http://imagej.273.s1.nabble.com/Background-correction-tp5019468p5019474.html
1. There is a global background (illumination) gradient in the sample image.
2. There is a light border or hem, especially on the right half, that
re 1. As others have noted already: Use better image acquisition
(illumination). Try highly diffuse illumination if possible.
re 2. What causes this surprisingly pronounced border?
> 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
>>
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>
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