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PhagoSight: an open-source MATLAB® package for the analysis of fluorescent neutrophil and macrophage migration in a zebrafish model

Henry, K. M., Pase, L., Ramos-Lopez, C. F., Lieschke, G. J., Renshaw, S. A. and Reyes-Aldasoro, C. C. (2013). PhagoSight: an open-source MATLAB® package for the analysis of fluorescent neutrophil and macrophage migration in a zebrafish model. PLoS One, 8(8), e72636. doi: 10.1371/journal.pone.0072636

Abstract

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.

Publication Type: Article
Publisher Keywords: Algorithms, Animals, Cell Movement, Cell Size, Databases as Topic, Fluorescence, Image Processing, Computer-Assisted, Macrophages, Models, Animal, Neutrophil Infiltration, Neutrophils, Reference Standards, Reproducibility of Results, Software, Time Factors, Wound Healing, Zebrafish
Subjects: T Technology > TA Engineering (General). Civil engineering (General)
Departments: School of Mathematics, Computer Science & Engineering > Engineering
School of Mathematics, Computer Science & Engineering > Engineering > Electrical & Electronic Engineering
Related URLs:
URI: http://openaccess.city.ac.uk/id/eprint/3735
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