TY - JOUR T1 - SMART: An Open-Source Extension of WholeBrain for Intact Mouse Brain Registration and Segmentation JF - eneuro JO - eNeuro DO - 10.1523/ENEURO.0482-21.2022 VL - 9 IS - 3 SP - ENEURO.0482-21.2022 AU - Michelle Jin AU - Joseph D. Nguyen AU - Sophia J. Weber AU - Carlos A. Mejias-Aponte AU - Rajtarun Madangopal AU - Sam A. Golden Y1 - 2022/05/01 UR - http://www.eneuro.org/content/9/3/ENEURO.0482-21.2022.abstract N2 - Mapping immediate early gene (IEG) expression across intact mouse brains allows for unbiased identification of brain-wide activity patterns underlying complex behaviors. Accurate registration of sample brains to a common anatomic reference is critical for precise assignment of IEG-positive (“active”) neurons to known brain regions of interest (ROIs). While existing automated voxel-based registration methods provide a high-throughput solution, they require substantial computing power, can be difficult to implement and fail when brains are damaged or only partially imaged. Additionally, it is challenging to cross-validate these approaches or compare them to any preexisting literature based on serial coronal sectioning. Here, we present the open-source R package SMART (Semi-Manual Alignment to Reference Templates) that extends the WholeBrain R package framework to automated segmentation and semi-automated registration of intact mouse brain light-sheet fluorescence microscopy (LSFM) datasets. The SMART package was created for novice programmers and introduces a streamlined pipeline for aligning, registering, and segmenting LSFM volumetric datasets across the anterior-posterior (AP) axis, using a simple “choice game” and interactive menus. SMART provides the flexibility to register whole brains, partial brains or discrete user-chosen images, and is fully compatible with traditional sectioned coronal slice-based analyses. We demonstrate SMART’s core functions using example datasets and provide step-by-step video tutorials for installation and implementation of the package. We also present a modified iDISCO+ tissue clearing procedure for uniform immunohistochemical labeling of the activity marker Fos across intact mouse brains. The SMART pipeline, in conjunction with the modified iDISCO+ Fos procedure, is ideally suited for examination and orthogonal cross-validation of brain-wide neuronal activation datasets. ER -