The Mouse Atlas Anatomy Atlas website provided interactive viewers for the 3D embryo models for each stage, viewers for the high-resolution section images used to develop the models, an interactive viewer for the embryo anatomy ontology and links providing information about embryo staging and links to movies of each embryo. Links to free download of these data are provided here with an additional link to a tutorial video on how to visualise the data on your own machine using ITK-Snap.

The eHistology Atlas with Kaufman Annotations is based on the “Atlas of Mouse Development” (Kaufman 1992) and additional coronal sections published in the later Supplement to this Atlas (1st Edition Baldock et al, 2016; 2nd Edition Morris-Kay and Srinivas, 2024) in a collaboration with Academic Press/Elsevier. The histological sections used for the original atlas have been scanned at high-resolution and provided online with the annotations transferred from the printed volume. Each high resoluton section image can be indiviually downloaded along with data files defining the text annotations and their positions within each image. In addition the eHistology atlas browser has been transferred to the HDBR Atlas resource in Newcastle who are hosting all of the Kaufman Atlas and Supplement images using the same annotaions as provided in the books. These can be accessed interactively as well as similar series for the human embryo. Finally the Placenta Atlas (Perez-Garcia et al, 2018) images, developed as part of the Wellcome DMDD project, are also published on the HDBR website.

The driving purpose for the Edinburgh Mouse Atlas of Anatomy comprising standard models for each stage of development was to enable capture by spatial mapping of 2-D and 3-D gene-expression data. Mapping the spatial patterns of expression onto a standard framework then enables direct pattern query, comparison and analysis in purely spatial terms. The EMAGE web-pages provided dynamic spatial matching allowing users to "draw" or import a spatial pattern to be used to query the expression data, it also provide spatial comparison between entries to find similar patterns. This capability relied on fast image-processing behind the web-application which is no longer available. All of the original images used for mapping and the resulting mapped patterns are available in the repositories listed below and the software used for comparison is available from the ma-tech GitHub repository (Additional Links and Resources). Download of this data and implementing the image software would enable the spatial analysis to be executed locally.

All of the ~32,600 eMAGE assay pages have been captured in pdf format and can be downloaded of local query. The spreadsheets of oll assays can be used to search and query the data in terms of gene, stage, data type, source etc. then the location of the corresponding pages, images and mapped data is given. All of the pages can be downloaded from DataShare and the image data from DataVault.

All of the data with text-annotated gene-expression patterns in eMAGE are also accessible from the Mouse Genome Informatics (MGI) gene-expression database GXD and the set of EurExpress data is also available the GenePaint resource.

Intro text here.