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PhagoSight: an open-source MATLAB package for the analysis of neutrophils and macrophage migration
To address the challenging task of analysing the motion and shape tracking of Neutrophils in Zebrafish we have developed PhagoSight, a software package based on MATLAB. The package provides semi-automated algorithms that read and transform large datasets into MATLAB format, segment and track neutrophils in time, and provide a large number of quantitative measurements from which users are able to analyse the behaviour of their datasets. The package performs many pre- and post-processing steps: intensity thresholds are pre-selected based on Otsu’s algorithm which the user then can verify manually if desired. Temporal variation of intensity is analysed as cells that disappear from their tracks and then re-appear a few points later. Collision of cells are analysed by measuring the volume of cells in time and splitting cells when their volume increases considerably. Finally, as the lack of proofreading and editing tools has been one of the main barriers to adopt automated and semi-automated methods we provide proofreading and editing tools, through which users can evaluate the output of algorithms and correct mistakes that can be visually detected.
The zebrafish, also known as Danio rerio, is a tropical freshwater fish, named for the five uniform, pigmented, horizontal blue stripes on the side of the body, all of which extend to the end of the caudal fin.
Two crucial advantages of zebrafish for in vivo cell observation make it a very attractive model: first, larval forms of the zebrafish are transparent, it is possible to see through the outer layers. Second, animals are readily genetically manipulated to allow labelling of individual cell populations with fluorescent tags. See Fish for Science for more details.
This website and its algorithms have evolved from a collaboration between the universities of Sheffield and City University London which started with a conference publication (PRIB 2009 ) but now several journal papers have been published. The main publication describing PhagoSight has been published in PLOS ONE .