Posted by
Rubiu, Elena (ext) on
Sep 17, 2014; 9:04am
URL: http://imagej.273.s1.nabble.com/Background-subtraction-tp5009655p5009660.html
Hi Karsten,
thank you for your answer. I guess then I should just apply the threshold - but what do you mean with "provided there is no shift"?
Kind regards
Elena
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Gesendet: Mittwoch, 17. September 2014 10:38
An:
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Betreff: Re: Background subtraction
Hi Elena Rubiu,
I think "subtract background" is not the tool do reduce noise. It is the choice to flatten uneven illumination or background. You should use it only if the background, after some smoothing, shows deviations AND these deviations are also influencing the object. In case of fluorescence you should better control your microscope to have an even exitation light!
For intensity estimation I think it would be sufficient to generate one mask by thresholding and to apply it to all three pictures of the same object, provided there is no shift, and measure with this mask the intensities.
If you are fixed to "subtract background" estimate the noise using one or more roi's in the background for measurement, really not recommended.
Regards
Karsten
Am 17.09.2014 um 10:01 schrieb Rubiu, Elena (ext) <
[hidden email]>:
> Hi everybody,
>
> I am trying to analyze the fluorescence intensity of some pictures.
> I usually have three different pictures of the same object, that not only differ in fluorescence intensity but also in background noise (the less the intensity, the more the noise). To deal with the noise I'm using the "subtract background" function (rolling ball algorithm), then I'm selecting the area of interest with the threshold.
>
> My idea was to use the same parameters for all three pics (same rolling ball radius, same threshold limit) but the problem is that if I subtract the background of a relatively non-noisy pic then the threshold selection is working in a different way than with a noisy picture where I subtracted the background.
>
> Is there a way to "quantify" noise in a picture, so that I can decide if I should subtract the background or not?
> Or should I just treat every picture in the same way, not caring if the non-noisy pic's data is completely affected by the subtraction?
>
> I hope I could explain myself clearly and that you will be willing to help me.
>
> Thank you for your time!
>
> Kind regards,
> Elena Rubiu
>
>
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