http://imagej.273.s1.nabble.com/Background-correction-tp5019468p5019477.html
Sorry for the late reply. As Herbie correctly pointed out, there is a
gradient in the background, and I want to remove that. The right side of
the image has more non-uniformity, which needs to be corrected. And as I
the mean intensity of the sample region properly. If I do without any
background, which is impossible as per the logic. The whole object is big,
Thanks for the suggestion Robert. I will check that shading corrector.
> Anu,
>
> As Herbie noted, there appears to be a shading issue. You might try
> Polynomial Shading Corrector,
http://www.optinav.info/> Polynomial_Shading_Corrector.htm <
http://www.optinav.info/> Polynomial_Shading_Corrector.htm>
>
> Bob
>
> > On Sep 30, 2017, at 11:20 AM, anusuya pal <
[hidden email]>
> wrote:
> >
> > Hello
> >
> > Here is the sample image (raw file) attached. I am using a polarizing
> > microscope. And I think for my other samples, BaSiC is working good. But
> > for particularly this type of image, I am not getting the background
> > intensity and sample intensity differently. The range is more or less
> same.
> > So, if I know any plugins that will solve this correction for the current
> > image, It will be helpful.
> >
> > Thanks
> > Anu
> >
> > On Sat, Sep 30, 2017 at 12:17 PM, Bill Christens-Barry <
>
[hidden email]>
> > wrote:
> >
> >> Anu,
> >>
> >> You mention wanting to reject reflected light; am I right in thinking
> that
> >> the light you do want to capture in the image is due to fluorescence? If
> >> so, two approaches come to mind:
> >>
> >> It might be possible to use linear polarizers. Reflected light often
> >> retains the same linear polarization as that of the illumination, while
> >> fluorescence emission is often highly depolarized. If you place a linear
> >> polarizer in front of the light source and place another in front of the
> >> camera, with its polarization axis perpendicular to that of the
> >> illumination polarizer, the reflected light will be greatly attenuated
> >> while the fluorescence emission will be decreased to a lesser extent (~
> 2x
> >> for full depolarization). This is especially true if the reflected light
> >> has been reflected from the surface alone; translucent materials will
> allow
> >> more penetration and consequent depolarization due to internal
> scattering,
> >> which reduces the effectiveness of this approach. Try rotating the
> >> illumination polarizer and the camera polarizer about their polarization
> >> axes together, i.e. by maintaining the 90ยบ difference between the
> >> orientations of their polarization axes as you rotate both. There will
> >> likely be a best orientation for the pair of polarizers.
> >>
> >> Alternatively, you might employ a long pass filter in front of the
> camera
> >> so that only the longer emissions are passed while the shorter
> illumination
> >> wavelengths are blocked. This presumes that you are illuminating with a
> >> range of wavelengths shorter than those you wish to capture, otherwise
> some
> >> of the illumination may be passed by the filter.
> >>
> >> Hope this helps,
> >>
> >> Bill Christens-Barry
> >>
> >> --
> >> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html> >>
> >
> > --
> > ImageJ mailing list:
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>
> Robert P. Dougherty
> President
> OptiNav, Inc.
> 1414 127th Pl NE #106
> Bellevue, WA 98005
> (425) 891-4883
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>
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>
>
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