Automated segmentation of in vivo and ex vivo mouse brain magnetic resonance images

Molecular Imaging

Volumn 8, Issue 1, 2009, Pages 35-44

  Dijkstra, Jouke ^a   Scheenstra, Alize E H ^b   Van De Ven, Rob C G ^b   Van Weerd, Louise Der ^b   Van Den Maagdenberg, Arn M J M ^b   Reiber, Johan H C ^b  

^a LEIDEN UNIVERSITY MEDICAL CENTER   (Netherlands)

^b NONE

Author keywords

[No Author keywords available]

Indexed keywords

AFFINE REGISTRATION; ATLAS-BASED SEGMENTATION; AUTOMATED SEGMENTATION; AUTOMATIC SEGMENTATIONS; CLUSTERING APPROACH; DIFFERENT STRUCTURE; EX-VIVO; GENERIC APPROACH; GOLD STANDARDS; IN-VIVO; KAPPA INDEX; LOW CONTRAST; LOW SIGNAL-TO-NOISE RATIO; MANUAL SEGMENTATION; MOUSE BRAIN; OTHER APPLICATIONS; PROCESSING TIME; ROUGH SEGMENTATION; SEGMENTATION METHODS; TIME POINTS; VOLUME QUANTIFICATION;

IMAGE REGISTRATION; IMAGE SEGMENTATION; MAGNETIC RESONANCE; MAGNETIC RESONANCE IMAGING; METAL REFINING;

SIGNAL TO NOISE RATIO;

ALGORITHM; ANIMAL; ARTICLE; AUTOMATED PATTERN RECOGNITION; BRAIN; C57BL MOUSE; COMPUTER SIMULATION; HISTOLOGY; IMAGE PROCESSING; METHODOLOGY; MOUSE; NUCLEAR MAGNETIC RESONANCE IMAGING; ORGAN SIZE; RADIOGRAPHY; VALIDATION STUDY;

ALGORITHMS; ANIMALS; BRAIN; COMPUTER SIMULATION; IMAGE PROCESSING, COMPUTER-ASSISTED; MAGNETIC RESONANCE IMAGING; MICE; MICE, INBRED C57BL; ORGAN SIZE; PATTERN RECOGNITION, AUTOMATED;

EID: 66449084990     PISSN: 15353508     EISSN: None     Source Type: Journal    
DOI: 10.2310/7290.2009.00004     Document Type: Article

References (30)

1. Anderson SA, Frank JA. MRI of mouse models of neurological disorders. NMR Biomed 2007;20:200-15.
2. Turnbull DH, Mori S. MRI in mouse developmental biology. NMR Biomed 2007;20:265-74.
3. Chen XJ, Kovacevic N, Lobaugh NJ, et al. Neuroanatomical differences between mouse strains as shown by high-resolution 3D MRI. Neuroimage 2005;29:99-105.
4. Meyer CR, Moffat BA, Kuszpit KK, et al. A methodology for registration of histological slide and in vivo MRI volume based on optimizing mutual information. Mol Imaging 2006;5:16-23.
5. Breen MS, Lazebnik RS, Wilson DL. Three-dimensional registration of magnetic resonance image data to histological sections with model-based evaluation. Ann Biomed Eng 2005;33:1100-12.
6. Geurts JJ, Bo L, Pouwels PJ, et al. Cortical lesions in multiple sclerosis: combined postmortem MR imaging and histopathology. AJNR Am J Neuroradiol 2005;26:572-7.
7. Bardinet E, Ourselin S, Dormont D, et al. Co-registration of histological, optical and MR data of the human brain. In: Dohi T, Kikinis R, editors. LNCS medical image computing and computer- assisted intervention-part I. Tokyo, Japan: Springer Berlin/ Heidelberg. 2002. p. 548-55.
8. Scheenstra AEH, Dijkstra J, van de Ven RCG, et al. Automated registration of histology sections with ex vivo MRM volumes. In: Proceedings of the International Society for Magnetic Resonance in Medicine (ISMRM). Seattle: 2006. p. 2012.
9. Gholipour A, Kehtarnavaz N, Briggs R, et al. Brain functional locatization: a survey of image registration techniques. IEEE Trans Med Imaging 2007;26:427-51.
10. Tohka J, Krestyannikov JE, Dinov ID, et al. Genetic algorithms for finite mixture model based voxel classification in neuroimaging. IEEE Trans Med Imaging 2007;26:696-711.
11. Ma Y, Smith D, Hof PR, et al. In vivo 3D digital atlas database of the adult C57BL/6J mouse brain by magnetic resonance microscopy. Front Neuroanat 2008;2:1-10.
12. Ma Y, Hof PR, Grant SC, et al. A three-dimensional digital atlas database of the adult C57BL/6J mouse brain by magnetic resonance microscopy. Neuroscience 2005;135:1203-15.
13. Kovacevic N, Henderson JT, Chan E, et al. A Three-dimensional MRI atlas of the mouse brain with estimates of the average and variability. Cereb Cortex 2005;15:639-45.
14. Bock NA, Kovacevic N, Lipina TV, et al. In vivo magnetic resonance imaging and semiautomated image analysis extend the brain phenotype for cdf/cdf mice. J Neurosci 2006;26:4455-9.
15. Lau JC, Lerch JP, Sled JG, et al. Longitudinal neuroanatomical changes determined by deformation-based morphometry in a mouse model of Alzheimer's disease. Neuroimage 2008;42:19-27.
16. Rohlfing T, Russakoff DB, Maurer CR. Performance-based classifier combination in atlas-based image segmentation using expectation-maximization parameter estimation. IEEE Trans Med Imaging 2004;23:983-94.
17. Ali AA, Dale AM, Badea A, Johnson GA. Automated segmentation of neuroanatomical structures in multispectral MR microscopy of the mouse brain. Neuroimage 2005;27:425-35.
18. Allan Johnson G, Ali-ShariefAA, Badea A, et al. High-throughput morphologic phenotyping of the mouse brain with magnetic resonance histology. Neuroimage 2007;37:82-9.
19. Sharief AA, Badea A, Dale AM, Allan Johnson G. Automated segmentation of the actively stained mouse brain using multi- spectral MR microscopy. Neuroimage 2008;39:136-45.
20. Duda RO, Hart PE, Stork DG. In Pattern classification. 2nd ed. John Wiley & Sons, Inc. New York; 2001. p. 528-30.
21. Geman S, Geman D. Stochastic relaxation, Gibbs distributions, and the Bayesian restoration of images. IEEE Trans Pattern Anal Mach Intell 1984;6:721-41.
22. Thirion JP. Image matching as a diffusion process: an analogy with Maxwell's demons. Med Image Anal 1998;2:243-60.
23. Joshi S, Davis B, Jomier M, Gerig G. Unbiased diffeomorphic atlas construction for computational anatomy. Neuroimage 2004;23: S151-60.
24. Thompson PM, Toga AW. Detection, visualization and animation of abnormal anatomic structure with deformable probabilistic brain atlas based on random vector field transformations. Med Image Anal 1997;1:271-94.
25. Maintz JBA, Viergever MA. A survey ofmedical image registration. Med Image Anal 1998;2:1-36.
26. Hill DLG, Batchelor PG, Holden M, Hawkes DJ. Medical image registration. Phys Med Biol 2001;46:R1-45.
27. Yoo TS, Ackerman MJ, Lorensen WE, et al. Engineering and algorithm design for an image processing API: a technical report on ITK - The Insight Toolkit. In: Westwood JD, et al, editors. Proceedings of Medicine Meets Virtual Reality. Amsterdam: ISO press; 2002. p. 586-92.
28. MacKenzie-Graham A, Lee E, Dinov ID, et al. A multimodal, multidimensional atlas of the C57BL/6J mouse brain. J Anat 2004; 205:71-149.
29. Kier LB. A shape index from chemical graphs. Quantitative Structure Activity Relationship 1985;4:109-16.
30. Lorenzen P, Prastawa M, Davis B, et al. Multi-model image set registration and atlas formation. Med Image Anal 2006;10: 440-51.