An ontology-based segmentation scheme for tracking postnatal changes in the developing rodent brain with MRI

NeuroImage

Volumn 67, Issue , 2013, Pages 375-384

  Calabrese, Evan ^a,b   Johnson, G Allan ^a,b   Watson, Charles ^c,d  

^a DUKE UNIVERSITY MEDICAL CENTER   (United States)

^b Duke University   (United States)

^c CURTIN UNIVERSITY   (Australia)

^d NEUROSCIENCE RESEARCH AUSTRALIA   (Australia)

Author keywords

Diffusion tensor imaging; MRI; Neurodevelopment; Postnatal; Rat brain

Indexed keywords

ADULT ANIMAL; AMYGDALOID NUCLEUS; ANIMAL EXPERIMENT; ANIMAL TISSUE; ARTICLE; BRAIN DEVELOPMENT; BRAIN SIZE; CONTROLLED STUDY; CORPUS CALLOSUM; FEASIBILITY STUDY; FOREBRAIN; GROWTH RATE; IMAGE ANALYSIS; IMAGE SEGMENTATION; MAGNETIC RESONANCE HISTOLOGY; MALE; MESENCEPHALON; NEOCORTEX; NEUROANATOMY; NEUROIMAGING; NONHUMAN; NUCLEAR MAGNETIC RESONANCE IMAGING; OLFACTORY BULB; POSTNATAL DEVELOPMENT; PRIORITY JOURNAL; RAT; RHOMBENCEPHALON; STRUCTURE ANALYSIS; WHITE MATTER;

AGING; ANIMALS; BRAIN; COMPUTER SIMULATION; IMAGE INTERPRETATION, COMPUTER-ASSISTED; MAGNETIC RESONANCE IMAGING; MALE; MODELS, ANATOMIC; MODELS, NEUROLOGICAL; RATS; RATS, WISTAR; REPRODUCIBILITY OF RESULTS; SENSITIVITY AND SPECIFICITY;

EID: 84871840316     PISSN: 10538119     EISSN: 10959572     Source Type: Journal    
DOI: 10.1016/j.neuroimage.2012.11.037     Document Type: Article

References (52)

1. Altman J. Postnatal development of the cerebellar cortex in the rat. I. The external germinal layer and the transitional molecular layer. J. Comp. Neurol. 1972, 145:353-397.
2. Asato M.R., Terwilliger R., Woo J., Luna B. White matter development in adolescence: a DTI study. Cereb. Cortex 2010, 20:2122-2131.
3. Ashwell K.W.S., Paxinos G. Atlas of the Developing Rat Nervous System 2008, Academic Press.
4. Autism and Developmental Disabilities Monitoring Network Surveillance Year 2006 Principal Investigators, Centers for Disease Control and Prevention (CDC) Prevalence of autism spectrum disorders - Autism and Developmental Disabilities Monitoring Network, United States, 2006. MMWR Surveill. Summ. 2009, 58:1-20.
5. Avants B.B., Epstein C.L., Grossman M., Gee J.C. Symmetric diffeomorphic image registration with cross-correlation: evaluating automated labeling of elderly and neurodegenerative brain. Med. Image Anal. 2008, 12:26-41.
6. Badea A., Ali-Sharief A.A., Johnson G.A. Morphometric analysis of the C57BL/6J mouse brain. Neuroimage 2007, 37:683-693.
7. Bailey S.A., Zidell R.H., Perry R.W. Relationships between organ weight and body/brain weight in the rat: what is the best analytical endpoint?. Toxicol. Pathol. 2004, 32:448-466.
8. Bota M., Swanson L.W. BAMS neuroanatomical ontology: design and implementation. Front. Neuroinform. 2008, 2:2.
9. Bowden D.M., Martin R.F. Neuronames brain hierarchy. Neuroimage 1995, 2:63-83.
10. Bug W.J., Ascoli G.A., Grethe J.S., Gupta A., Fennema-Notestine C., Laird A.R., Larson S.D., Rubin D., Shepherd G.M., Turner J.A., Martone M.E. The NIFSTD and BIRNLex vocabularies: building comprehensive ontologies for neuroscience. Neuroinformatics 2008, 6:175-194.
11. Centers for Disease Control and Prevention (CDC) Increasing prevalence of parent-reported attention-deficit/hyperactivity disorder among children-United States, 2003 and 2007. MMWR Morb. Mortal. Wkly Rep. 2010, 59:1439-1443.
12. Chuang N., Mori S., Yamamoto A., Jiang H., Ye X., Xu X., Richards L.J., Nathans J., Miller M.I., Toga A.W., Sidman R.L., Zhang J. An MRI-based atlas and database of the developing mouse brain. Neuroimage 2011, 54:80-89.
13. Clancy B., Finlay B.L., Darlington R.B., Anand K.J.S. Extrapolating brain development from experimental species to humans. Neurotoxicology 2007, 28:931-937.
14. Delnomdedieu M., Hedlund L.W., Johnson G.A., Maronpot R.R. Magnetic resonance microscopy-a new tool for the toxicologic pathologist. Toxicol. Pathol. 1996, 24:36-44.
15. Dong H.W. The Allen Reference Atlas: A Digital Color Brain Atlas of the C57Bl/6J Male Mouse 2008, John Wiley & Sons Inc.
16. Frederiksen K., McKay R.D. Proliferation and differentiation of rat neuroepithelial precursor cells in vivo. J. Neurosci. 1988, 8:1144-1151.
17. Giedd J.N., Rapoport J.L. Structural MRI of pediatric brain development: what have we learned and where are we going?. Neuron 2010, 67:728-734.
18. Giuliani N.R., Calhoun V.D., Pearlson G.D., Francis A., Buchanan R.W. Voxel-based morphometry versus region of interest: a comparison of two methods for analyzing gray matter differences in schizophrenia. Schizophr. Res. 2005, 74:135-147.
19. Herrmann M., King K., Weitzman M. Prenatal tobacco smoke and postnatal secondhand smoke exposure and child neurodevelopment. Curr. Opin. Pediatr. 2008, 20:184-190.
20. Hines M., Allen L.S., Gorski R.A. Sex differences in subregions of the medial nucleus of the amygdala and the bed nucleus of the stria terminalis of the rat. Brain Res. 1992, 579:321-326.
21. Jaaro-Peled H., Hayashi-Takagi A., Seshadri S., Kamiya A., Brandon N.J., Sawa A. Neurodevelopmental mechanisms of schizophrenia: understanding disturbed postnatal brain maturation through neuregulin-1-ErbB4 and DISC1. Trends Neurosci. 2009, 32:485-495.
22. Johnson G.A., Cofer G.P., Fubara B., Gewalt S.L., Hedlund L.W., Maronpot R.R. Magnetic resonance histology for morphologic phenotyping. J. Magn. Reson. Imaging 2002, 16:423-429.
23. Johnson G.A., Cofer G.P., Gewalt S.L., Hedlund L.W. Morphologic phenotyping with MR microscopy: the visible mouse. Radiology 2002, 222:789-793.
24. Johnson G.A., Ali-Sharief A., Badea A., Brandenburg J., Cofer G., Fubara B., Gewalt S., Hedlund L.W., Upchurch L. High-throughput morphologic phenotyping of the mouse brain with magnetic resonance histology. Neuroimage 2007, 37:82-89.
25. Johnson G.A., 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.
26. Johnson G.A., Calabrese E., Badea A., Paxinos G., Watson C. A multidimensional magnetic resonance histology atlas of the Wistar rat brain. Neuroimage 2012, 62:1848-1856.
27. Kelly P.H., Seviour P.W., Iversen S.D. Amphetamine and apomorphine responses in the rat following 6-OHDA lesions of the nucleus accumbens septi and corpus striatum. Brain Res. 1975, 94:507-522.
28. Knickmeyer R.C., Gouttard S., Kang C., Evans D., Wilber K., Smith J.K., Hamer R.M., Lin W., Gerig G., Gilmore J.H. A structural MRI study of human brain development from birth to 2years. J. Neurosci. 2008, 28:12176-12182.
29. Kochunov P., Lancaster J.L., Thompson P., Woods R., Mazziotta J., Hardies J., Fox P. Regional spatial normalization: toward an optimal target. J. Comput. Assist. Tomogr. 2001, 25:805-816.
30. Kovacevic N. A three-dimensional MRI atlas of the mouse brain with estimates of the average and variability. Cereb. Cortex 2004, 15:639-645.
31. Ma Y., Hof P.R., Grant S.C., Blackband S.J., Bennett R., Slatest L., McGuigan M.D., Benveniste H. A three-dimensional digital atlas database of the adult C57BL/6J mouse brain by magnetic resonance microscopy. Neuroscience 2005, 135:1203-1215.
32. Mori S., Itoh R., Zhang J., Kaufmann W.E., van Zijl P.C., Solaiyappan M., Yarowsky P. Diffusion tensor imaging of the developing mouse brain. Magn. Reson. Med. 2001, 46:18-23.
33. Mukherjee P., McKinstry R.C. Diffusion tensor imaging and tractography of human brain development. Neuroimaging Clin. N. Am. 2006, 16:19-43.
34. O'Leary-Moore S.K., Parnell S.E., Lipinski R.J., Sulik K.K. Magnetic resonance-based imaging in animal models of fetal alcohol spectrum disorder. Neuropsychol. Rev. 2011, 21:167-185.
35. Paxinos G., Watson C. The Rat Brain in Stereotaxic Coordinates 2007, Elsevier Academic Press, San Diego. 6th ed.
36. Petiet A.E., Kaufman M.H., Goddeeris M.M., Brandenburg J., Elmore S.A., Johnson G.A. High-resolution magnetic resonance histology of the embryonic and neonatal mouse: a 4D atlas and morphologic database. Proc. Natl. Acad. Sci. U. S. A. 2008, 105:12331-12336.
37. Puelles L., Rubenstein J.L.R. Forebrain gene expression domains and the evolving prosomeric model. Trends Neurosci. 2003, 26:469-476.
38. Puelles L., Martinez-de-la-Torre M., Paxinos G., Watson C., Martinez S. The Chick Brain in Stereotaxic Coordinates: An Atlas featuring Neuromeric Subdivisions and Mammalian Homologies 2007, Elsevier Academic Press, San Diego.
39. Puelles E., Martinez-de-la-Torre M., Watson C., Puelles L. Midbrain. The Mouse Nervous System 2012, 337-359. Elsevier Academic Press, San Diego. C. Watson, G. Paxinos, L. Puelles (Eds.).
40. Puelles L., Martinez-de-la-Torre M., Bardet S., Rubenstein J.L.R. Hypothalamus. The Mouse Nervous System 2012, 221-312. Elsevier Academic Press. C. Watson, G. Paxinos, L. Puelles (Eds.).
41. Puelles L., Martinez-de-la-Torre M., Ferran J.-L., Watson C. Diencephalon. The Mouse Nervous System 2012, 313-336. Elsevier Academic Press, San Diego. C. Watson, G. Paxinos, L. Puelles (Eds.).
42. Richards K., Watson C., Buckley R.F., Kurniawan N.D., Yang Z., Keller M.D., Beare R., Bartlett P.F., Egan G.F., Galloway G.J., Paxinos G., Petrou S., Reutens D.C. Segmentation of the mouse hippocampal formation in magnetic resonance images. Neuroimage 2011, 58:732-740.
43. Rosen G.D., Harry J.D. Brain volume estimation from serial section measurements: a comparison of methodologies. J. Neurosci. Methods 1990, 35:115-124.
44. Silbert L.C., Quinn J.F., Moore M.M., Corbridge E., Ball M.J., Murdoch G., Sexton G., Kaye J.A. Changes in premorbid brain volume predict Alzheimer's disease pathology. Neurology 2003, 61:487-492.
45. Sturm V., Lenartz D., Koulousakis A., Treuer H., Herholz K., Klein J.C., Klosterkötter J. The nucleus accumbens: a target for deep brain stimulation in obsessive-compulsive- and anxiety-disorders. J. Chem. Neuroanat. 2003, 26:293-299.
46. Tiemeier H., Lenroot R.K., Greenstein D.K., Tran L., Pierson R., Giedd J.N. Cerebellum development during childhood and adolescence: a longitudinal morphometric MRI study. Neuroimage 2010, 49:63-70.
47. Ullmann J.F.P., Keller M.D., Watson C., Janke A.L., Kurniawan N.D., Yang Z., Richards K., Paxinos G., Egan G.F., Petrou S., Bartlett P., Galloway G.J., Reutens D.C. Segmentation of the C57BL/6J mouse cerebellum in magnetic resonance images. Neuroimage 2012, 62:1408-1414.
48. Walker D.L., Toufexis D.J., Davis M. Role of the bed nucleus of the stria terminalis versus the amygdala in fear, stress, and anxiety. Eur. J. Pharmacol. 2003, 463:199-216.
49. Watson C. Hindbrain. The Mouse Nervous System 2012, 397-422. Elsevier Academic Press, San Diego. C. Watson, G. Paxinos, L. Puelles (Eds.).
50. Watson C., Paxinos G., Puelles L. The Mouse Nervous System 2012, Academic Press, San Diego.
51. White J.J., Sillitoe R.V. Development of the cerebellum: from gene expression patterns to circuit maps. WIREs Dev. Biol. 2013, 2(1):149-164. 10.1002/wdev.65.
52. Zhang J., Miller M.I., Plachez C., Richards L.J., Yarowsky P., van Zijl P., Mori S. Mapping postnatal mouse brain development with diffusion tensor microimaging. Neuroimage 2005, 26:1042-1051.