[Insight-users] Otsu Threshold

[Luis Ibanez]

Hi Radhika,

Luca kindly contributed his code yesterday at 12:47 pm

Thanks to the fact that he provided tests for his
classes the code is in the Toolkit today at 10:32 am.


IMAGINE publishing a paper in a Journal at that speed   :-)


---


You may want to look at the files:


    Insight/Code/Algorithms
         itkOtsuMultipleThresholdsCalculator.txx
         itkOtsuMultipleThresholdsCalculator.h
         itkHistogramAlgorithmBase.txx
         itkHistogramAlgorithmBase.h


    Insight/Code/BasicFilters
         itkThresholdLabelerImageFilter.txx
         itkThresholdLabelerImageFilter.h



and their test files:


    Insight/Testing/Code/Algorithms
         itkOtsuMultipleThresholdsCalculatorTest.cxx

    Insight/Testing/Code/BasicFilters
         itkThresholdLabelerImageFilterTest.cxx



Please let us know if you have further questions.


   Thanks


     Luis


-------------------------------
Radhika Sivaramakrishna wrote:

> Hi Luis,
> Thanks for the more detailed explanation of what the Otsu threshold 
> calculator does. When will Luca's code be available in ITK? Has that 
> been logged in as a new feature request?
> 
> Thanks
> Radhika
> 
> 
> -----Original Message-----
> From: Luis Ibanez [mailto:luis.ibanez at kitware.com]
> Sent: Saturday, February 28, 2004 8:26 AM
> To: Radhika Sivaramakrishna
> Cc: ITK
> Subject: Re: [Insight-users] Otsu Threshold
> 
> 
> Hi Radhika,
> 
> There may be a conceptual interpretation problem here.
> 
> The OtsuThreshold calculator is not supposed to return
> the mininum between two peaks in a histogram.
> 
> What this calculator computes is the intensity value
> that can be used to separate the histogram in two
> classes such that inter class variance is maximized.
> 
> In this context, the Otsu calculator doesn't care at
> all about peaks and valleys.  You could get a 'valid'
> threhold even for a uniform histogram.
> 
> ('valid' in terms of the definition of what an Otsu
>    threshold is).
> 
> 
> If you actually want to select a minimum in the histogram,
> the solution would be to write a variance of this calculator,
> (maybe taking advantage of the Statistics classes that already
> compute the histogram for you), and then parse the histogram
> in order to identify minima.  Note that there are scale-space
> issues here, you will have to smooth the histogram using a
> particular sigma that will define the minimum size of valley
> that you consider to be significant.
> 
> 
> If you write such a calculator, and you are willing to
> contribute it to the toolkit we will be happy to include
> it in the repository.
> 
> Note that Luca
> http://www.itk.org/pipermail/insight-users/2004-February/007040.html
> has developed a variant of this calculator in order to support
> multiple thresholds (still defined as those that maximize
> inter-class variability). His code will hopefully be included in
> the toolkit soon.
> 
> 
> 
> Regards,
> 
> 
>     Luis
> 
> 
> 
> -------------------------------
> Radhika Sivaramakrishna wrote:
> 
>  > Hi Luis,
>  >
>  > I am using Otsu threshold for segmenting tissue from from the
>  > background. It appears to work very well in most cases, however some
>  >
>  > Cases it fails for unknown reasons.
>  >
>  > In these cases, I have looked at the histogram, and I can clearly see
>  > two well distinguished peaks for background and tissue, however, it
>  > appears to give me a threshold that is past the 2^nd peak (tissue peak)
>  > instead of between the two peaks. Could you explain why this might be
>  > happening. I tried to play with the number of bins for this case but
>  > everytime it bypassed the actual threshold and gave back something past
>  > the tissue peak.
>  >
>  > Thanks
>  >
>  > Radhika
>  >
>  > 
>  >
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