[SciPy-User] watershed question

[Stéfan van der Walt]

Hi Emanuelle

The CellProfiler team has been very generous in sharing code so far:

http://stefanv.github.com/scikits.image/contribute.html#merge-code-provided-by-cellprofiler-team

I have just been too busy working on my PhD to get it all integrated
:(  [Of course, I'd be very happy if someone would help with this
task!]

I see the svn links on that page is broken; I'll see where the code is
hosted now.  I'm not sure if the watershed code is covered.

Cheers
Stéfan

On 29 April 2010 21:38, Emmanuelle Gouillart
<emmanuelle.gouillart at normalesup.org> wrote:
>        Hi Stéfan and Zach,
>
>        thank you for your answers. So it seems that
> ndimage.watershed_ift is quite buggy, maybe some warnings should be
> added to its docstring? We can't afford people spending too much time
> trying to use the function if it doesn't work.
>
>        Using the cellprofile/cpmath package is a neat trick, I tried it
> and it works perfectly. It even works for 3-D arrays (using the
> fast_watershed function)! Too bad that it's GPL-licensed and it's not
> possible to integrate the code in the image processing scikit :(.
>
>        Thanks again,
>
>        Emmanuelle
>
>
>
> On Wed, Apr 28, 2010 at 01:18:11PM -0400, Zachary Pincus wrote:
>> > Unless I'm also missing something obvious, the code returns an invalid
>> > result.  I even adjusted the depths of the two "pits", but always one
>> > region overruns the other---not what I would expect to happen.  I
>> > haven't delved into the ndimage code at all, but I wonder weather we
>> > shouldn't implement one of the simpler algorithms as part of
>> > scikits.image.segment for comparison?
>
>> Cellprofiler has a watershed algorithm, I believe. And like most of
>> the cellprofiler stuff, the implementation seems pretty high-quality
>> and well-thought-out.
>
>> I wound up extracting the cpmath sub-package, and (after a few
>> setup.py changes) it works great standalone with just scipy and numpy
>> as dependencies:
>> https://svn.broadinstitute.org/CellProfiler/trunk/CellProfiler/cellprofiler/cpmath/
>
>> Zach
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