Virtual Mouse Brain Atlas for iPad

The Center for in Vivo Microscopy at Duke University Medical Center led by Dr. G Allan Johnson, is investigating the use of new publishing media to expand the possibilities to share image data and their educational value. Last October, they released an iPad application that provides an atlas of 3D MR images of the C57BL/6J mouse brain in digital format with labels for 40 different brain structures.

Virtual Mouse Brain for iPAD_4

At the first INCF Digital Atlasing Task Force meeting in Waxholm, it was proposed to develop a magnetic resonance imaging (MRI) -based reference space to serve as a common platform for the integration of different digital images and other data on the mouse brain. Waxholm Space (WHS) was developed based on actively stained (using Gadolinum), high–resolution images acquired using high field (9.4T) MRI at the Duke Center for In Vivo Microscopy (CIVM). The 3 MR contrasts acquired at CIVM were accompanied by Nissl stainings that were performed at Drexel University in the lab of Johnatan Nissanov. Thirty-seven regions of the brain were manually traced onto the MR images and co-registered with the Nissl volume reconstructed brain.  In addition to WHS, an average population atlas was released at the same time with superior signal to noise ratio and the same 37 labels determined based on automated registration. These data sets were made available to the public from the CIVM and INCF servers (1).

The high resolution inherent to the MR microscopy datasets makes visualization of these large image matrices difficult on a regular desktop computer, so specialized visualization software tools, capable of holding into memory multiple large datasets like the WHS sets are computer resource demanding (in terms of memory), and in general expensive. Besides visualization resources, the datasets may require knowledge of modern digital image formats, such as NIFTI. To enable a broader community to access digital atlasing resources such as WHS, we thought of using one of the new forms of electronic media. The iPad is a user-friendly platform that has gained popularity extremely fast.

 With hope to increase accessibility to these datasets, an iPad application has been built to present the average WHS atlas, with enhanced T1, T2*, and T2 with contrast to noise ratios (relative to the single specimen atlas). The labeling is improved and the number of brain structures is increased to 40. Visualization is intuitive and the anatomical structures are presented overlaid on the MR images in the three cardinal planes, as well as 3D surface models. These regions are color-coded and are callable from a hierarchically organized list with multiple levels anatomical details. Other enhancements include a better alignment of the WHS mouse brain atlas to the traditional mouse brain atlas in stereotaxic coordinates that was developed by George Paxinos and Keith Franklin.

The 40 brain regions were manually defined using Avizo (VSG, Burlington, MA) on an average mouse brain template based on images from multiple specimens, as described in (2). The regions contours are color coded, to help identify the anatomy, and overlaid on top of the MR images. They can be switched on or off and can be called upon from a menu where the structures are arranges in a hierarchical fashion to facilitate the educational experience. Brain navigation is done interactively by manipulating a 3D surface representation of the brain and its subcomponents (rotating, slicing, and advancing through these object representations). The smooth visualization tools circumvent the need for desktop users to buy commercial software with capabilities to interactively visualize multiple, large datasets, and overlay manual label contours.

The project was developed over a couple of months through a collaboration between CIVM and Lunatic Fringe Design (Durham, NC). The team included:  Dr. G Allan Johnson - the director of CIVM, David Adcock from Lunatic Fringe Design, Matthew Sherrier - an intern at CIVM, and Alexandra Badea – an Assistant Professor member of the CIVM neuroimaging research group. 

Virtual Mouse Brain for iPAD_3

StartquoteWe find the Virtual Mouse Brain app handy as a neuroanatomical reference, easy to transport on the sleek iPad whenever histological atlases are not available, and at a fraction of their cost. The VMB offers complementary contrasts to add to the multitude of histological stains, and an unprecedented 3D visualization of the spatial relationship among brain structures, based on an undistorted MR acquisition in situ, where the brain was left in the skull Endquote explains Alexandra Badea.

The app can be downloaded from the iTunes store, for $4.99. The original MR mouse brain atlas was supported by NCRR to CIVM as a national Biomedical Technology Research Center (P41 RR005959) and NCI Small Animal Imaging Resource Program (U24 CA092656). Additional support was supplied by the Mouse Biomedical Informatics Research Network (MBIRN) (U24 RR021760) and the International Neuroinformatics Coordinating Facility (INCF).

A YouTube movie gives a brief intro to the app here


1. Access the WaxholmSpace data via the INCF Software Center:

 2.         Johnson GA, Badea A, Brandenburg J, Cofer G, Fubara B, Liu S, et al. Waxholm space: an image-based reference for coordinating mouse brain research. Neuroimage. 2010;53(2):365-72. Epub 2010/07/06. doi: S1053-8119(10)00927-4 [pii]10.1016/j.neuroimage.2010.06.067 [doi]. PubMed PMID: 20600960.


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