It would be useful if you provided a picture and explained how you labelled the nucleus and protein of interest and what sort of microscope you used to take the image etc. Qualitative analysis of protein localisation is fairly easy but quantitative analysis depends so much on how your sample is prepared for imaging and how you take your images. A lot depends on the question you want to answer as well. For example you can get numbers from software such as ImageJ (FIJI) (which is free) but you need to know what to measure.

I agree with David G Spiller . It completely depends on what you are going to study or analyze. For subcellular localization, generally a marker gene is labelled with a fluorescent protein encoding gene to verify the subcellular localization in a qualitative manner. You can quantify the signal by different co-localization experiments. Fiji/ImageJ is a free tool to conduct basic analysis. For higher level analysis, Cellpose, Imaris can help.

Best regards.

Thank you so much for taking the time to help me with this! I'll attach a picture for your reference. In the image, the protein I'm investigating is highlighted in green, while the nucleus stands out in blue. Because of time constraints during my doctoral research, I wasn't able to use different fluorescent dyes to distinguish between cell compartments. However, I've noticed a distinct pattern in the green fluorescence. I'm curious if this pattern might offer clues about the potential localization of the protein, based on typical appearances of different cell compartments in fluorescent microscopy. Do you happen to know of any software that could analyze the image and provide insights into where my protein might be located or where I could find advice on how to interpret the signals? Thank you very much.

This is the reference picture. Thank you very much.