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Neuroinformatics

, Volume 2, Issue 1, pp 3–18 | Cite as

Informatics approaches to functional MRI odor mapping of the rodent olfactory bulb

OdorMapBuilder and OdorMapDB
  • Nian LiuEmail author
  • Fuqiang Xu
  • Luis Marenco
  • Fahmeed Hyder
  • Perry Miller
  • Gordon M. Shepherd
Original Article

Abstract

The present study applies informatics tools to aid and extend fMRI analysis of the coding mechanism of neural signals in the rodent olfactory system. Odor stimulation evokes unique spatial patterns of activity in the glomerular layer of the mammalian olfactory bulb (OB). An open-source software program, OdorMapBuilder, has been developed to process the high resolution anatomical and functional MRI images of the OB and to generate single two-dimensional flat maps, called odor maps, that describe the spatial activity patterns in the entire glomerular layer. Odor maps help identify the spatial activity patterns from the tremendous amount of fMRI data and they serve as ideal representation of space coding for the olfactory signals in the OB in response to a given odor stimulation. Based on the fMRI technology, OdorMapBuilder provides comparable odor maps on the intra-subject basis, a significant step towards the detailed analyses of the effects of odor types and/or concentrations. In addition, a new database, OdorMapDB, is developed to provide a repository for the generated odor maps. Web interfaces to the database are provided for the data entry, modification and retrieval. OdorMapDB is based on the EAV/CR (entity-attribute-value with classes and relationships) architecture and it is integrated with two other SenseLab olfactory databases: the olfactory receptor and odor databases. Both OdorMapBuilder and OdorMapDB should serve as useful tools and resources for the field and help facilitate experimental research in understanding the olfactory system and the mechanism for smell perception.

Index entries

Odor map glomerular layer spatial activity pattern Java web-based database neuroinformatics 

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References

  1. Adrian, E. D. (1950) Sensory discrimination, with some recent evidence from the olfactory organ. Br. Med. Bull. 6, 330–333.PubMedGoogle Scholar
  2. Chicurel, M. (2000) Databasing the brain. Nature 406, 822–825.PubMedCrossRefGoogle Scholar
  3. Fissell, K., Tseytlin, E., Cunningham, D., et al. (2003) Fiswidgets: A graphical computing environment for neuroimaging analysis. Neuroinformatics 1, 111–126.PubMedCrossRefGoogle Scholar
  4. Guthrie, K. M., Anderson, A. J., Leon, M., and Gall, C. (1993) Odor-induced increases in c-fos mRNA expression reveal an anatomical “unit” for odor processing in olfactory bulb. Proc. Natl. Acad. Sci. USA 90, 3329–3333.PubMedCrossRefGoogle Scholar
  5. Huerta, M. F., Koslow, S. H., and Leshner, A. I. (1993) The Human Brain Project: an international resource. Trends Neurosci. 16, 436–438.PubMedCrossRefGoogle Scholar
  6. Johnson, S. B. (1996) Generic data modeling for clinical repositories. J. Am. Med. Inform. Assoc. 3, 328–339.PubMedGoogle Scholar
  7. Johnson, B.A., Woo, C.C., Hingco, E.E., Pham, K.L., and Leon, M. (1999) Multidimensional chemotopic responses to n-aliphatic acid odorants in the rat olfactory bulb. J. Comp. Neurol. 409, 529–548.PubMedCrossRefGoogle Scholar
  8. Johnson, B.A. and Leon, M. (2000) Modular representations of odorants in the glomerular layer of the rat olfactory bulb. J. Comp. Neurol. 422, 496–509.PubMedCrossRefGoogle Scholar
  9. Liu, N., Cigola, E., Tinti, C., et al. (1999) Unique regulation of immediate early gene and tyrosine hydroxylase expression in the odor-deprived mouse olfactory bulb. J. Biol. Chem. 274, 3042–3047.PubMedCrossRefGoogle Scholar
  10. Mombaerts, P., Wang, F., Dulac, C., et al. (1996) Visualizing an olfactory sensory map. Cell 87, 675–686.PubMedCrossRefGoogle Scholar
  11. Nadkarni, P., Brandt, C., Frawley, S.M., et al. (1998) Managing attribute-value clinical trials data using the ACT/DB client system. J. Am. Med. Inform. Assoc. 5, 139–151.PubMedGoogle Scholar
  12. Nadkarni, P., Marenco, L., Chen, R., Skoufos, E., Shepherd, G., and Miller, P. (1999) Organization of heterogeneous scientific data using the EAV/CR representation. J. Am. Med. Inform. Assoc. 6, 478–493.PubMedGoogle Scholar
  13. Niemeyer, P. and Peck, J. (1997) Exploring JAVA, 2nd ed., O’Reilly & Associates, Sebastopol, CA.Google Scholar
  14. Royet, J. P., Sicard, G., Souchier, C., and Jourdan, F. (1987) Specificity of spatial patterns of glomerular activation in the mouse olfactory bulb: computer-assisted image analysis of 2-deoxyglucose autoradiograms. Brain Res. 417, 1–11.PubMedCrossRefGoogle Scholar
  15. Rubin, B. D. and Katz, L. C. (1999) Optical imaging of odorant representations in the mammalian olfactory bulb. Neuron 23, 499–511.PubMedCrossRefGoogle Scholar
  16. Sallaz, M. and Jourdan, F. (1993) C-fos expression and 2-deoxyglucose uptake in the olfactory bulb of odour-stimulated awake rats. Neuroreport 4, 55–58.PubMedCrossRefGoogle Scholar
  17. Shepherd, G. M. (1985) The olfactory system: the uses of neural space for a non-spatial modality. Prog. Clin. Biol. Res. 176, 99–114.PubMedGoogle Scholar
  18. Stewart, W. B., Kauer, J. S., and Shepherd, G. M. (1979) Functional organization of rat olfactory bulb analysed by the 2-deoxyglucose method. J. Comp. Neurol. 185, 715–734.PubMedCrossRefGoogle Scholar
  19. Toga, A. W. (2002) Neuroimage databases: the good, the bad and the ugly. Nat. Rev. Neurosci. 3, 302–308.PubMedCrossRefGoogle Scholar
  20. Van Essen, D. C., Lewis, J. W., Drury, H. A., et al. (2001) Mapping visual cortex in monkeys and humans using surface-based atlases. Vision Res. 41, 1359–1378.PubMedCrossRefGoogle Scholar
  21. Wilson, D. A. and Leon, M. (1988) Spatial patterns of olfactory bulb single-unit responses to learned olfactory cues in young rats. J. Neurophysiol. 59, 1770–1782.PubMedGoogle Scholar
  22. Xu, F., Greer, C. A., and Shepherd, G. M. (2000a) Odor maps in the olfactory bulb. J. Comp. Neurol. 422, 489–495.PubMedCrossRefGoogle Scholar
  23. Xu, F., Kida, I., Hyder, F., and Shulman, R. G. (2000b) Assessment and discrimination of odor stimuli in rat olfactory bulb by dynamic functional MRI. Proc. Natl. Acad. Sci. USA 97, 10601–10606.PubMedCrossRefGoogle Scholar
  24. Yang, X., Renken, R., Hyder, F., et al. (1998) Dynamic mapping at the laminar level of odor-elicited responses in rat olfactory bulb by functional MRI. Proc. Natl. Acad. Sci. USA 95, 7715–7720.PubMedCrossRefGoogle Scholar

Copyright information

© Humana Press Inc 2004

Authors and Affiliations

  • Nian Liu
    • 1
    Email author
  • Fuqiang Xu
    • 2
  • Luis Marenco
    • 1
  • Fahmeed Hyder
    • 3
  • Perry Miller
    • 1
  • Gordon M. Shepherd
    • 2
  1. 1.Center for Medical InformaticsYale University School of MedicineNew Haven
  2. 2.Department of NeurobiologyYale University School of MedicineNew Haven
  3. 3.Department of Diagnostic RadiologyYale University School of MedicineNew Haven

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