IntelliR: A comprehensive and standardized pipeline for automated profiling of higher cognition in mice

In the rapidly evolving field of rodent behavior research, observer-independent methods facilitate data collection within a social, stress-reduced, and thus more natural environment. A prevalent system in this research area is the IntelliCage, which empowers experimenters to design individual tasks and higher cognitive challenges for mice, driven by their motivation to access reward. The extensive amount and diversity of data provided by the IntelliCage system explains the growing demand for automated analysis among users. Here, we introduce IntelliR, a standardized pipeline for analyzing raw data generated by the IntelliCage software, as well as novel parameters including the cognition index, which enables comparison of performance across various challenges. With IntelliR, we provide the tools to implement and automatically analyze 3 challenges that we designed, encompassing spatial, episodic-like, and working memory with their respective reversal tests. Using results from 3 independent control cohorts of adult female wildtype mice, we demonstrate their ability to comprehend and learn the tasks, thereby improving their proficiency over time. To validate the sensitivity of our approach for detecting cognitive impairment, we used adult female NexCreERT2xRosa26-eGFP-DTA mice after tamoxifen induced diphtheria toxin-mediated ablation of pyramidal neurons in cortex and hippocampus. We observed deterioration in learning capabilities and cognition index across several tests. IntelliR can be readily integrated into and adapted for individual research, thereby improving time management and reproducibility of data analysis. HIGHLIGHTSO_LIIntelliR is a standardized pipeline for analyzing raw data of IntelliCage software. C_LIO_LIDomains include spatial, episodic-like, and working memory with reversals. C_LIO_LIWT mice (3 cohorts) comprehend, learn and improve proficiency over time. C_LIO_LICognition index permits comparison of performance across cognitive domains. C_LIO_LIMice with ablation of pyramidal neurons decline mainly in working memory. C_LI