Posted by
Thomas Boudier on
Dec 09, 2014; 4:10am
URL: http://imagej.273.s1.nabble.com/Segmentation-of-yeast-cells-Please-help-tp5010855p5010856.html
Hi Guiseppe,
Usually for yeast cells, I use band pass filtering since almost all
cells have same area (FFT/BandPass). It will help enhance the cells and
get rid of the variation of intensities. But then what is your question
? Number of cells ? Sizes ?
Best,
Thomas
On 09/12/14 11:52, giuseppe3 wrote:
> Hi there,
>
> I am currently stuck on cell segmentation of my images. I deal with yeast
> cells and I am trying to get cell ROI using two consecutive filters on
> confocal fluorescence images of yeast cells. The cell express a fluorescent
> tag which localises close to the cell wall but it is not a continuous and
> homogeneous signal around the cell, it can be dotty creating voids in the
> cell "perimeter". I have attached an example image (1024x1024, 16-bit).
> WT_24h_-N_green.tif
> <
http://imagej.1557.x6.nabble.com/file/n5010855/WT_24h_-N_green.tif>
>
> So far I apply the filters (in this order):
> 1) Unsharp Mask,
> 2) Variance
>
> The parameters for these filters need to change in order to get most cells
> out of the different images.
>
> The problem is that I cannot come up with a strategy to find out which
> parameters to feed into the filters depending on some property of the image
> to be processed.
> I could loop the macro over a range of parameters and then use the
> parameters that lead to the highest number of cells being identified but
> this will take a long time especially because I have > 2000 images to
> process.
>
> Do you think I am using the right approach/filters? Do you have any
> suggestions?
> Should I try to segment cells from the brightfield image?
>
> Thanks a lot for your help.
>
>
>
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>
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Thomas Boudier, Associate Professor, UPMC,
Université Pierre et Marie Curie, Paris, France.
BioInformatics Institute (BII)/IPAL, Singapore.
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