Multi-atlas segmentation propagation has evolved quickly in recent years, becoming a state-of-the-art methodology for automatic parcellation of structural images. However, few studies have applied these methods to preclinical research. In this study, we present a fully automatic framework for mouse brain MRI structural parcellation using multi-atlas segmentation propagation. The framework adopts the similarity and truth estimation for propagated segmentations (STEPS) algorithm, which utilises a locally normalised cross correlation similarity metric for atlas selection and an extended simultaneous truth and performance level estimation (STAPLE) framework for multi-label fusion. The segmentation accuracy of the multi-atlas framework was evaluated using publicly available mouse brain atlas databases with pre-segmented manually labelled anatomical structures as the gold standard, and optimised parameters were obtained for the STEPS algorithm in the label fusion to achieve the best segmentation accuracy. We showed that our multi-atlas framework resulted in significantly higher segmentation accuracy compared to single-atlas based segmentation, as well as to the original STAPLE framework.
机构:
Univ Washington, Natl Primate Res Ctr, Seattle, WA 98195 USA
Univ Washington, Dept Psychiat & Behav Sci, Seattle, WA 98195 USAUniv Washington, Natl Primate Res Ctr, Seattle, WA 98195 USA
Bowden, Douglas M.
;
Johnson, G. Allan
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机构:
Duke Univ, Med Ctr, Duke Ctr In Vivo Microscopy, Durham, NC 27710 USAUniv Washington, Natl Primate Res Ctr, Seattle, WA 98195 USA
Johnson, G. Allan
;
Zaborsky, Laszlo
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h-index: 0
机构:
Rutgers State Univ, Ctr Mol & Behav Neurosci, Newark, NJ 07102 USAUniv Washington, Natl Primate Res Ctr, Seattle, WA 98195 USA
Zaborsky, Laszlo
;
Green, William D. K.
论文数: 0引用数: 0
h-index: 0
机构:
Univ Vienna, Fac Life Sci, A-1091 Vienna, AustriaUniv Washington, Natl Primate Res Ctr, Seattle, WA 98195 USA
Green, William D. K.
;
Moore, Eider
论文数: 0引用数: 0
h-index: 0
机构:Univ Washington, Natl Primate Res Ctr, Seattle, WA 98195 USA
Moore, Eider
;
Badea, Alexandra
论文数: 0引用数: 0
h-index: 0
机构:
Duke Univ, Med Ctr, Duke Ctr In Vivo Microscopy, Durham, NC 27710 USAUniv Washington, Natl Primate Res Ctr, Seattle, WA 98195 USA
Badea, Alexandra
;
Dubach, Mark F.
论文数: 0引用数: 0
h-index: 0
机构:
Univ Washington, Natl Primate Res Ctr, Seattle, WA 98195 USA
Univ Washington, Dept Psychiat & Behav Sci, Seattle, WA 98195 USAUniv Washington, Natl Primate Res Ctr, Seattle, WA 98195 USA
Dubach, Mark F.
;
Bookstein, Fred L.
论文数: 0引用数: 0
h-index: 0
机构:
Univ Vienna, Fac Life Sci, A-1091 Vienna, Austria
Univ Washington, Dept Stat, Seattle, WA 98195 USAUniv Washington, Natl Primate Res Ctr, Seattle, WA 98195 USA
机构:
UCL, Ctr Adv Biomed Imaging, Dept Med, London WC1E 6DD, England
UCL, UCL Inst Child Hlth, London WC1E 6DD, EnglandUCL, Ctr Adv Biomed Imaging, Dept Med, London WC1E 6DD, England
Cleary, Jon O.
;
Modat, Marc
论文数: 0引用数: 0
h-index: 0
机构:
UCL, Dept Med Phys & Bioengn, Ctr Med Image Comp, London WC1E 6BT, England
UCL, Dept Comp Sci, Ctr Med Image Comp, London WC1E 6BT, EnglandUCL, Ctr Adv Biomed Imaging, Dept Med, London WC1E 6DD, England
Modat, Marc
;
Norris, Francesca C.
论文数: 0引用数: 0
h-index: 0
机构:
UCL, Ctr Adv Biomed Imaging, Dept Med, London WC1E 6DD, England
UCL, UCL Inst Child Hlth, London WC1E 6DD, England
UCL, Ctr Math & Phys Life Sci & Expt Biol CoMPLEX, London WC1E 6BT, EnglandUCL, Ctr Adv Biomed Imaging, Dept Med, London WC1E 6DD, England
Norris, Francesca C.
;
Price, Anthony N.
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h-index: 0
机构:
UCL, Ctr Adv Biomed Imaging, Dept Med, London WC1E 6DD, England
UCL, UCL Inst Child Hlth, London WC1E 6DD, EnglandUCL, Ctr Adv Biomed Imaging, Dept Med, London WC1E 6DD, England
Price, Anthony N.
;
Jayakody, Sujatha A.
论文数: 0引用数: 0
h-index: 0
机构:
UCL, UCL Inst Child Health, Neural Dev Unit, London WC1N 1EH, EnglandUCL, Ctr Adv Biomed Imaging, Dept Med, London WC1E 6DD, England
Jayakody, Sujatha A.
;
Martinez-Barbera, Juan Pedro
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h-index: 0
机构:
UCL, UCL Inst Child Health, Neural Dev Unit, London WC1N 1EH, EnglandUCL, Ctr Adv Biomed Imaging, Dept Med, London WC1E 6DD, England
Martinez-Barbera, Juan Pedro
;
Greene, Nicholas D. E.
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h-index: 0
机构:
UCL, UCL Inst Child Health, Neural Dev Unit, London WC1N 1EH, EnglandUCL, Ctr Adv Biomed Imaging, Dept Med, London WC1E 6DD, England
Greene, Nicholas D. E.
;
Hawkes, David J.
论文数: 0引用数: 0
h-index: 0
机构:
UCL, Dept Med Phys & Bioengn, Ctr Med Image Comp, London WC1E 6BT, England
UCL, Dept Comp Sci, Ctr Med Image Comp, London WC1E 6BT, EnglandUCL, Ctr Adv Biomed Imaging, Dept Med, London WC1E 6DD, England
Hawkes, David J.
;
Ordidge, Roger J.
论文数: 0引用数: 0
h-index: 0
机构:
UCL, Wellcome Trust Adv MRI Grp, London WC1N 3BG, EnglandUCL, Ctr Adv Biomed Imaging, Dept Med, London WC1E 6DD, England
Ordidge, Roger J.
;
Scambler, Peter J.
论文数: 0引用数: 0
h-index: 0
机构:
UCL, UCL Inst Child Hlth, Mol Med Unit, London WC1N 1EH, EnglandUCL, Ctr Adv Biomed Imaging, Dept Med, London WC1E 6DD, England
Scambler, Peter J.
;
Ourselin, Sebastien
论文数: 0引用数: 0
h-index: 0
机构:
UCL, Dept Med Phys & Bioengn, Ctr Med Image Comp, London WC1E 6BT, England
UCL, Dept Comp Sci, Ctr Med Image Comp, London WC1E 6BT, England
Natl Hosp Neurol & Neurosurg, Dementia Res Ctr, London WC1N 3BG, EnglandUCL, Ctr Adv Biomed Imaging, Dept Med, London WC1E 6DD, England
Ourselin, Sebastien
;
Lythgoe, Mark F.
论文数: 0引用数: 0
h-index: 0
机构:
UCL, Ctr Adv Biomed Imaging, Dept Med, London WC1E 6DD, England
UCL, UCL Inst Child Hlth, London WC1E 6DD, EnglandUCL, Ctr Adv Biomed Imaging, Dept Med, London WC1E 6DD, England
机构:
Univ Washington, Natl Primate Res Ctr, Seattle, WA 98195 USA
Univ Washington, Dept Psychiat & Behav Sci, Seattle, WA 98195 USAUniv Washington, Natl Primate Res Ctr, Seattle, WA 98195 USA
Bowden, Douglas M.
;
Johnson, G. Allan
论文数: 0引用数: 0
h-index: 0
机构:
Duke Univ, Med Ctr, Duke Ctr In Vivo Microscopy, Durham, NC 27710 USAUniv Washington, Natl Primate Res Ctr, Seattle, WA 98195 USA
Johnson, G. Allan
;
Zaborsky, Laszlo
论文数: 0引用数: 0
h-index: 0
机构:
Rutgers State Univ, Ctr Mol & Behav Neurosci, Newark, NJ 07102 USAUniv Washington, Natl Primate Res Ctr, Seattle, WA 98195 USA
Zaborsky, Laszlo
;
Green, William D. K.
论文数: 0引用数: 0
h-index: 0
机构:
Univ Vienna, Fac Life Sci, A-1091 Vienna, AustriaUniv Washington, Natl Primate Res Ctr, Seattle, WA 98195 USA
Green, William D. K.
;
Moore, Eider
论文数: 0引用数: 0
h-index: 0
机构:Univ Washington, Natl Primate Res Ctr, Seattle, WA 98195 USA
Moore, Eider
;
Badea, Alexandra
论文数: 0引用数: 0
h-index: 0
机构:
Duke Univ, Med Ctr, Duke Ctr In Vivo Microscopy, Durham, NC 27710 USAUniv Washington, Natl Primate Res Ctr, Seattle, WA 98195 USA
Badea, Alexandra
;
Dubach, Mark F.
论文数: 0引用数: 0
h-index: 0
机构:
Univ Washington, Natl Primate Res Ctr, Seattle, WA 98195 USA
Univ Washington, Dept Psychiat & Behav Sci, Seattle, WA 98195 USAUniv Washington, Natl Primate Res Ctr, Seattle, WA 98195 USA
Dubach, Mark F.
;
Bookstein, Fred L.
论文数: 0引用数: 0
h-index: 0
机构:
Univ Vienna, Fac Life Sci, A-1091 Vienna, Austria
Univ Washington, Dept Stat, Seattle, WA 98195 USAUniv Washington, Natl Primate Res Ctr, Seattle, WA 98195 USA
机构:
UCL, Ctr Adv Biomed Imaging, Dept Med, London WC1E 6DD, England
UCL, UCL Inst Child Hlth, London WC1E 6DD, EnglandUCL, Ctr Adv Biomed Imaging, Dept Med, London WC1E 6DD, England
Cleary, Jon O.
;
Modat, Marc
论文数: 0引用数: 0
h-index: 0
机构:
UCL, Dept Med Phys & Bioengn, Ctr Med Image Comp, London WC1E 6BT, England
UCL, Dept Comp Sci, Ctr Med Image Comp, London WC1E 6BT, EnglandUCL, Ctr Adv Biomed Imaging, Dept Med, London WC1E 6DD, England
Modat, Marc
;
Norris, Francesca C.
论文数: 0引用数: 0
h-index: 0
机构:
UCL, Ctr Adv Biomed Imaging, Dept Med, London WC1E 6DD, England
UCL, UCL Inst Child Hlth, London WC1E 6DD, England
UCL, Ctr Math & Phys Life Sci & Expt Biol CoMPLEX, London WC1E 6BT, EnglandUCL, Ctr Adv Biomed Imaging, Dept Med, London WC1E 6DD, England
Norris, Francesca C.
;
Price, Anthony N.
论文数: 0引用数: 0
h-index: 0
机构:
UCL, Ctr Adv Biomed Imaging, Dept Med, London WC1E 6DD, England
UCL, UCL Inst Child Hlth, London WC1E 6DD, EnglandUCL, Ctr Adv Biomed Imaging, Dept Med, London WC1E 6DD, England
Price, Anthony N.
;
Jayakody, Sujatha A.
论文数: 0引用数: 0
h-index: 0
机构:
UCL, UCL Inst Child Health, Neural Dev Unit, London WC1N 1EH, EnglandUCL, Ctr Adv Biomed Imaging, Dept Med, London WC1E 6DD, England
Jayakody, Sujatha A.
;
Martinez-Barbera, Juan Pedro
论文数: 0引用数: 0
h-index: 0
机构:
UCL, UCL Inst Child Health, Neural Dev Unit, London WC1N 1EH, EnglandUCL, Ctr Adv Biomed Imaging, Dept Med, London WC1E 6DD, England
Martinez-Barbera, Juan Pedro
;
Greene, Nicholas D. E.
论文数: 0引用数: 0
h-index: 0
机构:
UCL, UCL Inst Child Health, Neural Dev Unit, London WC1N 1EH, EnglandUCL, Ctr Adv Biomed Imaging, Dept Med, London WC1E 6DD, England
Greene, Nicholas D. E.
;
Hawkes, David J.
论文数: 0引用数: 0
h-index: 0
机构:
UCL, Dept Med Phys & Bioengn, Ctr Med Image Comp, London WC1E 6BT, England
UCL, Dept Comp Sci, Ctr Med Image Comp, London WC1E 6BT, EnglandUCL, Ctr Adv Biomed Imaging, Dept Med, London WC1E 6DD, England
Hawkes, David J.
;
Ordidge, Roger J.
论文数: 0引用数: 0
h-index: 0
机构:
UCL, Wellcome Trust Adv MRI Grp, London WC1N 3BG, EnglandUCL, Ctr Adv Biomed Imaging, Dept Med, London WC1E 6DD, England
Ordidge, Roger J.
;
Scambler, Peter J.
论文数: 0引用数: 0
h-index: 0
机构:
UCL, UCL Inst Child Hlth, Mol Med Unit, London WC1N 1EH, EnglandUCL, Ctr Adv Biomed Imaging, Dept Med, London WC1E 6DD, England
Scambler, Peter J.
;
Ourselin, Sebastien
论文数: 0引用数: 0
h-index: 0
机构:
UCL, Dept Med Phys & Bioengn, Ctr Med Image Comp, London WC1E 6BT, England
UCL, Dept Comp Sci, Ctr Med Image Comp, London WC1E 6BT, England
Natl Hosp Neurol & Neurosurg, Dementia Res Ctr, London WC1N 3BG, EnglandUCL, Ctr Adv Biomed Imaging, Dept Med, London WC1E 6DD, England
Ourselin, Sebastien
;
Lythgoe, Mark F.
论文数: 0引用数: 0
h-index: 0
机构:
UCL, Ctr Adv Biomed Imaging, Dept Med, London WC1E 6DD, England
UCL, UCL Inst Child Hlth, London WC1E 6DD, EnglandUCL, Ctr Adv Biomed Imaging, Dept Med, London WC1E 6DD, England