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An alternative solution for analysing cell migration would be the
"phagokinetic track method"  developed by Guenter Albrecht-Buehler...
Here you get to observe all of the tracks of all of the cells in 2D.
For more on the method see below

http://www.basic.northwestern.edu/g-buehler/htmltxt.htm#point6

>Search the CONFOCAL archive at
>http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
>
>Dear Confocalists,
>
>We are studying cell migration, as a result, I am interested  in any
>suggestions on various motion tracking software solutions for the
>analysis of cell movement on a time-lapse stack of images.
>
>Thank you
>Judy
>
>
>Judy Trogadis
>Bio-Imaging Coordinator
>St. Michael's Hospital, 7Queen
>30 Bond St.
>Toronto, ON M5B 1W8
>Canada
>ph:  416-864-6060  x6337
>pager: 416-685-9219
>fax: 416-864-6043
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--
Steve Paddock, Ph.D.,
Howard Hughes Medical Institute,
Dept. Molecular Biology,
Univ. Wisconsin,
1525 Linden Drive,
Madison, WI 53706.
Tel: 608 262 7898 (lab.)
      608 242 7391 (home)
      608 770 1301 (cell)
FAX: 608 262 9343