SMART: An open source extension of WholeBrain for iDISCO+ LSFM intact mouse brain registration and segmentation

The SMART package was created with the novice programmer in mind and introduces a streamlined pipeline for aligning, registering, and segmenting large LSFM volumetric datasets with the CCF across the anterior-posterior axis, using a simple ‘choice game’ and interactive user-friendly menus. SMART further provides the flexibility to register partial brains or discrete user-chosen experimental images across the CCF, making it compatible with analysis of traditionally sectioned coronal brain slices. In addition to SMART, we introduce a modified tissue clearing protocol based on the iDISCO+ procedure that is optimized for uniform Fos antibody labeling and tissue clearing across whole intact mouse brains. Here we demonstrate the utility of the SMART-WholeBrain pipeline, in conjunction with the modified iDISCO+ Fos procedure, by providing example datasets alongside a full user tutorial. Finally, we present a subset of these data online in an interactive web applet. The complete SMART package is available for download on GitHub.