AMP: An Automated Marker Based Motion Capture Processing Pipeline for Kinematic Trajectory Label Scrubbing and Gaps Filling

Marker-based optical motion capture remains the gold standard for kinematic analysis across biomechanical research. However, when tracking dynamic movements, severe occlusions often create missing data and noisy signals that require time-consuming manual cleaning. Existing automated methods usually rely on predefined skeleton models or need massive training datasets for machine learning solutions. This study presents the AMP: an automated marker based motion capture processing pipeline. The AMP is a fully analytical approach that uses hierarchical algorithms including 1) rigid-body constraint, 2) Kalman Filter state estimation and 3) kinematic pattern match to label markers and fill data gaps without manual human intervention. First, the algorithm identifies and removes mislabeling markers before any data scrubbing. During the data cleaning process, our hierarchical algorithm uses a translation-based step to track segments even when there are insufficient donor markers to form a full rigid body. To reconstruct missing marker trajectories, the pipeline initially uses Piecewise Cubic Hermite Interpolating Polynomial (PCHIP) interpolation for short marker gaps. However, the PCHIP creates massive spatial errors during long occlusions, the system automatically switches to rigid-body tracking for gaps over 40 ms. Results showed the pipeline drastically reduced processing time compared to manual human expert methods by 73.5%. In addition, the AMP kept spatial errors within 10 mm of the manual ground truth. By using this combined hierarchical approach to match marker processing accuracy, the pipeline provides a fast, general-purpose tool that fully automates data cleaning and saves hours of manual effort.