CRCNS: Data Sharing: Open Web Atlas for High-Resolution 3D Mouse Brain Data Grant uri icon


  • This Project will support the web-based data sharing of high-resolution, high-quality, whole mouse brain data obtained from an innovative 3D microscopy technology called Knife-Edge Scanning Microscopy (KESM). Furthermore, the data from KESM will be linked to other existing, complementary data sets such as the Allen Brain Atlas containing extensive gene expression data, effectively multiplying the utility of the resource for neuroscientists studying the brain by relating structural data (microstructure) to functional data (gene expression). The central goal of this project is to devise a web-based data dissemination framework to link and to deliver massive amounts of mouse brain data (up to 2 terabytes per brain) to the neuroscience research community in an easily accessible form. To this end, the research team will design and develop a light-weight, web-based 3D visualization and annotation framework so that the KESM data can be viewed, annotated, and analyzed at multiple resolutions (imagine Google Maps in full 3D). The project is expected to result in a unique resource that provides an unprecedented look into the wiring of the entire mouse brain in the context of large-scale gene expression data. Such a resource can help scientists begin to unravel the intricate functions of the brain, and in the long term enable the construction of intelligent artifacts based on such an understanding. The project will involve graduate and undergraduate researchers, and a simplified version of the resource will be created to kindle interest and fascination for brain science in K12 students and in the general public. The framework developed in this project is expected to have broader application in geology, meteorology, and even in astronomy where huge amounts of 3D data are gathered routinely yet the access limited due to the massiveness and 3D nature of the data. All data and software resulting from this project will be released in the public domain, available in full at

date/time interval

  • 2012 - 2015