[SciPy-User] watershed question

[Stéfan van der Walt]

I've updated the links to the repository.

Lee, I assume the watershed code covered under the arrangement?  Looks
like we've got some hands to help!

Regards
Stéfan

2010/5/1 Stéfan van der Walt <stefan at sun.ac.za>:
> 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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