Segmentation of smFISH images by DAPI staining

Hi everyone,

I did some smFISH staining (using the HCR protocol), with a nuclear DAPI stain. I am wondering is there any way that I can use the nuclear DAPI stain as the primary object and perform segmentation to identify cell boundary, so that I can quantify the localization of the smFISH stains within each cells?

I’m very new to Cell Profiler, if anyone can point me to any place to learn how to better perform this, that will be much appreciated! Thank you!


If there is no cell staining you can define cells as secondary objects by expanding nuclei to a defined pixel distance using Distance-N method. This way you quantify locations of smFISH stain per cell basis.


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Dear Hamdah,

Thanks a lot for your suggestion! I was trying that and it seems to work very well!


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