Technical sheet of CellTracker

Operating System

Windows95/98

Windows 2000 and Windows XP

Windows NT 4.0 or higher

Hardware requirements

PCs that are able to run Win95/98/Win NT/2000/XP

512MB RAM, 1GB or above recommended

Hard disk space 35MB

Software requirement

Matlab component run time (MCR)

Input images

A stack of time series (Karl Zeiss LSM file; TIF; JPG; BMP; Matlab mat file)

Note that input images could have more than three channels

Language

English ( UK )

Boundary detection method

Level set (Vese 1998)

Snake(Kass 1987, Xu 1998)

Thresholding

Boundary tracking method

Particle filter based on image colour, edge features (Blake 1998, Isard 1998,Nummiaro 2003)

Snake(Kass 1987, Xu 1998)

Segmentation based (Jones 2005)

Cell tracking method

Combination of the above boundary tracking methods

Export format

AVI; Tiff; XML; XLS

 

Background Literature

Abraham, V. C., Taylor, D. L., Haskins, J. R. 2004 High content screening applied to large-scale cell biology. Trends Biotechnol 22 , 15-22.

Bailey, S. N., Ali, S. M., Carpenter, A. E., Higgins, C. O., Sabatini, D. M. 2006 Microarrays of lentiviruses for gene function screens in immortalized and primary cells. Nat Methods 3 , 117-22.

Nelson, D. E., Ihekwaba, A. E. C., Elliott, M., Gibney, C. A., Foreman, B. E., Nelson, G., See, V., Horton, C. A., Spiller, D. G., Edwards, S. W., McDowell, H. P., Unitt, J. F., Sullivan, E., Grimley, R., Benson, N., Broomhead, D. S., Kell, D. B. & White, M. R. H. 2004 Oscillations in NF- k B signalling control the dynamics of target gene expression. Science 306 , 704-708.

Method Literature

Blake, A. & Isard, M. 1998 Active contours : the application of techniques from graphics, vision, control theory and statistics to visual tracking of shapes in motion .

Doucet, A., De Freitas, N., Gordon, N. 2001 Sequential Monte Carlo methods in practice . Statistics for engineering and information science. New York ; London: Springer.

Isard, M., Blake, A. 1998 CONDENSATION - Conditional density propagation for visual tracking. Int. J. Comp. Vision 29 , 5-28.

Jones, T. R., Carpenter, A. & Golland, P. 2005 Voronoi-based segmentation of cells on image manifolds. In Computer Vision for Biomedical Image Applications. First International Workshop, CVBIA 2005. Proceedings, 21 Oct. 2005 , pp. 535-43 BN - 3 540 29411 2. Beijing, China: Springer-Verlag.

Kass, M., Witkin, A., Terzopoulos, D. 1987 Snakes: active contour models. International Journal of Computer Vision 1 , 321-31.

Nummiaro, K., Koller-Meier, E., Van Gool, L. 2003 An adaptive color-based particle filter. Image Vis. Comput. 21 , 99-110.

Shen, H., Nelson, G., Kennedy, S., Nelson, D., Johnson, J., Spiller, D., 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.

Vese, L. A.,Chan, T. F. 2002 A multiphase level set framework for image segmentation using the Mumford and Shah model. International Journal of Computer Vision 50, 271-93.

Xu, C., Prince, J. L. 1998 Generalized gradient vector flow external forces for active contours. Signal Processing 71 , 131-9.