We present an automated method for the tracking and dynamics modeling of microtubules -a major component of the cytoskeleton- which provides researchers with a previously unattainable level of data analysis and quantification capabilities. The proposed method improves upon the manual tracking and analysis techniques by i) increasing accuracy and quantified sample size in data collection, ii) eliminating user bias and standardizing analysis, iii) making available new features that are impractical to capture manually, iv) enabling statistical extraction of dynamics patterns from cellular processes, and v) greatly reducing required time for entire studies. An automated procedure is proposed to track each resolvable microtubule, whose aggregate activity is then modeled by mixtures of Hidden Markov Models to uncover dynamics patterns of underlying cellular and experimental conditions. Our results support manually established findings on an actual microtubule dataset and illustrate how automated analysis of spatial and temporal patterns offers previously unattainable insights to cellular processes.