Christopher Lau1, Lydia Ng1, Chihchau Kuan1, Changkyu Lee1, Mallar Chakravarty1, Allan Jones1, George Allan Johnson2, Michael Hawrylycz1
1Allen Institute for Brain Science, Seattle, WA, United States; 2Center for In Vivo Microscopy, Duke University
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.