The neuroterrain 3D mouse brain atlas

Frontiers in Neuroinformatics

Volumn 2, Issue JUL, 2008, Pages

  Bertrand, Louise ^a   Nissanov, Jonathan ^a  

^a DREXEL UNIVERSITY COLLEGE OF MEDICINE   (United States)

Author keywords

3D reconstruction; Atlas; Automated segmentation; Brain model; Neuroanatomy; Registration; Spatial normalization; Standard coordinate space

Indexed keywords

EID: 70349471430     PISSN: 16625196     EISSN: None     Source Type: Journal    
DOI: 10.3389/neuro.11.003.2008     Document Type: Article

References (43)

1. Ardekani, S. (2000). Inter-Animal Rodent Brain Alignment and Supervised 3D Reconstruction. Philadelphia, School of Biomedical Engineering, Science, and Health Systems, Drexel University, 92 p.
2. Baldock, R. A., Bard, J. B. L., Burger, A., Burton, N., Christiansen, J.,Feng, G., Hill, B., Houghton, D., Kaufman, M., Rao, J., Sharpe, J., Ross, A., Stevenson, P., Venkataraman, S., Waterhouse, A., Yang, Y., and Davidson, D. R. (2003). EMAP and EMAGE: a framework for understanding spatially organized data. Neuroinformatics 1, 309-326.
3. Beatty, J., and Laughlin, R. (2006). Genomic regulation of natural variation in cortical and noncortical brain volume. BMC Neurosci. 7, 16.
4. Boline, J., Bug, W., Zaslavsky, I., Williams, R., Martone, M., Anderson, S., Wong, W., Yuan, H., Memon, A., Ng, Q., Grethe, J., Sforza, D., MacKenzie-Graham, A., Nissanov, J., Gustafson, C., and Toga, A. (2007). Accessing a sharing infrastructure with the Mouse BIRN atlasing toolkit (MBAT). In Proceedings of the Society for Neuroscience 37th Annual Meeting, San Diego, CA, USA.
5. Bowden, D. M., and Dubach, M. F. (2003). NeuroNames 2002. Neuroinformatics 1, 43-59.
6. Bug, W., Gustafson, C., Shahar, A., Gefen, S., Fan, G. Y., Bertrand, L., and Nissanov, J. (2007a). Brain spatial normalization: indexing neuroanatomical databases. In Neuroinformatics, C. Crasto, ed. (Totowa, Humana Press), pp. 211-234.
7. Bug, W., Wong, W., Gustafson, C., Johnson, G., Martone, M., Price, D., Rosen, G., Williams, R., Zaslavsky, I., and Nissanov, J. (2007b). Integration of brain atlasing tools: NeuroTerrain-Smart Atlas synergistic visualization and analysis environment. In Proceedings of the 3rd International IEEE EMBS Conference on Neural Engineering, Kohala Coast, Hawaii, pp. 280-283.
8. Dougherty, D. A., Nissanov, J., and Gindi, G. R. (1998). Autoradiographic-based rat brain phantom for emission tomography. In Proceedings of the IEEE Nuclear Science Symposium and Medical Imaging conference, Toronto, Canada, Vol. 2, pp. 1250-1254.
9. Fox, P., Mikiten, S., Davis, G., and Lancaster, J. (1994). Brainmap: a database of human functional brain mapping. In: Functional Neuroimaging Technical Foundation, R. Thatcher et al., eds (San Diego, Academic Press), pp. 95-105.
10. Franklin, K., and Paxinos, G. (1997). The Mouse Brain in Stereotaxic Coordinates. San Diego, Academic Press.
11. Gefen, S., Kiryati, N., Bertrand, L., and Nissanov, J. (2006). Planar-to-curved-surface image registration. In Proceedings of the 2006 Conference on Computer Vision and Pattern Recognition Workshop, IEEE, 72 p.
12. Gefen, S., Kiryati, N., and Nissanov, J. (2008). Atlas-based indexing of brain sections via 2-D to 3-D image registration. IEEE Trans. Biomed. Eng. 55, 147-156.
13. Gefen, S., Tretiak, J. O., and Nissanov, J. (2003). Elastic 3D alignment of rat brain histological images. IEEE Trans. Med. Imaging 22, 1480-1489.
14. Gefen, S., Tretiak, O., Bertrand, L., Rosen, G., and Nissanov, J. (2004). Surface alignment of an elastic body using a multi-resolution wavelet representation. IEEE Trans. Biomed. Eng. 51, 1230-1241.
15. Gupta, A., Astakhov, V., Boline, J., Bug, B., Fennema-Notestine, C., Grethe, J., Kennedy, D., Martone, M., Rubin, D., Sanders, B., and Turner, J. (2007). Data Federation in the Biomedical Informatics Research Network: Tools for semantic annotation and query of distributed multiscale brain data. In Proceedings of the Society for Neuroscience 37th Annual Meeting, San Diego, 37, p. 100.116.
16. Gustafson, C., Bug, W. J., and Nissanov, J. (2007). NeuroTerrain - a client-server system for browsing 3D biomedical image data sets. BMC Bioinform. 8, 40.
17. Gustafson, C., Tretiak, O., Bertrand, L., and Nissanov, J. (2004). Design and implementation of software for assembly and browsing of 3D brain atlases. Comput. Methods Programs Biomed. 74, 53-61.
18. Hjornevik, T., Leergaard, T., Darine, D., Moldestad, O., Dale, A., Willoch, F., and Bjaalie, J. (2007). Three-dimensional atlas system for mouse and rat brain imaging data. Front. Neuroinform. 1, 4.
19. Hof, P., Young, W., Bloom, F., Belichenko, P., and Celio, M. (2000). Comparative Cytoarchitectonic Atlas of the C57BL6 and 129 Sv Mouse Brains. Amsterdam, Elsevier.
20. Johnson, G. A., Ali-Sharief, A., Badea, A., Brandenburg, J., Cofer, G., Fubara, B., Gewalt, S., Hedlund, L. W., and Upchurch, L. (2007). High-throughput morphologic phenotyping of the mouse brain with magnetic resonance histology. Neuroimage 37, 82-89.
21. Kim, B., Boes, J. L., Frey, K. A., and Meyer, C. R. (1997). Mutual information for automated unwarping of rat brain autoradiographs. Neuroimage 5, 31-40.
22. Lander, E., and Schork, N. (1994). Genetic dissection of complex traits. Science 265, 2037-2048.
23. Lee, E. F., Jacobs, R. E., Dinov, I., Leow, A., and Toga, A. W. (2005). Standard atlas space for C57BL/6J neonatal mouse brain. Anat. Embryol. (Berl.) 210, 245-263.
24. Lein, E. S., Hawrylycz, M. J., Ao, N., Ayres, M., Bensinger, A., Bernard, A., Boe, A. F., Boguski, M. S., Brockway, K. S., Byrnes, E. J., Chen, L., Chen, T. M., Chin, M. C., Chong, J., Crook, B. E., Czaplinska, A., Dang, C. N. et al. (2007). Genome-wide atlas of gene expression in the adult mouse brain. Nature 445, 168-176.
25. Lo, C.-C. (1996). Section Thickness Determination and Evaluation of a New Gray Value Normalization Technique for Brain Reconstruction, Vol. MS. Philadelphia, School of Biomedical Engineering, Science, and Health Systems, Drexel University, 49 p.
26. Ma, Y., Hof, P. R., Grant, S. C., Blackband, S. J., Bennett, R., Slatest, L., McGuigan, M. D., and Benveniste, H. (2005). A three-dimensional digital atlas database of the adult C57BL/6J mouse brain by magnetic resonance microscopy. Neuroscience 135, 1203-1215.
27. MacKenzie-Graham, A., Boline, J., and Toga, A. (2007). Brain atlases and neuroanatomic imaging. In Neuroinformatics, Vol. 401, C. Crasto, ed. (Totowa, Humana Press), pp. 183-194.
28. MacKenzie-Graham, A., Lee, E. F., Dinov, I. D., Bota, M., Shattuck, D. W., Ruffi ns, S., Yuan, H., Konstantinidis, F., Pitiot, A., Ding, Y., Hu, G., Jacobs, R. E., and Toga, A. W. (2004). A multimodal, multidimensional atlas of the C57BL/6J mouse brain. J. Anat. 204, 93-102.
29. Martone, M., Zhang, S., Gupta, A., Qian, X., He, H., Price, D., Wong, M., Santini, S., and Ellisman, M. (2003). The cell-centered database: a database for multiscale structural and protein localization data from light and electron microscopy. Neuroinformatics 1, 379-395.
30. Nissanov, J., Bertrand, L., Gefen, S., Bakare, P., Kane, C., Gross, K., and Baird, D. (2006). Cryoplane fl uorescence microscopy. In Proceedings of the 24th IASTED International Multi-Conference on Biomedical Engineering, Innsbruck, Austria, pp. 362-366.
31. Nissanov, J., Bertrand, L., and Tretiak, O. (2001). Cryosectioning distortion reduction using tape support. Microsc. Res. Tech. 53, 239-240.
32. Nissanov, J., and McEachron, D. L. (1991). Advances in image processing for autoradiography. J. Chem. Neuroanat. 4, 329-342.
33. Palombi, O., Shin, J. W., Watson, C., and Paxinos, G. (2006). Neuroanatomical affi liation visualization-interface system. Neuroinformatics 4, 299-317.
34. Paxinos, G., and Franklin, K. (2001). The Mouse Brain in Stereotaxic Coordinates. San Diego, Academic Press.
35. Rosen, G., Porte, N. L., Diechtiareff, B., Pung, C., Nissanov, J., Gustafson, C., Bertrand, L., Gefen, S., Fan, Y., Tretiak, O., Manly, K. F., Park, M. R., Williams, A. G., Connolly, M. T., Capra, J. A., and Williams, R. W. (2003). Informatics center for mouse genomics: the dissection of complex traits of the nervous system. Neuroinformatics 1, 327-342.
36. Seecharan, D. J., Kulkarni, A. L., Lu, L., Rosen, G. D., and Williams, R. W. (2003). Genetic control of interconnected neuronal populations in the mouse primary visual system. J. Neurosci. 23, 11178-11188.
37. Shambra, U., Lauder, J., and Silver, J. (1992). Atlas of the Prenatal Mouse Brain. San Diego, Academic Press.
38. Toga, A. W. (1999). Brain Warping. San Diego, Academic Press.
39. Valverde, F. (1998). Golgi Atlas of the Postnatal Mouse Brain. Vienna, Springer-Verlag.
40. Venkataraman, S., Stevenson, P., Yang, Y., Richardson, L., Burton, N., Perry, T. P., Smith, P., Baldock, R. A., Davidson, D. R., and Christiansen, J. H. (2008). EMAGE - Edinburgh Mouse Atlas of Gene Expression: 2008 update. Nucleic Acids Res. 36, D860-D865.
41. Williams, R. W., Airey, D. C., Kulkarni, A., Zhou, G., and Lu, L. (2001). Genetic dissection of the olfactory bulbs of mice: QTLs on four chromosomes modulate bulb size. Behav. Genet. 31, 61-77.
42. Woods, R. P., Grafton, S. T., Holmes, C. J., Cherry, S. R., and Mazziotta, J. C. (1998a). Automated image registration: I. General methods and intrasubject, intramodality validation.J. Comput. Assist. Tomogr. 22, 139-152.
43. Woods, R. P., Grafton, S. T., Watson, J. D., Sicotte, N. L., and Mazziotta, J. C. (1998b). Automated image registration: II. Intersubject validation of linear and nonlinear models. J. Comput. Assist. Tomogr. 22, 153-165.