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

[Lassi Paavolainen]

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