[Insight-users] Watershed Behavior

[Richard Beare]

The png I get from the website is 8 bit - I can't see the problem.

Can you try unsigned short tif or your current pixel type as nii.

Thanks

On 2/9/07, Albert Huang <alberth+itk at ece.ubc.ca> wrote:
> Thanks for the fast reply Richard.
>
> I quickly remove the relabel filter and save the output of watershed as
> unsigned int. As you can see with the grayscale image here:
>     http://www.ece.ubc.ca/~alberth/watershed_morph2.png
> The outputs are labeled as:
>     001 002 003 004 005 006 007 ... 018 <---------- topmost
>     325 326 327 328 329 330 331 ... 342
>             ..........
>     019 020 021 022 023 024 025 ... 036
>     001 002 003 004 005 006 007 ... 018 <---------- bottommost
> Where the topmost and bottommost rows are labeled as the same numbers or
> wrap around as I called it.
>
> Albert
>
> ----- Original Message -----
> From: "Richard Beare" <richard.beare at gmail.com>
> To: "Albert Huang" <alberth+itk at ece.ubc.ca>
> Cc: "Gaetan Lehmann" <gaetan.lehmann at jouy.inra.fr>; <insight-users at itk.org>
> Sent: Thursday, February 08, 2007 2:58 PM
> Subject: Re: [Insight-users] Watershed Behavior
>
> Hi,
> I'm having difficulty determining what you mean by wrap around - from
> the example it looks as though it could be wrap around of the
> colormap, rather than the watershed.
>
> Try saving the output of the watershed filter, rather than the
> relabeller/coloring step and probe the values. For example, save as
> unsigned short tif and use the ImageView or some other tool to check
> the values. There shouldn't be any wrap around, but you never know.
>
> On 2/9/07, Albert Huang <alberth+itk at ece.ubc.ca> wrote:
> > Thanks Richard and Gaetan
> >
> > The new filter works very well on the edges for my application. However,
> > when I relabel my image after the morphological watershed, I get a wrap
> > around on the very top and bottom grids (even though they are alternating
> > intensity blocks). Is that a known behavior?
> >
> >         http://www.ece.ubc.ca/~alberth/watershed_morph.png
> >
> > The left and right image edge labels are ok with no wrap around. Checking
> > the gradient magnitude image, all image edges have 0 gradient (top,
> > bottom,
> > left, right).
> >
> > My morphological watershed filter has
> >     input (double)
> >     output (unsigned long)
> >     SetMarkWatershedLine=false.
> > My relabel component image filter has
> >     input (unsigned long)
> >     output (unsigned int)
> > The relabeler outputs for my example are [1...342] which seems to be still
> > well within the range of my output type.
> >
> > Albert
> >
> > ----- Original Message -----
> > From: "Gaetan Lehmann" <gaetan.lehmann at jouy.inra.fr>
> > To: "Albert Huang" <alberth+itk at ece.ubc.ca>
> > Cc: <Richard.Beare at ieee.org>; <insight-users at itk.org>
> > Sent: Thursday, February 08, 2007 1:48 AM
> > Subject: Re: [Insight-users] Watershed Behavior
> >
> >
> > Hi,
> >
> > You may also want to test the morphological watershed Richard and I have
> > contributed, and see if it gives better results.
> >
> > http://hdl.handle.net/1926/202
> >
> > You can also found this new filter in ITK cvs now.
> >
> > Regards,
> >
> > Gaetan
> >
> >
> > On Thu, 08 Feb 2007 04:34:39 +0100, Richard Beare
> > <richard.beare at gmail.com> wrote:
> >
> > > Have a look at the gradient image and dheck whether there are plateaus
> > > in the zig-zag area. The behaviour of the standard itk watershed is
> > > somewhat arbitary in the presence of plateaus.
> > >
> > >
> > > On 2/8/07, Albert Huang <alberth+itk at ece.ubc.ca> wrote:
> > >>
> > >>
> > >> Dear experts
> > >>
> > >> I was just playing with the watershed pipeline a few days ago using a
> > >> checkerboard pattern (with uint8 grids of black=64, gray=153,
> > >> white=192),
> > >> and observed a zig-zaggy pattern on some edges (see
> > >> http://www.ece.ubc.ca/~alberth/watershed.png). Adding a
> > >> smooth field on the checkboard results in more zig-zaggy behaviors on
> > >> edges
> > >> that seem fairly strong in the input image. I am wondering if this is
> > >> normal
> > >> behavior for the itkWatershedImageFilter?
> > >>
> > >> My pipeline (ITK 3.0.1) setup is as below:
> > >>     file reader ->
> > >>     vector gradient magnitude image filter (pca off) ->
> > >>     watershed (level=0.2, threshold=0.0) ->
> > >>     relabel component
> > >>
> > >> p.s. The black regions in the outputs are colormap problems and not a
> > >> watershed issue. =)
> > >>
> > >> Thanks
> > >> Albert
> > >>
> > >> _______________________________________________
> > >> Insight-users mailing list
> > >> Insight-users at itk.org
> > >> http://www.itk.org/mailman/listinfo/insight-users
> > >>
> > >>
> > > _______________________________________________
> > > Insight-users mailing list
> > > Insight-users at itk.org
> > > http://www.itk.org/mailman/listinfo/insight-users
> >
> >
> >
> > --
> > Gaëtan Lehmann
> > Biologie du Développement et de la Reproduction
> > INRA de Jouy-en-Josas (France)
> > tel: +33 1 34 65 29 66    fax: 01 34 65 29 09
> > http://voxel.jouy.inra.fr
> >
> >
>