[Insight-users] ultimate erode set (erode up to object centres)

[Prashanth Ravindran]

Hi -

When faced with a problem that required a complete erosion leaving only the center, I used the Label Geometry filter from the journal article http://www.insight-journal.org/browse/publication/301. This filter returns the centroids of the various objects in the binary image that I supply to it (along with various other parameters). I pick the centroids and use that as an estimate for my next step.

Hope this helps,

Thanks,
--Prashanth



----- Original Message ----
> From: Richard Beare <richard.beare at gmail.com>
> To: lynx.abraxas at freenet.de
> Cc: insight-users at itk.org
> Sent: Friday, July 24, 2009 5:42:08 AM
> Subject: Re: [Insight-users] ultimate erode set (erode up to object centres)
> 
> Hi,
> I'm not sure if this is exactly what you're after, but it might be
> close. The "standard" approach for circle splitting that Gaetan
> mentioned is to do a distance transform of the blobs and apply a
> watershed to the result (or inverse of the result). If the blobs are
> perfect circles the DT will be a cone with a well defined peak and
> you'll end up with one region per circle.
> 
> In practice, of course, things are rarely that simple. The objects
> aren't perfect circles, so you end up with a few peaks in the distance
> transform per object and therefore break objects up more than you
> want. There are a few ways of merging these peaks to reduce the
> problem, and these may be what you are after
> 
> 1)  Require that peaks in the DT must be different by some margin or
> else they get merged - you can do this by a kind of top hat filter -
> subtract a scalar from the distance map, reconstruct against the
> original, take the difference between reconstruction and the original,
> threshold this and use the blobs as markers for your watershed.
> 
> 2) Simply dilate the peaks in the dt and use the resulting blobs as markers.
> 
> 3) Threshold the distance transform and use the resulting blobs as
> markers - this is equivalent to a binary erosion (so see previous
> messages about doing this quickly) and will discard small objects by
> not giving them a marker.
> 
> Probably loads of other options as well.
> 
> On Fri, Jul 24, 2009 at 7:55 AM, wrote:
> > Dear Gaëtan Lehmann,
> >
> >
> > Thank You very much for Your answer.
> >
> > On 23/07/09 22:27:28, Gaëtan Lehmann wrote:
> >>> In total I want to create a small program that separates and labels
> >>> pores/particles by watersheds.
> >>
> >> How do you use the ultimated eroded for that task?
> >> Usually, the watershed on the distance map is quite good for this task.
> >
> > Well in the end I want to get the markers for the watershed that lie within a 
> defined distance to be grouped to only one marker (or just one marker of these 
> to be left over).
> >
> > After thinking more about this, I think using the ultimated eroded and a 
> closing filter for this is wrong. (MAVI docs: 
> http://www.itwm.fhg.de/bv/projects/MAVI/Documents/MAVI.pdf)
> >
> >>>> I'm looking for a filter that iteratively erodes until only the
> >>>> centres are left over. In the mavi docs it's discrribed as: "
> >>>> The Ultimate Eroded (Dilated) Set is defined only for MONO images.
> >>>> It is the union of all connected components of foreground
> >>>> (background)
> >>>> pixels that disappear completely in each step of successive erosions
> >>>> (dilations) performed on the input image. The structuring element is
> >>>> defined
> >>>> by the neighborhood, which can be chosen in the dialog."
> >>>>
> >>>>
> >>>> Is there such a filter in ITK? Or can it be implemented easily?
> >>>> I couldn't find any hint searching in the user's guide nor in the
> >>>> doxygen docs nor in the insight journal.
> >>
> >> I don't think there is such a filter in ITK. It shouldn't be that hard
> >> to implement though, and would make a great contribution to the insight
> >> journal!
> >
> > I'll wait a little more until I got more familiar with ITK but I'd be very 
> happy if I could contribute a little to this great project.
> >
> > Regards,
> > Lynx
> >
> >
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