Animal pose estimation (APE) is utilized in preclinical research settings for various neurological disorders such as Parkinson's disease (PD), Huntington's disease (HD) and multiple sclerosis. The technique includes real-time scoring of impairment in the animals during testing or video recording. This is a time-consuming operation prone to errors due to visual fatigue. To overcome these shortcomings, APE automation by deep learning has been studied. The field of APE has gone through significant development backed by improvements in deep learning techniques. These developments have improved 2D and 3D pose estimation, 3D mesh reconstruction and behavior prediction capabilities. As a result, there are numerous sophisticated tools and datasets available today. Despite these developments, APE still lags behind human observer scoring with respect to accuracy and flexibility under complex scenarios. In this project, two critical challenges are being addressed within the context of neurological research focusing on PD. The first challenge is about the lack of comprehensive diverse datasets necessary for accurate training as well as for fine-tuning deep learning models. This is compounded by the inherent difficulty in working with uncooperative rodent subjects, whose unpredictable behaviors often impede reliable data collection. The second challenge focuses on reduction in variation of scores that result from being scored by different evaluators. This will also involve tackling bias and reducing human error for the purpose of reliable and accurate assessments. In order to address these issues, systematic data collection and deep learning in APE have been utilized to automate manual scoring procedures. This project will contribute to neurological research, particularly in understanding and treating disorders like PD. The goal is to improve methods used in assessing rodent behavior which could aid in developing effective therapeutics. The successful implementation of an automated scoring mechanism could set a new standard in neurological research, offering insights and methodologies that are more accurate and reliable.