Signal to noise Ratio and Signal to Background Ratio in fluorescent images


I am interest in calculating signal to noise and signal to background ratios from my fluorescent images. I am doing PLA experiments on cells. As results, I got Signal-dots around the nucleus, count and measure their intensity via Cell Profiler.

First, I add the module “maskObject” to exclude all signals from the image and then I add the module “measureImageIntensity” to get the background intensity of the image. Next, I add “measureImageIntensity” one more time with the option “measure intensity only from areas enclosed by objects”, to measure the signal intensity. To calculate the SBR I divide the mean intensity of the Signal intensity through the mean intensity of the background intensity.

To determine the Signal to Noise ratio I used the module “MeasureObjectIntensity”. Then I divided the values IntensityMaxIntensity through Intensity STDIntensity, to get the SNR for each signal.

My question is if the calculation way is correct or if someone has experience with these calculations using cell profiler results. I am thankful for any advices!

Thank you very much for your help,


Hi Juli,

It seems to me that you are using a correct approach conceptually. It will be able to help you more if you share your images and pipeline with me.


Dear Hamdah

Thank you for your answer!

I used the module “identifyPrimaryObjact” to detect the signals, by setting a size limit of 3 to 20 pixels and the follwoing treshold: global treshhold strategie, minimal crossentropy, lower bound of trshhold: 0,003.