Cell Tracking Profiler – a user-driven analysis framework for evaluating 4D live-cell imaging data

Claire A. Mitchell, Lauryanne Carof, Jose Solis-Lemus, Constantino Reyes-Aldosoro, Alessandra Vigilante, Fiona Warburton, Fabrice Chaumont, Alexandre Dufour, Stephane Dallongeville, Jean-Christophe Olivo-Marin, Robert Knight

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Accurate measurements of cell morphology and behaviour are fundamentally important for understanding how disease, molecules and drugs affect cell function in vivo. Using muscle stem cell (muSC) responses to injury in zebrafish as our biological paradigm we established a ground truth for muSC behaviour. This revealed segmentation and tracking algorithms from commonly used programs are error-prone, leading us to develop a fast semi-automated image analysis pipeline that allows user defined parameters for segmentation and correction of cell tracking. Cell Tracking Profiler (CTP) is a package that runs two existing programs, HK Means and Phagosight within the Icy image analysis suite, to enable user-managed cell tracking from 3D time-lapsed datasets to provide measures of cell shape and movement. We demonstrate how CTP can be used to reveal changes to cell behaviour of muSCs in response to manipulation of the cell cytoskeleton by small molecule inhibitors. CTP and the associated tools we have developed for analysis of outputs thus provide a powerful framework for analysing complex cell behaviour in vivo from 4D datasets that are not amenable to straightforward analysis.
Original languageEnglish
Article numberjcs241422
Number of pages12
JournalJournal of Cell Science
Early online date22 Oct 2020
Publication statusPublished - 22 Nov 2020


  • muscle
  • zebrafish
  • Cell Tracking
  • segmentation
  • In vivo imaging
  • Phagosight
  • Icy
  • Imaris


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