problems with tracking cells & looking for best plugins

[Cammer, Michael]

Hi.

We are trying to track cells imaged by reflection microscopy and are having problems.  Help appreciated!

Our first goal is to do simple paths.

Using a combination of median filtering and thresholding we've done a decent job of segmenting the cells of interest.
http://www.flickr.com/photos/mcammer/7979766642/

Also posted online is an STDEV projection to give an idea of the paths.
http://www.flickr.com/photos/mcammer/7979765917

When mTrack2 outputs the paths to a large text file, many of the paths are split into smaller paths.
http://www.flickr.com/photos/mcammer/7979766566/

We tried increasing the maximum allowable speed to connect some of these paths, but this connects other unrelated paths.
http://www.flickr.com/photos/mcammer/7979789006/

Are there ways to work with mTrack2 to make the results more robust or do you have recommendations for other plugins to try?

Thank you!!

________________________________________________________
Michael Cammer, Assistant Research Scientist
Skirball Institute of Biomolecular Medicine
Lab: [phone]  Cell: [phone]


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[Alexandre Dufour]

Hi Michael,

I'm doing quite a bit of cell tracking myself. Would you have two or three consecutive time points (raw data) to post somewhere for me (or the list) to have a look ?

Thx.
Alexandre

On 12 sept. 2012, at 17:51, "Cammer, Michael" <[hidden email]> wrote:

> Hi.
>
> We are trying to track cells imaged by reflection microscopy and are having problems.  Help appreciated!
>
> Our first goal is to do simple paths.
>
> Using a combination of median filtering and thresholding we've done a decent job of segmenting the cells of interest.
> http://www.flickr.com/photos/mcammer/7979766642/
>
> Also posted online is an STDEV projection to give an idea of the paths.
> http://www.flickr.com/photos/mcammer/7979765917
>
> When mTrack2 outputs the paths to a large text file, many of the paths are split into smaller paths.
> http://www.flickr.com/photos/mcammer/7979766566/
>
> We tried increasing the maximum allowable speed to connect some of these paths, but this connects other unrelated paths.
> http://www.flickr.com/photos/mcammer/7979789006/
>
> Are there ways to work with mTrack2 to make the results more robust or do you have recommendations for other plugins to try?
>
> Thank you!!
>
> ________________________________________________________
> Michael Cammer, Assistant Research Scientist
> Skirball Institute of Biomolecular Medicine
> Lab: [phone]  Cell: [phone]
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html