Segmentation propagation using a 3D embryo atlas for high-throughput MRI phenotyping: Comparison and validation with manual segmentation

Magnetic Resonance in Medicine

Volumn 69, Issue 3, 2013, Pages 877-883

  Norris, Francesca C ^a   Modat, Marc ^a   Cleary, Jon O ^a   Price, Anthony N ^a   McCue, Karen ^b   Scambler, Peter J ^b   Ourselin, Sebastien ^a,c   Lythgoe, Mark F ^a  

^a UNIVERSITY COLLEGE LONDON   (United Kingdom)

^b UNIVERSITY COLLEGE LONDON   (United Kingdom)

^c NATIONAL HOSPITAL FOR NEUROLOGY AND NEUROSURGERY   (United Kingdom)

Author keywords

automated segmentation; magnetic resonance microscopy; mouse embryo atlas; mouse embryo phenotyping

Indexed keywords

AUTOMATION; MAGNETIC RESONANCE; MAGNETIC RESONANCE IMAGING; VOLUMETRIC ANALYSIS;

AUTOMATED SEGMENTATION; EMERGING APPLICATIONS; HIGH THROUGHPUT SCREENING; MAGNETIC RESONANCE MICROSCOPY; MORPHOMETRIC ANALYSIS; MOUSE EMBRYOS; PHENOTYPING; SEGMENTATION PROPAGATION;

DATA FLOW ANALYSIS;

ACCURACY; ANIMAL EXPERIMENT; ARTICLE; BRAIN SIZE; CONTROLLED STUDY; EMBRYO; EMBRYO SEGMENTATION; HIGH THROUGHPUT SCREENING; KIDNEY SIZE; MORPHOMETRICS; MOUSE; NONHUMAN; NUCLEAR MAGNETIC RESONANCE IMAGING; PHENOTYPE; SIGNAL NOISE RATIO; THREE DIMENSIONAL IMAGING;

EID: 85027945051     PISSN: 07403194     EISSN: 15222594     Source Type: Journal    
DOI: 10.1002/mrm.24306     Document Type: Article

References (42)

1. Mouse Genome Sequencing Consortium. Initial sequencing and comparative analysis of the mouse genome. Nature 2002; 420: 520-562.
2. Capecchi MR,. Generating mice with targeted mutations. Nat Med 2001; 7: 1086-1090.
3. International Mouse Knockout Consortium., Collins FS, Rossant J, Wurst W,. A mouse for all reasons. Cell 2007; 128: 9-13.
4. Holdsworth DW, Thornton MM,. Micro-CT in small animal and specimen imaging. Trends Biotechnol 2002; 20: 34-39.
5. Johnson JT, Hansen MS, Wu I, Healy LJ, Johnson CR, Jones GM, Capecchi MR, Keller C,. Virtual histology of transgenic mouse embryos for high-throughput phenotyping. PLoS Genet 2006; 2: e61.
6. Sharpe J, Ahlgren U, Perry P, Hill B, Ross A, Hecksher-Sorensen J, Baldock R, Davidson D,. Optical projection tomography as a tool for 3D microscopy and gene expression studies. Science 2002; 296: 541-545.
7. Weninger WJ, Mohun T,. Phenotyping transgenic embryos: a rapid 3-D screening method based on episcopic fluorescence image capturing. Nat Genet 2002; 30: 59-65.
8. Schneider JE, Bhattacharya S,. Making the mouse embryo transparent: identifying developmental malformations using magnetic resonance imaging. Birth Defects Res C Embryo Today 2004; 72: 241-249.
9. Schneider JE, Bose J, Bamforth SD, Gruber AD, Broadbent C, Clarke K, Neubauer S, Lengeling A, Bhattacharya S,. Identification of cardiac malformations in mice lacking Ptdsr using a novel high-throughput magnetic resonance imaging technique. Biomed Chromatogr Dev Biol 2004; 4: 16.
10. Smith BR, Johnson GA, Groman EV, Linney E,. Magnetic resonance microscopy of mouse embryos. Proc Natl Acad Sci USA 1994; 91: 3530-3533.
11. Petiet A, Johnson GA,. Active staining of mouse embryos for magnetic resonance microscopy. Methods Mol Biol 2010; 611: 141-149.
12. Zhang X, Schneider JE, Portnoy S, Bhattacharya S, Henkelman RM,. Comparative SNR for high-throughput mouse embryo MR microscopy. Magn Reson Med 2010; 63: 1703-1707.
13. Parnell SE, O'Leary-Moore SK, Godin EA, Dehart DB, Johnson BW, Allan Johnson G, Styner MA, Sulik KK,. Magnetic resonance microscopy defines ethanol-induced brain abnormalities in prenatal mice: effects of acute insult on gestational day 8. Alcohol Clin Exp Res 2009; 33: 1001-1011.
14. Schneider JE, Bamforth SD, Grieve SM, Clarke K, Bhattacharya S, Neubauer S,. High-resolution, high-throughput magnetic paragraph sign resonance imaging of mouse embryonic paragraph sign anatomy using a fast gradient-echo sequence. MAGMA 2003; 16: 43-51.
15. Dorr AE, Lerch JP, Spring S, Kabani N, Henkelman RM,. High resolution three-dimensional brain atlas using an average magnetic resonance image of 40 adult C57Bl/6J mice. Neuroimage 2008; 42: 60-69.
16. Johnson GA, Badea A, Brandenburg J, Cofer G, Fubara B, Liu S, Nissanov J,. Waxholm space: an image-based reference for coordinating mouse brain research. Neuroimage 2010; 53: 365-372.
17. Ma Y, Hof PR, Grant SC, Blackband SJ, Bennett R, Slatest L, McGuigan MD, Benveniste H,. A three-dimensional digital atlas database of the adult C57Bl/6J mouse brain by magnetic resonance microscopy. Neuroscience 2005; 135: 1203-1215.
18. Chen XJ, Kovacevic N, Lobaugh NJ, Sled JG, Henkelman RM, Henderson JT,. Neuroanatomical differences between mouse strains as shown by high-resolution 3D MRI. Neuroimage 2006; 29: 99-105.
19. Ali AA, Dale AM, Badea A, Johnson GA,. Automated segmentation of neuroanatomical structures in multispectral MR microscopy of the mouse brain. Neuroimage 2005; 27: 425-435.
20. Sharief AA, Badea A, Dale AM, Johnson GA,. Automated segmentation of the actively stained mouse brain using multi-spectral MR microscopy. Neuroimage 2008; 39: 136-145.
21. Lerch JP, Carroll JB, Spring S, Bertram LN, Schwab C, Hayden MR, Henkelman RM,. Automated deformation analysis in the YAC128 Huntington disease mouse model. Neuroimage 2008; 39: 32-39.
22. Cleary JO, Modat M, Norris FC, Price AN, Jayakody SA, Martinez-Barbera JP, Greene ND, Hawkes DJ, Ordidge RJ, Scambler PJ, Ourselin S, Lythgoe MF,. Magnetic resonance virtual histology for embryos: 3D atlases for automated high-throughput phenotyping. Neuroimage 2010; 54: 769-778.
23. Bock NA, Kovacevic N, Lipina TV, Roder JC, Ackerman SL, Henkelman RM,. In vivo magnetic resonance imaging and semiautomated image analysis extend the brain phenotype for cdf/cdf mice. J Neurosci 2006; 26: 4455-4459.
24. Ellegood J, Pacey LK, Hampson DR, Lerch JP, Henkelman RM,. Anatomical phenotyping in a mouse model of fragile X syndrome with magnetic resonance imaging. Neuroimage 2010; 53: 1023-1029.
25. Dhenain M, Ruffins SW, Jacobs RE,. Three-dimensional digital mouse atlas using high-resolution MRI. Dev Biol 2001; 232: 458-470.
26. Petiet AE, Kaufman MH, Goddeeris MM, Brandenburg J, Elmore SA, Johnson GA,. High-resolution magnetic resonance histology of the embryonic and neonatal mouse: a 4D atlas and morphologic database. Proc Natl Acad Sci USA 2008; 105: 12331-12336.
27. Bondiau PY, Malandain G, Chanalet S, Marcy PY, Habrand JL, Fauchon F, Paquis P, Courdi A, Commowick O, Rutten I, Ayache N,. Atlas-based automatic segmentation of MR images: validation study on the brainstem in radiotherapy context. Int J Radiat Oncol Biol Phys 2005; 61: 289-298.
28. Chupin M, Mukuna-Bantumbakulu AR, Hasboun D, Bardinet E, Baillet S, Kinkingnehun S, Lemieux L, Dubois B, Garnero L,. Anatomically constrained region deformation for the automated segmentation of the hippocampus and the amygdala: method and validation on controls and patients with Alzheimer's disease. Neuroimage 2007; 34: 996-1019.
29. Jurck V, Fripp J, Engstrom C, Walker D, Salvado O, Ourselin S, Crozier S,. Atlas based automated segmentation of the quadrates lumborum muscle using non-rigid registration on magnetic resonance images of the thoracolumbar region. 5th IEEE International Symposium on Biomedical Imaging-From Nano to Macro, Paris, France, 2008; 113-116.
30. Molyneux P, Tofts P, Fletcher A, Gunn B, Robinson P, Gallagher H, Moseley I, Barker G, Miller D,. Precision and reliability for measurement of change in MRI lesion volume in multiple sclerosis: a comparison of two computer assisted techniques. J Neurol Neurosurg Psychiatry. 1998; 65: 42-47.
31. Kaus MR, Warfield SK, Nabavi A, Black PM, Jolesz FA, Kikinis R,. Automated segmentation of MR images of brain tumors. Radiology 2001; 218: 586-591.
32. Heijman E, Aben JP, Penners C, Niessen P, Guillaume R, van Eys G, Nicolay K, Strijkers GJ,. Evaluation of manual and automatic segmentation of the mouse heart from CINE MR images. J Magn Reson Imaging 2008; 27: 86-93.
33. Riegler J, Cheung KK, Man YF, Cleary JO, Price AN, Lythgoe MF,. Comparison of segmentation methods for MRI measurement of cardiac function in rats. J Magn Reson Imaging 2010; 32: 869-877.
34. Cleary JO, Price AN, Thomas DL, Scambler PJ, Kyriakopoulou V, McCue K, Schneider JE, Ordidge RJ, Lythgoe MF,. Cardiac phenotyping in ex vivo murine embryos using microMRI. NMR Biomed 2009; 22: 857-866.
35. Ourselin S, Roche A, Subsol G, Pennec X, Ayache N,. Reconstructing a 3D structure from serial histological sections. Image Vis Comput 2001; 19: 25-31.
36. Modat M, Ridgway GR, Taylor ZA, Lehmann M, Barnes J, Hawkes DJ, Fox NC, Ourselin S,. Fast free-form deformation using graphics processing units. Comput Methods Programs Biomed 2010; 98: 278-284.
37. Bland JM, Altman DG,. Statistical methods for assessing agreement between two methods of clinical measurement. Lancet 1986; 1: 307-310.
38. Baghdadi L, Bishop J, Henkelman M, Sled JG,. Automated measurement of kidney volumes for MRI based whole mouse screening. In Proceedings of the 13th Annual Meeting of ISMRM, Miami Beach, Florida, USA, 2005. p. 1904.
39. Hadjidemetriou S, Reichardt W, Hennig J, Buechert M, von Elverfeldt D,. Volumetric analysis of MRI data monitoring the treatment of polycystic kidney disease in a mouse model. MAGMA 2011; 24: 109-119.
40. Mazziotta JC, Toga AW, Evans A, Fox P, Lancaster J,. A probabilistic atlas of the human brain: theory and rationale for its development. The International Consortium for Brain Mapping (ICBM). Neuroimage 1995; 2: 89-101.
41. Huang S, Liu C, Dai G, Kim YR, Rosen BR,. Manipulation of tissue contrast using contrast agents for enhanced MR microscopy in ex vivo mouse brain. Neuroimage 2009; 46: 589-599.
42. Zamayadi M, Baghdadi L, Lerch JP, Bhattacharya S, Schneider JE, Henkelman RM, Sled JG,. Mouse embryonic phenotyping by morphometric analysis of MR images. Physiol Genomics 2010; 42A: 89-95.