[Insight-users] Image filtering and feature detection-

[Dan Mueller]

Hi Ryan,

Indeed, I computed the regional maxima of the distance map.

Perhaps you could post your code (or a minimal example) and input data?

Dan

On 13 September 2010 22:50, Ryan Smith <ryanleesmith at gmail.com> wrote:
> 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
>> >> >> >
>> >> >> >
>> >> >> > _____________________________________
>> >> >> > Powered by www.kitware.com
>> >> >> >
>> >> >> > Visit other Kitware open-source projects at
>> >> >> > http://www.kitware.com/opensource/opensource.html
>> >> >> >
>> >> >> > Kitware offers ITK Training Courses, for more information visit:
>> >> >> > http://www.kitware.com/products/protraining.html
>> >> >> >
>> >> >> > Please keep messages on-topic and check the ITK FAQ at:
>> >> >> > http://www.itk.org/Wiki/ITK_FAQ
>> >> >> >
>> >> >> > Follow this link to subscribe/unsubscribe:
>> >> >> > http://www.itk.org/mailman/listinfo/insight-users
>> >> >> >
>> >> >> >
>> >> >
>> >> >
>> >
>> >
>
>