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

[Lassi Paavolainen]

Hi Nick,

On Wed, 7 Oct 2009, Nicholas Tustison wrote:

> 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.

That really did the trick. Thanks Nick for all the help and for 
implementing this nice filter.

Lassi

> 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_____________________________________
>> Powered by www.kitware.com
>> 
>> Visit other Kitware open-source projects at
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>> 
>> Please keep messages on-topic and check the ITK FAQ at: 
>> http://www.itk.org/Wiki/ITK_FAQ
>> 
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>

-- 
Lassi Paavolainen, M.Sc.
Software Engineer
BioImageXD (http://www.bioimagexd.net)
lassi.paavolainen at jyu.fi