MAPaint Technical Report:
Introduction

Introduction

The essence of the gene-expression database being developed at the MRC Human Genetics Unit, is the ability to map the complex patterns of expression, see figure 1, from many experiments at different times and places onto a standard geometric space in order to allow comparison both with the expression patterns of other genes, the extent ot developing anatomy and indeed any other spatially organised information of interest. Furthermore by mapping onto a standard framework it becomes possible to enter the information into a database and to pose both textual and spatial (including image processing) queries. Much of the existing gene expression data is known only in textual terms by reference to the anatomy but in general the anatomical descriptions will be limited in detail and less specific than actual image data. To enable the inclusion of this data and to allow comparison with the known anatomical structures and tissue properties we need a digital Atlas of the developing mouse embryo onto which we can independently map the anatomy and gene-expression. The development of this atlas is part of Mouse Atlas and Gene Expression Database project[1,7,2] at the MRC in collaboration with the Department of Anatomy, University of Edinburgh.

  

Figure: Example expression patterns in a: the 12 day and b: the 9-day mouse embryo

The underlying reference image at each stage must be a full grey-level reconstruction of the histology so that the atlas can be resectioned in any arbitrary plane to compare with the experimental sections. The anatomy forms a rich spatial and temporal structure with each anatomical component identified as a 3D spatial domain at every developmental stage at which it is present so it is possible to go from anatomical name to spatial region. The reverse is also possible because every voxel is part of an anatomical domain so by straightforward search it is possible to go from spatial region to anatomy. For this to be possible we must segment and label the entire 3D volume image for each embryonic stage in the atlas. The 3D paint program has been developed for this purpose. The links between text, anatomy domain and histology as represented by the grey-level voxel reconstruction is shown in figure 2.

The basic assumption is that the final decision for the labelling of any particular voxel must be made by the biologist and therefore the result of any image processing or analysis tools must be subject to review. The structure of the program reflects this assumption and it is assumed that the user will be actively ``painting'' the reference image, calling on ``power-assist'' as required.

  

Figure: The LHS of the figure shows a screen shot of the anatomy database browser with a selection of the 9-day tissues. The RHS shows a 3D view of the reference image in ``cut-block'' view to display orthogonal and arbitrary sections through the data, none of which are in the original sectioning planes. The RHS also shows in surface rendered mode selected anatomical components identified by the connecting lines.

A second important aspect of the program is that from a pilot studies it is clear that the optimum viewing plane for identifying and painting structures is often not one of the standard sectioning planes and that it must be possible to paint in any arbitrary planes, preferably more than one at the same time. This is also required when the painting method is used for inputting section gene-expression data. It will not be possible or desirable to constrain the sectioning of the experimental embryos to the section planes of the atlas reconstructions.

The purpose of this document is to describe in some detail the mechanics of the painting program in order to provide a deeper understanding for the user and to get down in writing the precise definitions of the geometric quantities used to define the views. It is not intended as documentation of the code or as a user-guide. A user help/manual is provided as a set of html documents accessible externally or from within the program, the code is documented as manual pages and within the source code files.