[Insight-users] Image filtering and feature detection-

[Ryan Smith]

Hi Dan-
My itkSignedMaurerDistanceMapImageFilter now matches your output (I invoked
the SetInsideIsPositive(true); method as my initial result was the inverse
of yours).  With that said, my RegionalMaxima filter is not producing
quality results.  You are sending the distance map output to the to the
RegionalMaxima filter, not any of the other results in the chain, right?
 Upon saving the output of my RegionalMaximaImageFilter to disk I cannot
open the mha file with any of the readers I use.  I get an error. Any idea
on where I am going wrong?  I think I am close, however this one has me
stumped.  Thanks again for your continued support-
-Ryan

On Fri, Aug 20, 2010 at 11:05 PM, Dan Mueller <dan.muel at gmail.com> wrote:

> Hi Ryan,
>
> It looks like you have a problem with pixel type. Consider using a
> real pixel type (eg. float or double).
>
> HTH
>
> Cheers, Dan
>
> On 20 August 2010 22:06, Ryan Smith <ryanleesmith at gmail.com> wrote:
> > Thanks again for all the help Dan.  I tried your suggestion for using
> > the itkSignedMaurerDistanceMapImageFilter and got different results.  I
> sent
> > in my BinaryThresholdImageFilter output and got the following from
> > my itkSignedMaurerDistanceMapImageFilter
> > http://i.imgur.com/jZ1AN.png
> >
> > Are there any other inputs I need to set for my Mauerer Distance Map?
>  This
> > one is new to me and I didn't find much in the documentation.  Thanks-
> > -Ryan
> > p.s. You were right about my previous lossy compression woes
> > On Thu, Aug 19, 2010 at 2:51 PM, Dan Mueller <dan.muel at gmail.com> wrote:
> >>
> >> Hi Ryan,
> >>
> >> 1. The output of the connected component filter you provided does not
> >> seem right. Are you doubly sure you are passing the binary image to
> >> the connected component filter? I have attached the output you should
> >> get.
> >>
> >> 2. That said, if you just need to extract seeds for further
> >> processing, I don't think you need to use the connected component
> >> filter. This filter simply assigns a unique identifier (Eg. 1, 2, 3,
> >> 4, etc) to each component or "blob" in the image. One way of obtaining
> >> seeds is to take the binary image, compute the distance transform (try
> >> Code/BasicFilters/itkSignedMaurerDistanceMapImageFilter.h), and the
> >> apply the regional maxima filter
> >> (Code/Review/itkRegionalMaximaImageFilter.h). I have attached the
> >> output from this chain.
> >>
> >> HTH
> >>
> >> Cheers, Dan
> >>
> >> On 19 August 2010 21:20, Ryan Smith <ryanleesmith at gmail.com> wrote:
> >> > Hi Dan-
> >> > The white top hat worked great at removing my extra features, and the
> >> > binary
> >> > thresholding cleaned everything else up, however I am still having
> some
> >> > trouble using the ConnectedComponentFilter.  I found this article
> which
> >> > is
> >> > trying to do exactly what I am attempting:
> >> > http://www.itk.org/pipermail/insight-users/2007-January/020532.html
> >> > I want the position and full width half max (FWHM) of each intensity
> >> > maxima
> >> > in the image.  I tried using the connected component filter and got
> the
> >> > output found at the following URL: http://i.imgur.com/TCqL8.png
> >> > It appears each feature is being tagged as several different features.
> >> >  Just
> >> > to confirm I am sending the binary thresholded image, not the
> >> > original Gaussian spot image into the ConnectedComponentFilter.
> >> > I feel like I am going down the wrong path here.  I don't necessarily
> >> > need
> >> > to segment my points, I just need to clean up the image (done) and
> >> > potentially use techniques such as those in other ITK problems I have
> >> > read
> >> > to find 'seed points' for some region growing algorithms based on the
> >> > intensity maxima of my image.  Any thoughts? Thanks in advance-
> >> > -Ryan
> >> >
> >> >
> >> > On Sun, Aug 15, 2010 at 11:22 PM, Dan Mueller <dan.muel at gmail.com>
> >> > wrote:
> >> >>
> >> >> Hi Ryan,
> >> >>
> >> >> You might consider using the "white top hat" operation to remove the
> >> >> background:
> >> >>    WhiteTopHat = I - Dilate( Erode(I) )
> >> >> where I is the image, Erode is morphological erosion, and Dilate is
> >> >> morphological dilation.
> >> >>
> >> >> You can find an implementation of this operation in:
> >> >>    Code/BasicFilters/itkWhiteTopHatImageFilter.h
> >> >>
> >> >> Once the background is removed, a simple global intensity threshold
> >> >> should suffice to segment the spots. The following filters may be
> >> >> helpful for that task:
> >> >>    Code/BasicFilters/itkBinaryThresholdImageFilter.h
> >> >>    Code/Algorithms/itkOtsuThresholdImageFilter.h
> >> >>    Code/Review/itkKappaSigmaThresholdImageFilter.h
> >> >>
> >> >> HTH
> >> >>
> >> >> Cheers, Dan
> >> >>
> >> >> On 15 August 2010 23:04, Ryan Smith <ryanleesmith at gmail.com> wrote:
> >> >> > Hi-
> >> >> > I am attempting to remove the background and detect features in the
> >> >> > following image:
> >> >> > http://i.imgur.com/wd3Yt.jpg
> >> >> >
> >> >> > I have a series of images in which the white circular spots travel
> >> >> > and
> >> >> > the
> >> >> > white vertical stripes remain stationary.  I would like to apply
> some
> >> >> > simple
> >> >> > background subtraction to remove the white stripes then autodetect
> >> >> > the
> >> >> > intensity maxima associated with the circular features.
> >> >> >
> >> >> > A brief search provided the following results which address similar
> >> >> > problems
> >> >> > using itkConnectedComponentFilter.  Is this what I want after my
> >> >> > background
> >> >> > is subtracted?  Any example code on how to get the location and
> sizes
> >> >> > of
> >> >> > the
> >> >> > components? Thanks in advance-
> >> >> >
> >> >> > -Ryan
> >> >> >
> >> >> >
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