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CellTracker software is a platform for tracking nuclear and cytoplasmic fluorescence intensities from live cell microscopy time series data.

A prime application is studying the dynamics of NFkappa-B, a transcription factor which periodically shuttles in and out of the cell nucleus (Ashall et al., Science, 2009).

The software has formerly been developed in the group of Douglas Kell (Manchester University) by Hailin Shen in collaboration with Mike White (formerly University of Liverpool). Since 2009 CellTracker is developed further in the group of Till Bretschneider (Warwick Systems Biology Centre) by Chengjin Du.

Major improvements of the current version are a semi-automatic interactive cell segmentation method for initialization and a novel cellcut tracking algorithm, which allows to track more complex sequences.

CellTracker is freely available and can be dowloaded here, but you need to register.

You can download a preliminary manual with instructions for installation here (CellTracker manual). It should be read in conjunction with the following papers and the help file of the old version (Old CellTracker Help File). The functionality of the old version (available at is maintained for compatibility.

C.-J., Du, M., Marcello, D. G., Spiller, M. R. H., White, & T. Bretschneider (2010). Interactive segmentation of clustered cells via geodesic commute distance and constrained density weighted Nyström method. Cytometry Part A, 77A, 1137-1147, 2010.

C.-J., Du, M., Marcello, D. G., Spiller, M. R. H., White, & T. Bretschneider (2011). CellCut: A framework for interactive tracking of protein translocations between cell nucleus and cytoplasm. The eighth IEEE International Symposium on Biomedical Imaging, March 30 – April 2, Chicago Illinois, USA, 2011.

Shen, H., Nelson, G., Kennedy, S., Nelson, D. E., Johnson, J., Spiller, D. G., White, M. R. H. & Kell, D. B. (2006) Automatic tracking of biological cells and compartments using particle filters and active contours. Chemometrics and Intelligent Laboratory Systems 82, 276-282.

Shen, H., Nelson, G., Nelson, D. E., Kennedy, S., Spiller, D. G., Johnson, J., Griffith, T., Paton, N., Oliver, S. G., White, M. R. H. & Kell, D. B. (2006) Automated tracking of gene expression in individual cells and cell compartments. Journal of The Royal Society Interface 3, 787-794.





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