The mouse atlas project has developed a number of imaging tools and techniques. The underlying imaging software is based on the woolz image processing library. Most of the histology images have been digitised with in-house imaging systems and software (MAXmgrab) using a XilliX microimager 1400 camera mounted on a Zeiss Axioplan microscope. The 3D reconstruction from sections is performed using a number of tools: Reconstruct, mawarp and MAPaint. MAWarpPaint complement MAPaint by enabling the use of the warping software to rapidly "paint" (manually segment) an image stack. MA3DView is for reviewing 16 bit 3D datasets, setting optimal 16-8 bit conversion parameters and for defining a suitable bounding box. Recently Dr Jame Sharpe has developed Optical Projection Tomography (OPT) a novel and non-destructive way of capturing true 3D image data from an intact specimen. More detail of these imaging resources are given below.

	Optical Projection Tomography (OPT) is a novel microscopic imaging technique which captures 3D data directly without the need to physically section the specimen. The technique is likely to deliver images with pixel resolution from 1-20 microns with a specimen size range from 1-40 mm. It also allows the use of standard whole-mount staining protocols and has been tested for live-cell imaging. The specimen is undamaged and can be used for further analysis including microtome sectioning for high-resolution microscopy and detailed in situ staining (e.g. hybridisation or immunohistochemistry).
	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.
	MAWarpPaint - use warping for rapid segmentation map fitting
	3D Confocal Reconstruction of Gene Expression in the Mouse