[Insight-users] Correction of non-uniform illumination in EM data

[Nicholas Tustison]

Hi Lassi,

Considering that you were looking at the corners, my initial  
suggestion was going to be to try a mask where all the voxels have a  
value of 1.  Let me know what that does and, based on the results, we  
can try different things from there.

Nick


On Oct 7, 2009, at 6:18 PM, Lassi Paavolainen wrote:

> Hi Nick,
>
> On Wed, 7 Oct 2009, Nick Tustison wrote:
>
>> Hi Lassi,
>> In general, inspection of the corners in an image probably does not
>> constitute a proper assessment of bias correction algorithms.  Can  
>> you
>> describe your data a little more and perhaps I can point you to some
>> variations you might want to try?
>
> Ok. I explained it badly. This example dataset has its brightest  
> illumination in lower left area of the image. Average intensities  
> then go lower to the upper part of the image and to the right part  
> of the image. Its some sort of Gaussian distribution where the  
> center is in lower left part of the image. I measured those average  
> intensities by calculating mean of area about 512x512 in five  
> different places (left-top, right-top, center, right-bottom, left- 
> bottom).
>
> Even though mask image is said not to be that important, could it be  
> the solution for this problem? In this case using Otsu just masks  
> upper right part of the image and elsewhere some noisy parts of the  
> data. At least this mask image is quite different of what you would  
> expect to get from MRI data. I tested bias correction in EM data.
>
> Lassi
>
>> On Wed, Oct 7, 2009 at 8:46 AM, Lassi Paavolainen <lassi.paavolainen at jyu.fi 
>> >
>> wrote:
>>      Hi Nick,
>>
>>      On Thu, 24 Sep 2009, Nicholas Tustison wrote:
>>
>>            Hi Lassi,
>>
>>            You might want to take a look at the N3 algorithm
>>            implemented in ITK.  It might provide what you're
>>            looking for.
>>
>>            http://www.midasjournal.org/browse/publication/640
>>
>>            Good luck,
>>            Nick
>> I have played around with that now. It looks promising but doesn't do
>> its job completely. I have tested it with one dataset where mean
>> intensity is around 130 in lower left corner and around 100 in upper
>> right corner.
>> When I run test program from your publication using shrinkFactor = 4
>> and using default iteration number and number of fitting levels
>> values, I get image where difference between those areas is about 20.
>> Running it five times difference is subtracted to around 10. I have
>> changed the number of iterations and fitting levels without making a
>> much of a difference in results.
>> So it looks really promising but I would like to get the job done by
>> running it only once. Of course results cannot be perfect (there is  
>> no
>> perfect solution in image analysis). Do you have any idea where I
>> should look into to make it converge to some sort of optimal result  
>> by
>> running the filter just once?
>> Lassi
>>
>>      On Sep 24, 2009, at 4:23 AM, Lassi Paavolainen wrote:
>>
>>            Hi,
>>
>>            Does anyone know about ITK method to correct
>>            non-uniform illumination? There seems to be
>>            MRIBiasCorrection class and an example of it
>>            in InsightApplications. I'm not sure if this
>>            class can help me and anyway it doesn't seem
>>            to be very easy to use.
>>
>>            I have read following technical report
>>            (www.sci.utah.edu/~tolga/pubs/UUSCI-2005-008.pdf).
>>            One of the authors seems to be Ross Whitaker
>>            who is involved in ITK too. Is there ITK
>>            implementation of that method?
>>
>>            Lassi
>>
>>            --
>>            Lassi Paavolainen, M.Sc.
>>            Software Engineer
>>            BioImageXD (http://www.bioimagexd.net)
>>            lassi.paavolainen at jyu.fi
>>
>>            _____________________________________
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>> --
>> Lassi Paavolainen, M.Sc.
>> Software Engineer
>> BioImageXD (http://www.bioimagexd.net)
>> lassi.paavolainen at jyu.fi
>>
>
> -- 
> Lassi Paavolainen, M.Sc.
> Software Engineer
> BioImageXD (http://www.bioimagexd.net)
> lassi.paavolainen at jyu.fi_____________________________________
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