http://imagej.273.s1.nabble.com/correction-for-stray-light-on-epifluorescence-images-tp5005196p5005199.html
I think your idea with median is feasible, provided your objects of interest are small enough to be smoothed away and the artifacts are large enough not to be smoothed away.
However, why not using "Background Subtract"? If you think division is better, than logarithm the image before. Be careful in this case with resulting values less than 1!
Still I have a problem of understanding: You say you perform shading correction! In fluorescence? with which background image? Illumination is the excitation light, if there is any background, I think you should better inspect your microscope and improve the settings. Even the amount of stray light could be reasonably reduced!
> Dear all,
> I've got epifluorescence images, on which I am to quantify the total
> fluorescence (integrated density) of ROIs. On some of the images there are
> bright glowing artifacts. I exclude them from measurement however the stray
> light from them affects the neighbouring pixels. So i am searching for a
> way to neutralize this influence.
> My images are corrected for illumination irregularities (shading
> correction) at the acquisition.
> I was wondering would it be legitimate to do this correction dividing all
> my images by their smoothed with a big median filter (>100px) versions. I
> would do this using the Image calculator plus divide formula (i1/12)*k1
> where k1 would be the maximum grey value of the smoothed version.
>
> Best regards!
>
> Stoyan Pavlov
> ---
> Dr. Stoyan P. Pavlov, MD, PhD
> Departament of Anatomy, Histology and Embryology
> Medical University "Prof. Dr. Paraskev Stoyanov", Varna
> Prof. Marin Drinov Str.55
> 9002 Varna
> Bulgaria
> Tel: +359 (0) 52 - 677 - 052
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