Advertisement

Management of Spatially Organized Biological Data using EMAGE

  • Jeffrey H. ChristiansenEmail author
  • Duncan R. Davidson
  • Richard A Baldock

Abstract

Images are used to record the outcomes of many biological experiments, including those that employ in situ hybridization and immunohistochemistry assays. The most widespread method currently used to describe these images for archiving and analysis purposes is employing a text based description, whereby the pattern of staining observed in each image is described by a human using a standardized vocabulary of anatomical terms.

In this chapter, we describe a complementary approach, whereby, the spatially organized information inherently contained in data images is extracted and spatially integrated via a semi-automated process and then housed in a three-dimensional atlas of biological structure. Thus, spatial data from multiple assays can be interrogated directly by spatial based approaches to find patterns that display similarities or differences of patterns over local or entire regions of the specimen.

Keywords

Biological images Gene expression Spatial Database in situ hybridization Immunohistochemistry Mouse Embryo 

References

  1. 1.
    Bard, JB. Anatomics: the intersection of anatomy and bioinformatics. J Anat 2005;206(1):1–16.CrossRefPubMedGoogle Scholar
  2. 2.
    Davidson, D, Baldock, R. Bioinformatics beyond sequence: mapping gene function in the embryo. Nat Rev Genet 2001;2(6):409–417.CrossRefPubMedGoogle Scholar
  3. 3.
    Baldock, RA, Bard, JB, Burger, A, et al. EMAP and EMAGE: a framework for understanding spatially organized data. Neuroinformatics 2003;1(4):309–325.CrossRefPubMedGoogle Scholar
  4. 4.
    Sunkin, SM. Towards the integration of spatially and temporally resolved murine gene expression databases. Trends Genet 2006;22(4):211–217.CrossRefPubMedGoogle Scholar
  5. 5.
    Wilkinson DG, Nieto, MA. Detection of messenger RNA by in situ hybridization to tissue sections and whole mounts. Methods Enzymol 1993;225:361–373.CrossRefPubMedGoogle Scholar
  6. 6.
    Hsu, SM. Immunohistochemistry. Methods Enzymol 1990;184:357–363.CrossRefPubMedGoogle Scholar
  7. 7.
    Theiler, K. The House Mouse: Atlas of Embryonic Development. New York: Springer-Verlag; 1989.Google Scholar

Copyright information

© Humana Press, a part of Springer Science+Business Media, LLC 2009

Authors and Affiliations

  • Jeffrey H. Christiansen
    • 1
    Email author
  • Duncan R. Davidson
    • 2
  • Richard A Baldock
    • 2
  1. 1.MRC Human Genetics Unit, Western General HospitalUK
  2. 2.MRC Human Genetics Unit, Western General HospitalUK

Personalised recommendations