Segmenting yeast cells?

[Florian Jug]

Hello ,

I am looking for some plugin or workflow in Fiji that should solve a relatively simple image analysis task.

The screenshot below shows 3 yeast cells, the left one is a bit 'older', the right two just divided.
The goal is two-fold:
1) the nuclei should be tracked and the average intensity be plotted over time. This is relatively well solved by using TrackMate plus some obvious post-processing.
2) For all cells we would also like to measure the 'length' of the cell during the entire cell cycle. The position of the nuclei could be used as seeding points for some kind of segmentation.
It would be acceptable to have a semi-automated solution since the data is definitively finite. ;)
So far we are using the line selection tool and manually measure the length.
We have played with thresholding and 'Analyze Particles...', after thresholding also hoped to get better separation with binary watershed. It always felt as being almost there, but it never really worked out smoothly.
We also briefly tried 'Level Set Segmentation', but got also not lucky with that...

Since it seems to be a relatively achievable task we hope that some of you know about just the right existing plug-in or macro for this usecase.



(Slightly larger stack can be downloaded here: https://dl.dropboxusercontent.com/u/1222319/sample.tif)

Any pointers highly appreciated!
Thanks,
Florian & Tobias

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MPI of Molecular Cell Biology and Genetics
Group: Gene Myers
Pfotenhauer Strasse 108
01307 Dresden
Germany

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