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