Waxholm Space: An image-based reference for coordinating mouse brain research

Abstract

We describe an atlas of the C57BL/6 mouse brain based on MRI and conventional Nissl histology. Magnetic resonance microscopy was performed on a total of 14 specimens that were actively stained to enhance tissue contrast. Images were acquired with three different MR protocols yielding contrast dependent on spin lattice relaxation (T1), spin spin relaxation (T2), and magnetic susceptibility (T2*). Spatial resolution was 21.5 microns (isotropic). Conventional histology (Nissl) was performed on a limited set of these same specimens and the Nissl images were registered (3D-to-3D) to the MR data. Probabilistic atlases for 37 structures are provided, along with average atlases. The availability of three different MR protocols, the Nissl data, and the labels provides a rich set of options for registration of other atlases to the same coordinate system, thus facilitating data-sharing. All the data is available for download via the web.

Assembling models of embryo development: Image analysis and the construction of digital atlases

“…Mouse is the major mammalian model organism for biomedical investigations and much effort has been devoted to the reconstruction of their development (MacKenzieGraham et al, 2004;Carson et al, 2005;Kovac;evic;Ma et al, 2005;Lein et al, 2007;Johnson et al, 2010;Richardson et al, 2010;Hawrylycz et al, 2011). The relatively large size of the mouse embryo makes it difficult to capture the whole specimen in a single-shot, in-toto imaging strategy ("Imaging modalities" section) with sufficient spatial resolution ("Spatial scopes and resolutions" section).…”

“…Examples of such methods can be found in Ma et al (2005), Kovacevic et al (2005), Dorr et al (2008), Johnson et al (2010), andUllmann etal. (2010).…”

“…Although average templates usually imply a better signalto-noise ratio than individual specimens and exhibit a better definition in very similar regions between specimens, they fail to faithfully model fine features and regions with a high variability, lowering their definition (Kovacevic et al, 2005;Dorr et al, 2008). Finally, some approaches used a probabilistic template (Johnson et al, 2010) where specimens' variability is represented by statistical confidence limits.…”

“…Multiresolution approaches are also employed to optimize the mapping procedure in a coarse-to-fine strategy (Smith et al, 2004;Kovacevic et al, 2005;Tomer et al, 2010). Finally, multimodal approaches combine information coming from different imaging modalities, merging, for instance, histology and MRI (MacKenzie-Graham et al, 2004;Johnson et al, 2010). Such approaches provide multiple entry points to match different individuals and heterogeneous populations into the same coordinate system.…”

Magnetic Resonance Microscopy

“…Analogous to efforts in human brain imaging, the mouse neuroimaging community has developed brain atlases, for several mouse strains including C57BL/6, 129S1/SvIm [4,59,[74][75][76]. The digital imaging task force of the International Neuroinformatics Coordinating Facility (INCF, www.incf.org) is developing tools to facilitate the international sharing of data from the mouse brain [46].…”