Re: cell lineage software

Posted by Till Bretschneider-2 on Sep 08, 2015; 8:48am
URL: http://imagej.273.s1.nabble.com/cell-lineage-software-tp5014257p5014262.html

Dear Jeremy,

we have developed LineageTracker software for ImageJ which has been used to semi-automatically track cell cycle and clock markers.
http://www2.warwick.ac.uk/fac/sci/systemsbiology/staff/bretschneider/lineagetracker/

It has been described in this paper:
Downey MJ, Jeziorska DM, Ott S, Tamai TK, Koentges G, Vance KW, Bretschneider T. Extracting fluorescent reporter time courses of cell lineages from high-throughput microscopy at low temporal resolution. PLoS One. 2011;6(12):e27886 (12 pages). doi: 10.1371/journal.pone.0027886. Epub 2011 Dec 15.

An application can be found here:
Feillet C, Krusche P, Tamanini F, Janssens RC, Downey MJ, Martin P, Teboul M, Saito S, Lévi FA, Bretschneider T, van der Horst GT, Delaunay F, Rand DA. Phase locking and multiple oscillating attractors for the coupled mammalian clock and cell cycle. Proc Natl Acad Sci U S A. 2014 Jul 8;111(27):9828-33. doi: 10.1073/pnas.1320474111. Epub 2014 Jun 23.


We have an additional script to export only a selected range of frames. I can send you that if you think LineageTracker is something for you.
To be on the safe side I would try it with an older version of ImageJ. We have experienced some problems, mostly related to Java. Java 8 seems to fix most of it.

Best wishes,

Till

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