Identify cells

Hi there,

I’m new to cellprofiler and I am having some diffuclities.
I need to count cells, and I have something like 2000 cells in the pic.
The problem is that part of the pic the identifyprimary doesn’t identify the cell because they are very bright,
so it can identify only part of the cells. How can i make part of hte pic that is bright because of the kight darker?
so it will look like the rest of the pic? and that i can identify all of the cells in the pic?
I added the segmention that i’m getting.

I would really appreciated any help.

Thank you,
problem.pdf (424 KB)

(Moved post to appropriate forum)

Hi Hilla,

Please post your original image that are using, plus the pipeline that you have put together so far.


hi, I’m adding the files you asked for.
I hope I was clear about my problem. I have 208 pics of growing cells, when i run my pipeline on the first pic that has only 300 cells, it works fine, but when it has 2000 cells it miss a lot of cell in a specific area.
I hope I was clear now.
Thank you!

DefaultOUT__128.mat (145 KB)

Hi Hila,

I’ve get together a pipeline that should get you started. I perform some basic illumination correction compensate for what looks like a large illumination gradient from bottom left to top-right.

I should mention that your image is fairly saturated in areas (i.e, there are large regions that are at the maximum pixel intensity value). The more saturated your image is, the less likely you are to detect cells properly, so you should check the exposure of your image acquisition system.

2013_04_16.cp (4.8 KB)


Thanks a lot for your response.
I’m still having some problems with the identify primary objects.
How can I separate the objects in the file attached?

Thanks in advance,

DefaultOUT__291.mat (961 KB)
problem_det_291.pdf (206 KB)