title: Associating approximate paths and temporal sequences of noisy detections: Application to the recovery of spatio-temporal cancer cell trajectories.
abstract: In this paper we address the problem of recovering spatio-temporal trajectories of cancer cells in phase contrast video-microscopy where the user provides the paths on which the cells are moving. The paths are purely spatial, without temporal information. To recover the temporal information associated to a given path we propose an approach based on automatic cell detection and on a graph-based shortest path search. The nodes in the graph consist of the projections of the cell detections onto the geometrical cell path. The edges relate nodes which correspond to different frames of the sequence and potentially to the same cell and trajectory. In this directed graph we search for the shortest path and use it to define a temporal parametrization of the corresponding geometrical cell path. An evaluation based on 286 paths of 7 phase contrast microscopy videos shows that our algorithm allows to recover 92% of trajectory points with respect to the associated ground truth. We compare our method with a state-of-the-art algorithm for semi-automated cell tracking in phase contrast microscopy which requires interactively placed starting points for the cells to track. The comparison shows that supporting geometrical paths in combination with our algorithm allow us to obtain more reliable cell trajectories.
authors.affiliation: Knowledge-Based Vision Systems, Software Competence Center Hagenberg GmbH, Softwarepark 21, Hagenberg 4232, Austria.
authors.forename: Matthias
authors.initials: M
authors.lastname: Dorfer
authors.affiliation: Knowledge-Based Vision Systems, Software Competence Center Hagenberg GmbH, Softwarepark 21, Hagenberg 4232, Austria.
authors.forename: Tomáš
authors.initials: T
authors.lastname: Kazmar
authors.affiliation: Knowledge-Based Vision Systems, Software Competence Center Hagenberg GmbH, Softwarepark 21, Hagenberg 4232, Austria.
authors.forename: Matěj
authors.initials: M
authors.lastname: Šmíd
authors.affiliation: Knowledge-Based Vision Systems, Software Competence Center Hagenberg GmbH, Softwarepark 21, Hagenberg 4232, Austria.
authors.forename: Sanchit
authors.initials: S
authors.lastname: Sing
authors.affiliation: Institut für Allgemeine Pathologie und Pathologische Anatomie, Technische Universität München, Germany.
authors.forename: Julia
authors.initials: J
authors.lastname: Kneißl
authors.affiliation: Institut für Allgemeine Pathologie und Pathologische Anatomie, Technische Universität München, Germany.
authors.forename: Simone
authors.initials: S
authors.lastname: Keller
authors.affiliation: LISA-image, Université Libre de Bruxelles, Belgium.
authors.forename: Olivier
authors.initials: O
authors.lastname: Debeir
authors.affiliation: Institut für Allgemeine Pathologie und Pathologische Anatomie, Technische Universität München, Germany.
authors.forename: Birgit
authors.initials: B
authors.lastname: Luber
authors.affiliation: Knowledge-Based Vision Systems, Software Competence Center Hagenberg GmbH, Softwarepark 21, Hagenberg 4232, Austria. Electronic address: Julian.Mattes@scch.at.
authors.forename: Julian
authors.initials: J
authors.lastname: Mattes
mesh_terms: D000465:Algorithms; D045744:Cell Line, Tumor; D002465:Cell Movement; D058948:Cell Tracking / Q000379:methods*; D003198:Computer Simulation; D006801:Humans; D007089:Image Enhancement / Q000379:methods; D007090:Image Interpretation, Computer-Assisted / Q000379:methods*; D008858:Microscopy, Phase-Contrast / Q000379:methods*; D018715:Microscopy, Video / Q000379:methods*; D015233:Models, Statistical; D010363:Pattern Recognition, Automated / Q000379:methods*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D012815:Signal Processing, Computer-Assisted; D059629:Signal-To-Noise Ratio; D062211:Spatio-Temporal Analysis; D013274:Stomach Neoplasms / Q000473:pathology* / Q000503:physiopathology; D013382:Subtraction Technique
keywords: Cancer cell; Graph; Phase-contrast microscopy; Shortest path; Tracking