│   └── digibreast_tablelookup.m
└── LICENSE_BSD.txt

3.2. Data -- DigiBreast.mat

DigiBreast.mat is a MAT-file that contains all essential components of the digital breast phantom, 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:

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.

3.3. 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 mesh data is in the public domain.

If you use this mesh in your publication, please cite the mesh version number to avoid conflict to any further updates of this mesh. We are also appreciated if you can cite the papers for iso2mesh or CGAL in your publication.

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

[Fang2009] Q. Fang and D. Boas, “Tetrahedral mesh generation from volumetric binary and gray-scale images,” Proceedings of IEEE International Symposium on Biomedical Imaging 2009, 1142–1145 (2009).

[CGAL2009] L. Rineau, S. Tayeb, and M. Yvinec. 3D Mesh Generation. In CGAL Editorial Board, Ed, CGAL User and Reference Manual. 3.5 edition, 2009.

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