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Updated: May 20, 2026

Mining Spatial Transcriptomics Datasets using DeepSpaceDB
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Mining Spatial Transcriptomics Datasets using DeepSpaceDB

Published on: September 5, 2025

eMouseAtlas, EMAGE, and the spatial dimension of the transcriptome.

Chris Armit1, Shanmugasundaram Venkataraman, Lorna Richardson

  • 1MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, Scotland, UK. Chris.Armit@igmm.ed.ac.uk

Mammalian Genome : Official Journal of the International Mammalian Genome Society
|August 1, 2012
PubMed
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This summary is machine-generated.

eMouseAtlas offers enhanced visualization of mouse embryo development and gene expression through its redesigned Mouse Anatomy Atlas and EMAGE databases. New tools enable interactive 3D viewing and spatial analysis of gene expression patterns.

Area of Science:

  • Developmental Biology
  • Bioinformatics
  • Genomics

Background:

  • eMouseAtlas is a resource for mouse embryo visualization and gene expression analysis.
  • Existing tools require large file downloads for 3D image exploration.

Purpose of the Study:

  • To introduce a redesigned Mouse Anatomy Atlas website with enhanced visualization tools.
  • To improve spatial analysis of gene expression data within mouse embryo models.

Main Methods:

  • Development of the IIP3D web tool for interactive 3D embryo reconstruction viewing.
  • Integration of EMAGE (Edinburgh Mouse Atlas of Gene Expression) with spatial mapping of gene expression data.
  • Implementation of optical projection tomography and WlzWarp software for 3D gene expression mapping.

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Main Results:

  • The redesigned website allows interactive viewing of 3D embryo reconstructions and histological sections.
  • The IIP3D tool provides web-based access to large 3D image datasets without downloads.
  • EMAGE now spatially maps gene expression patterns, including 3D data, enabling comparative analysis.

Conclusions:

  • The updated eMouseAtlas platform enhances the study of mouse development and gene expression.
  • New interactive tools facilitate deeper investigation of spatial transcriptomic data.
  • eMouseAtlas provides a valuable, integrated resource for developmental biology research.