High-throughput morphologic phenotyping of the mouse brain with magnetic resonance histology

NeuroImage

Volumn 37, Issue 1, 2007, Pages 82-89

  Johnson, G Allan ^a   Ali Sharief, Anjum ^a   Badea, Alexandra ^a   Brandenburg, Jeffrey ^a   Cofer, Gary ^a   Fubara, Boma ^a   Gewalt, Sally ^a   Hedlund, Laurence W ^a   Upchurch, Lucy ^a  

^a DUKE UNIVERSITY MEDICAL CENTER   (United States)

Author keywords

Autosegmentation; Brain; Magnetic resonance histology; Mouse; MR

Indexed keywords

ALGORITHM; ANIMAL TISSUE; ARTICLE; BRAIN; DATA BASE; HISTOLOGY; IMAGE PROCESSING; IMAGE RECONSTRUCTION; KNOCKOUT MOUSE; MORPHOLOGY; MOUSE; NEUROANATOMY; NONHUMAN; NUCLEAR MAGNETIC RESONANCE IMAGING; PHENOTYPE; PRIORITY JOURNAL; STANDARD; STRAIN DIFFERENCE; TISSUE FIXATION;

ANIMALS; BRAIN; DATABASES; DOMINANCE, CEREBRAL; IMAGE ENHANCEMENT; IMAGE PROCESSING, COMPUTER-ASSISTED; IMAGING, THREE-DIMENSIONAL; MAGNETIC RESONANCE IMAGING; MICE; MICE, INBRED C57BL; PHENOTYPE; SENSITIVITY AND SPECIFICITY; SOFTWARE;

EID: 34447577998     PISSN: 10538119     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.neuroimage.2007.05.013     Document Type: Article

References (25)

1. Ali A.A., Dale A.M., Badea A., and Johnson G.A. Automated segmentation of neuroanatomical structures in multispectral MR microscopy of the mouse brain. NeuroImage 27 (2005) 425-435
2. Badea A., Nicholls P.J., Johnson G.A., and Wetsel W.C. Neuroanatomical phenotypes in the reeler mouse. NeuroImage 34 (2007) 1363-1374
3. Badea A., Ali Sharief A.A., Dale A.M., and Johnson G.A. Morphometric analysis of the C57BL/6J mouse brain. NeuroImage (2007)
4. Benveniste H., Kim K., Zhang L., and Johnson G.A. Magnetic resonance microscopy of the C57BL/6 mouse brain. NeuroImage 11 (2000) 601-611
5. Callaghan P.T. Principles of Nuclear Magnetic Resonance Microscopy. 1st ed. (1991), Oxford Univ. Press, New York
6. Conturo T.E., and Smith G.D. Signal-to-noise in phase angle reconstruction: dynamic range extension using phase reference offsets. Magn. Reson. Med. 15 (1990) 420-437
7. Haacke E.M., Brown R.W., Thompson M.R., and Venkatesan R. Magnetic Resonance Imaging: Physical Principles and Sequence Design (1999), Wiley-Liss, New York, NY
8. Hurlston S.E., Cofer G.P., and Johnson G.A. Optimized receiver coils for increased SNR in MR microscopy. Int. J. Imaging Syst. Technol. 8 (1997) 277-284
9. Johnson G., Hutchison J.M.S., Redpath T.W., and Eastwood L.M. Improvements in performance time for simultaneous three-dimensional NMR imaging. J. Magn. Reson. 54 (1983) 374-384
10. Johnson G.A., Benveniste H., Black R.D., Hedlund L.W., Maronpot R.R., and Smith B.R. Histology by magnetic resonance microscopy. Magn. Reson. Q 9 (1993) 1-30
11. Johnson G.A., Cofer G.P., Fubara B., Gewalt S.L., Hedlund L.W., and Maronpot R.R. Magnetic resonance histology for morphologic phenotyping. JMRI 16 (2002) 423-429
12. Johnson G.A., Cofer G.P., Gewalt S.L., and Hedlund L.W. Morphologic phenotyping with magnetic resonance microscopy: the visible mouse. Radiology 222 (2002) 789-793
13. Kovacevic N., Henderson J.T., Chan E., Lifshitz N., Bishop J., Evans A.C., Henkelman R.M., and Chen X.J. A three-dimensional MRI atlas of the mouse brain with estimates of the average and variability. Cereb. Cortex 15 (2005) 639-645
14. Ma Y., Hof P.R., Grant S.C., Blackband S.J., Bennett R., Slatest L., McGuigan M.D., and Benveniste H. A three-dimensional digital atlas database of the adult C57BL/6J mouse brain by magnetic resonance microscopy. Neuroscience 135 (2005) 1203-1215
15. MacFall J.R., Pelc N.J., and Vavrek R.M. Correction of spatially dependent phase shifts for partial Fourier imaging. Magn. Reson. Imaging 6 (1988) 143-155
16. MacKenzie-Graham A., Lee E.F., Dinov I.D., Bota M., Shattuck D.W., Ruffins S., Yuan H., Konstantinidis F., Pitiot A., Ding Y., Hu G., Jacobs R.E., and Toga A.W. A multimodal, multidimensional atlas of the C57BL/6J mouse brain. J. Anat. 204 (2004) 93-102
17. Martone M.E., Gupta A., and Ellisman M.H. E-neuroscience: challenges and triumphs in integrating distributed data from molecules to brains. Nat. Neurosci. 7 (2004) 467-472
18. Maudsley A.A. Dynamic range improvement in NMR imaging using phase scrambling. J. Magn. Reson. 76 (1987) 287-305
19. Paxinos G., and Franklin K.B.J. The Mouse Brain in Stereotaxic Coordinates. 2nd ed. (2001), Academic Press, New York
20. Sharief A.A., and Johnson G.A. Enhanced T2 contrast for MR histology of the mouse brain. Magn. Reson. Med. 56 (2006) 717-725
21. Stenger V.A., Noll D.C., and Boada F.E. Partial Fourier reconstruction for three-dimensional gradient echo functional MRI: comparison of phase correction methods. Magn. Reson. Med. 40 (1998) 481-490
22. Suddarth S.A., and Johnson G.A. Three-dimensional MR microscopy with large arrays. Magn. Reson. Med. 18 (1991) 132-141
23. Wedeen V.J., Chao Y.S., and Ackerman J.L. Dynamic range compression in MRI by means of a nonlinear gradient pulse. Magn. Reson. Med. 6 (1988) 287-295
24. Woods R., Grafton S., Holmes C., Cherry S., and Mazziotta J. Automated image registration: I. General methods and intrasubject, intramodality validation. J. Comput. Assist. Tomogr. 22 (1998) 139-152
25. Xu Y., and Haacke E.M. Partial Fourier imaging in multi-dimensions: a means to save a full factor of two in time. J. Magn. Reson. Imaging 14 (2001) 628-635