Systems and methods for the analysis of the diverse behaviors of animal subjects in defined areas are provided, including tools for filtering and analysis of high-resolution behavioral data. These systems and methods provide an opportunity to examine behavioral patterns with levels of precision and quantization that have not been previously achieved. Methods and systems for managing and analyzing the very large and unique datasets produced by behavioral monitoring systems, including quality assessment and control, archiving, data query, data reduction, analytical procedures and visualization techniques are provided. Such detailed analyses of spontaneous behavior provide fundamental insights into the neural organization of behavior and enable detection of genetic, pharmacological and environmental influences on brain function with high sensitivity.