Hello! If you are using ImageJ (as your tag suggests) you should record your images as 8-bit greyscale images. When you import them into ImageJ you can analyse the fluorescence intensity by looking at the pixel values - high values translate to a bright signal. You may select and area and use ImageJ tools to measure pixel intensity values for instance. Just to give you an idea of whats possible.

Thank you for your answer Susanne Bähr . These days I'm trying to use different ImageJ tools also converting the image to 8-bit (grayscale) but I don't know if they are correct. I am attaching an example image, maybe it could help you to try to resolve my doubt. Thank you

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Alessandro Montesi I suggest you take the images “in grey scale” so monochromatic already if you can. That provides better information for the analysis. I would then proceed to draw an ROI around the region you are interested in and then let ImageJ do the measurements for you. I don’t know the settings by heart and don’t have access to my computer at the moment.

Ok, thanks a lot.

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