[Insight-users] Image filtering and feature detection-

[Ryan Smith]

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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