[Insight-users] Re: Watershed success & VolView Plugins

[Luis Ibanez]

Hi Robert,

You are right, I missed that.
This Watershed RGB plugin was added after the release of VolView.

However, here is where you can take advantage of one of the
nice features of VolView plugins: You can simply download the
shared library of this new plugin and load it into VolView.

The binary versions of the plugins are available at the following
FTP site:

       ftp://public.kitware.com/pub/itk/VolViewPlugins/

You can download the .dll files from there and copy those files
into the VolView20/Plugins subdirectory. This will typically be
something like:

         C:\Program Files\VolView20\Plugins

Note that you must take the ITKCommon.dll along with any of the
.dll plugins you want to install.

--

You can also build the plugins by yourself, the only thing you
need to have is a built version of ITK, and of course CMake.

In your case, it will be interesting to write a plugin that performs
the preprocessing that you want to apply before using Watersheds.
Once you have such a plugin, you can use VolView for running first
your (preprocessing) plugin and then run the Watershed plugin on
the resulting image.  This will give you a very fast development
and testing cycle.


Please let us know if you encounter any problems,



   Thanks


     Luis


--------------------------
Atwood, Robert C wrote:

> Luis:
> That is not what I have on the menu group "Segmentation Level Set" as
> you can see from the attached screen shot, did I miss downloading a plug
> in?
> 
> Though, I like the control over the process that programming directly
> allows me, I am using my own algorithm for the input into the watershed
> filter (but I think I should try this Danielsson distance map filter as
> well)
> 
> On the other hand, most of the students and other research staff are not
> programmers and do not have the background to work with the library
> directly (I have even had to learn a lot about c++ as opposed to c,
> template classes, etc. are all new to me)
> --Robert
> 
> 
> 
> 
> 
> 
> -----Original Message-----
> From: Luis Ibanez [mailto:luis.ibanez at kitware.com] 
> Sent: 10 April 2004 17:59
> To: Atwood, Robert C
> Cc: Insight-users at itk.org
> Subject: Re: Watershed success
> 
> 
> 
> Hi Robert,
> 
> There are two Watershed plugins in VolView,
> both of them under the group:
> 
>        "Segmentation Level Set"
> 
> The first plugin to try is the
> 
>      Watershed RGB Module (ITK)
> 
> This module only has the Watershed filter
> followed by the color encoding filter.
> It is up to you to prepare the input image,
> typically by running a gradient magnitude
> filter on it. With this filter you may want
> to start exploring the image at water levels
> around 0.2, and then increase the water level
> if you get too many small regions, or decrease
> the water level if you get regions that are
> too large.
> 
> Once you feel comfortable with this plugin,
> you can use the
> 
>      Watershed Module (ITK)
> 
> which has a pre-processing and post-processing
> steps.  In preprocessing it computes the gradient
> magnitude of the input image for you. Then runs
> the Watershed filter on it and finally use the
> seed point that you provided in order to extract
> the specific watershed where the seed point is
> located.  The output of this module is a binary
> mask representing only the basin associated to
> the seed point. (Note that the seed point is not
> directly used by the watershed filter, but by
> the post-processing of its output.
> 
> ----
> 
> Please let us know if you still find any
> difficulties running these plugins.
> 
> 
>    Thanks
> 
> 
> 
>       Luis
> 
> 
> 
> ------------------------
> Atwood, Robert C wrote:
> 
> 
>>I could not use the watershed module in VolView , it did not do what I
> 
> 
>>wanted. I don't quite understand how the module uses the watershed 
>>filter, it does not seem to return an image with the watersheds 
>>coloured as in Fig 9.9 of the software guide? Anyways, I took another 
>>stab at programming using the ITK filters directly, using the 
>>Watershed1 example and 9.2 of the guide but substituting my own 
>>algorithm instead of all that diffusion-gradient-filter stuff.
>>
>>
>>I went back and coded a 'pipeline' to use the WatershedFilterType on 
>>my own generated "height-map" generated on my algorithm, and ... looks
> 
> 
>>good so far, even without prefiltering and with just the first guess 
>>at parameters to use. (see attatched screen shot) Still some 
>>'dumb-bell' shapes are not separated but , a bit of parameter 
>>adjustment (and manual
>>line-drawing) should do the trick. (It starts as one connected region)
>>
>>The result seems to come out flipped on some axes, though, I haven't 
>>figured out which ones yet.
>>
>>
>>
>>--Robert
>>
>>
>>
>>
>> 
> 
> 
> 
> 
> 
> ------------------------------------------------------------------------
>