SMART: An Open-Source Extension of WholeBrain for Intact Mouse Brain Registration and Segmentation.

ABSTRACT: 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 t

SUBMITTER: Jin M 

PROVIDER: S-EPMC9070730 | biostudies-literature | 2022 May-Jun

REPOSITORIES: biostudies-literature