Software developed as part of the Mouse Atlas Project at the Human Genetics Unit MRC was initially aimed at a Solaris Unix platform with an X11/Motif user interface. More recent software uses Java to provide the GUI and is therefore available for all platforms and operatiing systems that support the Java Virtual Machine. We are moving to a fully open-source licencing and in the interim the software can be obtained by emailing Richard Baldock.

Some code currently available can be found on the MRC Human Genetics Unit anonymous ftp server.

	WlzIIP server and viewer provide a novel fast method to access large 3D volumetric data sets of biological or medical imaging atlases. These tools have been developed as part of the NIH funded Human Brain Project (NIH) "Electronic Atlas of the developing Human Brain".
	Java tools for browsing Atlas image data, format conversion and reconstruction. These are prototype tools that have been developed as part of the NIH funded Human Brain Project (NICHD and NIMH) "Electronic Atlas of the developing Human Brain".
	The Woolz image processing library has been developed in the MRC Human Genetics Unit originally for high-speed microscope slide scanning and chromosome classification. It is an interval based image processing system with associated Unix binaries and is used throughout the project. We have developed a version of this library to be used with the persistant objects held in an ObjectStore ODBMS from Object Design Inc.
	Interactive image capture program for the an MRC Xillix camera interface for Solaris. This is now being ported to the Engineering Design Team (EDT) camera interface. The software includes some assistance for section alignment/registration and support for patched images as well as all the required shade corrections and calibrations.
	Reconstruct provides interactive registration and reconstruction of a voxel image from a series of 3D digital images. The 2D image input format is Woolz for which conversion filters are available. The voxel output can be in a range of 3D formats.
	The warping program will warp a stack of images to correct random sectioning distortions. The process is fully automatic and is based on an elastic sheet model for each 2D image with distorting forces arising from matching between sections. The equilibrium "warped" state is found using the finite element method (FEM).
	MAPaint is a program to allow manual and "power-assisted" delineation or painting of a 3D voxel image. The program can be used to review the anatomy and reconstructions of the Edinburgh Mouse Atlas as well as defining new (arbitrary) domains e.g. gene-expression. The programs allows painting onto any arbitrary section through the volume as well as a number of automatic tracking and segmentation methods.
	VTK is a toolkit for 2D and 3D image display. We use it for volume rendering the grey-level reconstructions and painted volumes, especially to generate the embryto views on the CD-ROM. These are produced by scripts then visualised using a Java applet/application developed here at the Human Genetics Unit. Example scripts are available on the ftp site ftp.hgu.mrc.ac.uk:/pub/MouseAtlas/vtk_scripts, please see the UsingVtk page for some hints on how to install vtk and run the programs.