cell lineage software

[Jeremy Adler]

We are looking for software that tracks individual cells in a developing cell culture that includes dividing cells and then allows for measurements to be made from two channels in the nuclei.
The nuclei are identifiable and will be the basis of the lineage tracing. The tracing needs to produce the location and outline of each nucleus at each timepoint and the outlines used to measure and output the mean intensity from two channels.

Suggestions.

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[Michael Doube-4]

On 07/09/15 15:08, Jeremy Adler wrote:
> We are looking for software that tracks individual cells in a developing cell culture that includes dividing cells and then allows for measurements to be made from two channels in the nuclei.
> The nuclei are identifiable and will be the basis of the lineage tracing. The tracing needs to produce the location and outline of each nucleus at each timepoint and the outlines used to measure and output the mean intensity from two channels.
>
> Suggestions.

TrackMate may do some of what you need:
http://fiji.sc/TrackMate

(we have used it to track dentine tubules)

Michael



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[Richard Mort-2]

Hi Jeremy,
It sounds like you are using Fucci? We wrote some semi-manual not very
sophisticated scripts to do this for following single cells. I can send
them if they might be useful. I also remember reading a paper that
described software based on ImageJ called FucciJ to do this but I don't
think the code ever appeared......

http://dev.biologists.org/content/suppl/2012/12/18/dev.086215.DC1/DEV086215.pdf

Best
R

On 07/09/15 14:30, Jeremy Adler wrote:
> We are looking for software that tracks individual cells in a developing cell culture that includes dividing cells and then allows for measurements to be made from two channels in the nuclei.
> The nuclei are identifiable and will be the basis of the lineage tracing. The tracing needs to produce the location and outline of each nucleus at each timepoint and the outlines used to measure and output the mean intensity from two channels.
>
> Suggestions.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html


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[Till Bretschneider-2]

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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