http://imagej.273.s1.nabble.com/Background-correction-tp5019468p5019491.html
> Good day Anu,
>
> you have to decide whether you improve image acquisition or use post hoc
> image correction, e.g. Shading Correction as proposed by Robert Dougherty.
>
> I would vote for better image acquisition.
>
> My impression is that you work with transmitted light and uneven
> illumination but you should also consider highly diffuse incident
> illumination.
> (For 5x magnification an inverted photographic macro lens system may be
> sufficient.)
>
> Good luck
>
> Herbie
>
> :::::::::::::::::::::::::::::::::::::::::
> Am 02.10.17 um 05:30 schrieb anusuya pal:
>
> 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
>>>
>>>
>>> --
>>> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>>>
>>>
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>> ImageJ mailing list:
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>>
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