Integrating MR with 3D Gene Expression Data in the Mouse Brain

Christopher Lau¹, Lydia Ng¹, Chihchau Kuan¹, Changkyu Lee¹, Mallar Chakravarty¹, Allan Jones¹, George Allan Johnson², Michael Hawrylycz¹

The Allen Brain Atlas (ABA) adult C56BL/6J mouse brain database of over 20,000 in situ gene expression patterns was registered with a set of multispectral 21.5 micron resolution target MR volumes (T1, T2, and T2*). We developed a 3D viewing application that enables comparison of gene expression patterns with MR data. The application can search for genes expressing in regions of interest defined in MR images, and co-visualize gene expression or histology with MR. This application forms a bridge between the transcriptome and MR data in the mouse brain.