Segmentation of yeast cells. Please help!

Posted by Giuseppe Lucarelli on Dec 09, 2014; 3:52am
URL: http://imagej.273.s1.nabble.com/Segmentation-of-yeast-cells-Please-help-tp5010855.html

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

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.