PHAGOSIGHT

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..

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