http://imagej.273.s1.nabble.com/Background-correction-tp5019468p5019482.html
image correction, e.g. Shading Correction as proposed by Robert Dougherty.
> Hello,
>
> 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
> mentioned before, the background (shading) needs to be corrected properly
> so that we don't lose any information about the sample but also, I can know
> the mean intensity of the sample region properly. If I do without any
> correction, it happens that the sample intensity is less than that of the
> background, which is impossible as per the logic. The whole object is big,
> the portion is taken with the background (which is the microscopic glass)
> and the objective used is 5X.
>
> Thanks for the suggestion Robert. I will check that shading corrector.
>
>
> Thanks
> Anu
>
> On Sun, Oct 1, 2017 at 10:46 PM, Robert Dougherty <
[hidden email]> wrote:
>
>> 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:
http://imagej.nih.gov/ij/list.html>>> <0 or 360.tif>
>>
>> Robert P. Dougherty
>> President
>> OptiNav, Inc.
>> 1414 127th Pl NE #106
>> Bellevue, WA 98005
>> (425) 891-4883
>> FAX (425) 467-1119
>>
[hidden email]
>> www.optinav. com
>>
>>
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>> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>>
>
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