PhagoSight: An Open-Source MATLAB® Package for the Analysis of Fluorescent Neutrophil and Macrophage Migration in a Zebrafish Model

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Henry, Katherine M. ; Pase, Luke ; Ramos-Lopez, Carlos Fernando ; Lieschke, Graham J. ; Renshaw, Stephen A. ; Reyes-Aldasoro, Constantino Carlos (2013)
  • Publisher: Public Library of Science
  • Journal: PLoS ONE, volume 8, issue 8 (eissn: 1932-6203)
  • Related identifiers: doi: 10.1371/journal.pone.0072636, pmc: PMC3758287
  • Subject: Computational Biology | Algorithms | Animal Models | Research Article | Biology | Immune Physiology | Developmental Biology | Immune Cells | Immunity | Programming Languages | TA | Anatomy and Physiology | Morphogenesis | Model Organisms | Computer Science | Inflammation | Immune Response | Biological Data Management | Cell Migration | Software Engineering | Zebrafish | Software Tools | Immunology

Neutrophil migration in zebrafish larvae is increasingly used as a model to study the response of these leukocytes to different determinants of the cellular inflammatory response. However, it remains challenging to extract comprehensive information describing the behaviour of neutrophils from the multi-dimensional data sets acquired with widefield or confocal microscopes. Here, we describe PhagoSight, an open-source software package for the segmentation, tracking and visualisation of migrating phagocytes in three dimensions. The algorithms in PhagoSight extract a large number of measurements that summarise the behaviour of neutrophils, but that could potentially be applied to any moving fluorescent cells. To derive a useful panel of variables quantifying aspects of neutrophil migratory behaviour, and to demonstrate the utility of PhagoSight, we evaluated changes in the volume of migrating neutrophils. Cell volume increased as neutrophils migrated towards the wound region of injured zebrafish. PhagoSight is openly available as MATLAB® m-files under the GNU General Public License. Synthetic data sets and a comprehensive user manual are available from http://www.phagosight.org.
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