Three-dimensional digital mouse atlas using high-resolution MRI

We present an archetypal digital atlas of the mouse embryo based on microsc opic magnetic resonance imaging. The atlas is composed of three modules: (1 ) images of fixed embryos 6 to 15.5 days postconception (dpc) [Theiler Stag es (TS) 8 to 24]; (2) an annotated atlas of the anterior portion of a 13.5 dpc (TS 22) mouse with anatomical structures delineated and linked to expla natory files; and (3) three-dimensional renderings of the entire 13.5 dpc e mbryo and specific organ systems. The explanatory files include brief descr iptions of the structure at each volume element in the image and links to 3 D reconstructions, allowing visualization of the shape of the isolated stru ctures. These files can also contain or be linked to other types of informa tion and data including detailed anatomical and physiological information a bout structures with pointers to online references, relationships between s tructures, temporal characteristics (cell lineage patterns, size, and shape changes), and gene expression patterns (both spatial and temporal). As an example, we have "painted" in the expression pattern of D1x5/D1x6 genes. Th is digital atlas provides a means to put specific data within the context o f normal specimen anatomy, to analyze the information in 3D, and to examine relationships between different types of information. (C) 2001 Academic Pr ess.