Re: Uneven illumination of background

Posted by rtas on
URL: http://imagej.273.s1.nabble.com/Uneven-illumination-of-background-tp5005529p5005543.html

Hi,

I guess i am confused between the intensity of illumination and color of illumination.
Is the code that i posted for correcting the intensity of illumination, isn't it?

I saw some published paper used similar code that i posted previously but image was divided by the brightfield and multiply 255 instead of mean of brightfield. They said it is for correcting the background and then applied the color deconvolution. So I assumed that what i was doing for correcting background was correct despite of giving the result not what i wanted.

I tried the subtracting background on my histological sections.
Probably i should be more clear what i want to do first. I'm focused on the tissue level segmentation not cell level, so the histological images are taken not-high magnification, like 1X (see attached image).
So the rolling ball radius is difficult to apply because the radius become large and does not seem to effectively remove uneven illumination.
Also i am not interested in quantifying the data, also due to bit of variability of staining I would probably end up manually segmenting the region of interests, cartilages in blue and mineralized bone in dark blown.

Is it wrong to process the color deconvolution for uncorrected background images to just "help" segment specific stain color regions? If this is fine, I could reduce the time of manual segmentation later on.

Rui