WELCOME TO THE EDINBURGH MOUSE ATLAS SOFTWARE CD-ROM PAGES

The CD-ROM contains software that can be installed on a users own computer.

The software includes the MAPaint and Java WlzViewer programs. These programs allow the user to view the Mouse Atlas 3D models and anatomy domains in any plane. MAPaint can also be used to paint and define arbitrary regions in 2D and 3D space. A suite of utility programs is also included, that enables manipulation of spatial data, and conversion from the Mouse Atlas woolz image format to more common image formats (jpg, tif, etc.).

The software should be used along with the companion Atlas Data CD-ROM that contains the MouseAtlas Models and anatomy domains.

Please read our Copyright and License agreement for the terms and conditions applicable to using the software.

Help documentation is not complete, so please contact us for more information regarding the use of the software or for help with the CD.

Software Installation Instructions

JWlzViewer Installation Instructions

Using The Software

MAPaint
Help With Mapping
Help With Woolz Programs

Contact

Software Installation Instructions

The software on the CD-ROM has been tested using several operating systems.
The installation and use of the software varies depending on which operating system is used on your computer.

Please choose the link below that most closely matches your operating system.

The operating systems currently available are:-

MAC OSX 10.3.x (Panther) We cannot support versions of OSX older than v10.3 as the necessary downloads from Apple are no longer available.
Linux
Solaris (sparc)
Windows
Other

JWlzViewer Installation Instructions

JWlzViewer is a 3D image viewer program. It allows the user to view MouseAtlas Woolz format images and anatomy domains. It will run on Unix, MacOSX and Windows computers.

JWlzViewer is a self contained package and is located on the CD-ROM in the JWlzViewer folder. JWlzViewer can run directly from the CD, but it will run much more efficiently if installed on your own computer.

To install, simply copy the JWlzViewer folder from the CD-ROM to your own computer. Open the readme.htm file in the JWlzViewer folder with any web browser to find instructions on how to start the program. The readme.htm file also contains links to a tutorial on how to use JWlzViewer.

Using The Software

MAPaint

MAPaint is an interactive program that allows a user to examine a 3D data volume, such as the EMAP Models. It also allows users to define 3D domains (regions of interest) by the use of painting tools.

Using MAPaint to Browse a 3D Model - shows an example of how to look at a 3D volume.

Help With Mapping

Step by step instruction guides on how to use MAPaint to spatially map data into the virtual space of an EMAP Atlas embryo model are available for coloured section data (eg. NBT/BCIP stained) and wholemount data.

These guides are also available as pdf format colouredsection.pdf and wholemount.pdf
or as MS-Word format colouredsection.doc and wholemount.doc.

If you wish to try the exercises in the guides, the data files used in the examples are here - AP2.jpg Msx2.bf.jpg Msx2.df.jpg sox10.jpg.

Help With Woolz Programs

Woolz programs manipulate 3D (and 2D) data volumes that have been created in the EMAP Woolz format.
The Index of woolz commands contains a summary description of each program and links to pages that give a fuller description, including the syntax required to run the program from the unix command line.

Contact

If you need help with the CD-ROM please contact:-

ma-edit@hgu.mrc.ac.uk

MRC Human Genetics Unit
Western General Hospital
Crewe Road
Edinburgh
EH4 2XU, UK.

Phone +44 (0)131 332 2471