title: UltraTrack: Software for semi-automated tracking of muscle fascicles in sequences of B-mode ultrasound images.
abstract: BACKGROUND
  Dynamic measurements of human muscle fascicle length from sequences of B-mode ultrasound images have become increasingly prevalent in biomedical research. Manual digitisation of these images is time consuming and algorithms for automating the process have been developed. Here we present a freely available software implementation of a previously validated algorithm for semi-automated tracking of muscle fascicle length in dynamic ultrasound image recordings, "UltraTrack".
  
  
  METHODS
  UltraTrack implements an affine extension to an optic flow algorithm to track movement of the muscle fascicle end-points throughout dynamically recorded sequences of images. The underlying algorithm has been previously described and its reliability tested, but here we present the software implementation with features for: tracking multiple fascicles in multiple muscles simultaneously; correcting temporal drift in measurements; manually adjusting tracking results; saving and re-loading of tracking results and loading a range of file formats.
  
  
  RESULTS
  Two example runs of the software are presented detailing the tracking of fascicles from several lower limb muscles during a squatting and walking activity.
  
  
  CONCLUSIONS
  We have presented a software implementation of a validated fascicle-tracking algorithm and made the source code and standalone versions freely available for download.
authors.affiliation: School of Human Movement & Nutrition Sciences, Level 5, Building 26B, Blair Drive, The University of Queensland, Brisbane, QLD 4072, Australia. Electronic address: d.farris@uq.edu.au.
authors.forename: Dominic James
authors.initials: DJ
authors.lastname: Farris
authors.affiliation: School of Human Movement & Nutrition Sciences, Level 5, Building 26B, Blair Drive, The University of Queensland, Brisbane, QLD 4072, Australia. Electronic address: g.lichtwark@uq.edu.au.
authors.forename: Glen A
authors.initials: GA
authors.lastname: Lichtwark
mesh_terms: D000465:Algorithms; D019295:Computational Biology; D003201:Computers; D015444:Exercise; D006801:Humans; D007091:Image Processing, Computer-Assisted; D009068:Movement; D009119:Muscle Contraction / Q000502:physiology; D018482:Muscle, Skeletal / Q000000981:diagnostic imaging*; D010363:Pattern Recognition, Automated; D011381:Programming Languages; D015203:Reproducibility of Results; D012984:Software; D014463:Ultrasonography; D016138:Walking
keywords: Affine optic flow; Automated; Fascicle; Matlab; Tracking; Ultrasound