Databases and Systems

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plate spline [19] or polynomial [20], to map the experimental data onto the atlas
image. If the resultant transformation is not correct then the user can add additional
tie-points or directly edit the resulting domain using painting. There are many
possibilities for determining the warp transform including a fully automatic matching
[8]. In practice the mechanism must be fast enough to allow interactive adjustment
and editing.
So far we have considered section data which assumes that the experimental
section corresponds to a planar section through the atlas embryo. If the experimental
data is in the form of a 3D image then full 3D warping will be necessary e.g. [13].
Data Extensions
The initial implementation of the image-mapped database will store the domains
(binary image) of gene-expression only. This means that expression strength
information can only be encoded as separate domains, e.g. weak, medium and strong,
or by storing a dithered version of the grey-level image. The Woolz image format
includes a simple extension to grey-level types within the image domain and
therefore we plan to extend the schema to allow full grey-level images of gene
expression data to be submitted. This means that the query language can be extended
to use grey-level operations such as gradient and intensity.
References
1. Theiler, K. The House Mouse: Atlas of Embryonic Development, (Springer-
Verlag, 1989).
2. Baldock, R A, Bard J, Kaufman, M H & Davidson D, A Real Mouse for your
Computer, BioEssays 14(1992)501-502.
3. Ringwald M, Baldock R, Bard J, Kaufman M, Eppig J, Richardson J E, Nadeau J
& Davidson D, A Database for Mouse Development, Science 265(1994) 2033-
2034.
4. Davidson D, Baldock R, Bard J, Kaufman M, Richardson J E, Eppig J T &
Ringwald M, Gene-Expression Databases, In Situ Hybridisation: A Practical
Approach, ed. Wilkinson D, (IRL press, Oxford, 1998).
5. Davidson D, Bard J B L, Brune R M, Burger A, Dubreuil C, Kaufman M, Quinn
J, Stark M & Baldock R A, The Mouse Atlas and Graphical Gene Expression
Database, Sem. Cell & Dev. Biol. 8(1997)509-517.
6. Eppig J T & Richardson J E, MGD and GXD, this issue.
7. Guest E&Baldock R A, Automatic Reconstruction of Serial Sections Using the
Finite Element Method, Bioimaging 3(1995)154-167.
8. Baldock R A, Verbeek F J & Vonesch J-L, 3-D Reconstruction for Graphical
Databases of Gene-Expression, Sem. Cell& Dev. Biol. 8(1997)499-507.