| In this page are a number of images and movies generated as part of the
Mouse Atlas Gene Expression Database Project. The project is a collaboration
between the MRC Human Genetics Unit and the University of Edinburgh Department
of Anatomy. The Human Genetics Unit is the co-ordinating site - principal
investigators, R.A. Baldock (computing) and D.R. Davidson (biology).
The principal investigators at the Department of Anatomy are M.H. Kaufman
and J.B.L. Bard. See the People page for all
the members of the project.
The images shown below illustrate the reconstruction process and a number
of preliminary results. Most of these images have appeared as illustrations
in journal papers or as parts of posters or conference presentations.
In all of the images below, click on the image to get a larger version
or the corresponding movie sequence.
The images have been divided into the categories:
- Processing:- sample images from the processing
steps to generate the atlas.
- 3-D Voxel Reconstructions:- images
of the voxel models.
- Anatomy:- images of the defined anatomy using
different visualisation methods
- Database Interfaces:- picture
of some of the prototype image database interfaces.
- Gene Expression:- picture of some
gene expression domains mapped onto the 9-day embryo.
- Movies:- some movie sequences.
This page is under construction and the numbers of images and movies will
be extended to cover the range of embryos now completed within the atlas
(most of TS1-TS14).
Processing
The software show in the images below has been developed as part of the
Mouse Atlas project. The image processing is based on the "woolz" system
developed at the MRC by many authors. This will become a public domain
system in 1998. The user interfaces are implemented in C and C++ and use
Motif for the graphical interface. More details are available from the
primary author for the programs listed in the caption.
More details of the reconstruction process are also available.
3-D Voxel Reconstructions
At each stage of development grey-level voxel reconstructions of the embryo
are made from images of serial histological sections. For embryos older
than 8 days of development (Theiler Stage12; Theiler, K. (1989) The House
Mouse, Atlas of development. Springer-Verlag, New York) the sections are
cut from wax-embedded embryos at a nominal section thickness of 7 um. The
younger embryos are cut from plastic with section thickness of 2 um. The
original digitsations are at roughly 3 times the final resolution so that
the image processing steps of registration and warping do not degrade the
information content of the image. All the reconstructions below were
made using the MRC woolz software. The wax histological sections are from
Professor M Kaufman, Department of Anatomy and the serial plastic sections
cut by Allyson Ross at the Human Genetics Unit.
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Block view of part of the digitised 9-day embryo model
(based on 307, 7um wax sections)displayed using SunVision (Sun Microsystems).
The view illustrates sections made digitally through the surface of
the block containing the embryo model. |
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A similar block view of the digitised 8.5-day embryo
model (based on 243 7um wax sections)displayed using SunVision (Sun
Microsystems). |
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A block view of the 7.5 day embryo model showing arbitrary
digital sections through the voxel model. This reconstruction is based
on plastic sections and has voxel size 2x2x2um. |
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Anatomy
The anatomical structures of the nomenclature database are defined within
the corresponding voxel model by a process of image segmentation.
In the earlier embryos this is primarily a manual process of painting the
voxel images to define the anatomical domains. All the anatomy displayed
below has been defined, using the paint program, by Renske
Brune at the Department of Anatomy, University of Edinburgh. The images
are displayed using paint and using AVS
5 (contact Margaret Stark,
MRC HGU, for more information of our use of AVS5 and AVS Viz).
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Selected anatomical domains of the 9-day embryo model displayed
in section mode with overlaid anatomical components. Colours are re-used
for different painted domains, these images show the resolution of
the Mouse Atlas painted domains.
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This pseudo-3D view of the TS14 (E9.0) embryo model displays the
painted domains of the neural tube (yellow), gut (red), heart (light
blue), somites (green), optic vesicles (dark blue), otic pit (lime
green) and primitive streak (mauve). These tissues of the embryo are
enclosed in translucent surface ectoderm.
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This pseudo-3D view of the TS13 (E8.5) embryo model displays the
painted domains of the neural tube (yellow), gut (red), heart (light
blue), somites (green), optic vesicles (dark blue), otic placode (lime
green) and streak (mauve). These tissues of the embryo are enclosed
in translucent surface ectoderm.
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Stereo pair of images showing selected vessels of the 9-day embryo
model. The stereo view can be seen by crossing your eyes and
merging the two images, either with this view or the enlarged version.
The angular separation between the two views is 12 degrees. |
Database Interfaces
The Object Oriented Database and the interfaces have been developed by Christophe
Dubreuil at the MRC Human Genetics Unit. The pictures below are of a number
of prototype interfaces providing access to the anatomical nomenclature
as well as the reconstructions and anatomical domains. The section viewers
are the first example of a WWW interface giving access to arbitrary sections
views of embryo images held in a central database. The user is able to highlight
specific tissues or simply move the mouse over the image to display the
corresponding tissue name.
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The standard nomenclature database has been implemented as an Object-Oriented
database using ObjectStore. The
components for each Theiler stage are organised as a hierarchy and
can be displayed as a tree of components. This interface allows the
user to browse the tree, expanding/collapsing it as required. This
is an early prototype without and additional facilities for display
of other data (e.g. lineage, groups, annotations etc.). The Theiler
Info button links to further information on the specific stage.
Author: Christophe Dubreuil |
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The database can be searched for any specific named component. The
results are returned as a simple time-ordered list. Author:
Christophe Dubreuil |
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Identifying tissues in sections
The database will be delivered via a CORBA interface and the interfaces
for submission, query, and analysis of gene expression data will be
implemented in java. This prototype interface accesses a database
of grey-level reconstructions and the defined anatomy. Arbitrary section
views of the reconstruction can be selected and will be returned as
well as the anatomy components present. As the cursor is passed
over the section view the corresponding anatomy is displayed.
Individual components can be selected and highlighted or the fully
"painted" image displayed. Author: Christophe Dubreuil |
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An alternative section viewer has also been implemented that provides
a 3D navigational block that shows the current section plane to indicate
the context of the histological section being viewed. This interface
allows the user to interactively set the fixed points used for navigation.
If two fixed points are set (a fixed line) then the section viewing
controls become a single control slider for the rotation about that
line. Elements of this interface will be integrated with the anatomy
database tree and domain viewer. Author: Oystein Sorensen
and Christophe Dubreuil |
Gene Expression
The database currently encodes domains of gene-expression in the same
way that anatomical domains are mapped onto the reference voxel model.
Gene expression domains can be defined using MAPaint in the same way but,
whereas tissues are defined to be non-overlapping, no such restriction
applies to gene-expression. In future versions of the database the gene-expression
data will be extended to include grey-value (strength) information.
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WT1 expression (red) on a section of the E9 (Theiler Stage 14) embryo
from the Edinburgh Mouse Atlas. The gut epithelium is shown in yellow
and the neural tube in a blue overlay. WT1 is expressed in the presumptive
mesothelium of the coelom and in the intermediate mesoderm (ventral
to the somites).
Reference: Armstrong et al, .... |
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Mapped gene-expression data in the 9.5 dpc (Theiler stage 15)
mouse embryo. The expression pattern of MSX1 is shown in green,
MSX2 in red and the region showing co-expression of the genes is
displayed in orange.
The gene-expression data has been mapped from an experimental embryo
onto the standard atlas reconstruction using sofware developed at
the MRC HGU to warp the signal image onto an arbitrary section through
the standard Atlas model. For more information of the mapping process
used to produce this image see /Documentation/Technical/ge_mapping.html |
Movies
All the movies below are in MPEG format for which viewers can be obtained
for all machine architectures (see for example http://www.mpeg.org/index.html/).
Some of the movie files below are quite large so be prepared to wait for
the data to download. These sequences show best on a 24-bit display and
when viewed on an 8-bit (256 colours) display may appear degraded. If you
have problems viewing these files please seek help from your local computing
administrator/services.
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