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Proceedings Paper

Computerized segmentation algorithm with personalized atlases of murine MRIs in a SV40 large T-antigen mouse mammary cancer model
Author(s): Adam R. Sibley; Erica Markiewicz; Devkumar Mustafi; Xiaobing Fan; Suzanne Conzen; Greg Karczmar; Maryellen L. Giger
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Paper Abstract

Quantities of MRI data, much larger than can be objectively and efficiently analyzed manually, are routinely generated in preclinical research. We aim to develop an automated image segmentation and registration pipeline to aid in analysis of image data from our high-throughput 9.4 Tesla small animal MRI imaging center. T2-weighted, fat-suppressed MRIs were acquired over 4 life-cycle time-points [up to 12 to 18 weeks] of twelve C3(1) SV40 Large T-antigen mice for a total of 46 T2-weighted MRI volumes; each with a matrix size of 192 x 256, 62 slices, in plane resolution 0.1 mm, and slice thickness 0.5 mm. These image sets were acquired with the goal of tracking and quantifying progression of mammary intraepithelial neoplasia (MIN) to invasive cancer in mice, believed to be similar to ductal carcinoma in situ (DCIS) in humans. Our segmentation algorithm takes 2D seed-points drawn by the user at the center of the 4 co-registered volumes associated with each mouse. The level set then evolves in 3D from these 2D seeds. The contour evolution incorporates texture information, edge information, and a statistical shape model in a two-step process. Volumetric DICE coefficients comparing the automatic with manual segmentations were computed and ranged between 0.75 and 0.58 for averages over the 4 life-cycle time points of the mice. Incorporation of these personalized atlases with intra and inter mouse registration is expected to enable locally and globally tracking of the morphological and textural changes in the mammary tissue and associated lesions of these mice.

Paper Details

Date Published: 29 March 2016
PDF: 8 pages
Proc. SPIE 9788, Medical Imaging 2016: Biomedical Applications in Molecular, Structural, and Functional Imaging, 97882M (29 March 2016); doi: 10.1117/12.2217425
Show Author Affiliations
Adam R. Sibley, The Univ. of Chicago (United States)
Erica Markiewicz, The Univ. of Chicago (United States)
Devkumar Mustafi, The Univ. of Chicago (United States)
Xiaobing Fan, The Univ. of Chicago (United States)
Suzanne Conzen, The Univ. of Chicago (United States)
Greg Karczmar, The Univ. of Chicago (United States)
Maryellen L. Giger, The Univ. of Chicago (United States)


Published in SPIE Proceedings Vol. 9788:
Medical Imaging 2016: Biomedical Applications in Molecular, Structural, and Functional Imaging
Barjor Gimi; Andrzej Krol, Editor(s)

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