watershed

[Juan Nunez-Iglesias]

Hi Daniel,

Actually there's a known bug [1]_ in the scikit-image implementation (which
is originally from CellProfiler). I haven't figured it out yet, nor do I
know what the exact differences are to the paper. (And most images are
unaffected.) Are you looking to *use* the implementation or are you trying
to implement your own as a learning strategy? If the latter, you might want
to have a look at my own implementation [2]_ in gala, for which I tried to
follow the paper exactly. But it's way slower.

Juan.

.. [1] https://github.com/scikit-image/scikit-image/issues/803
.. [2] https://github.com/janelia-flyem/gala/blob/master/gala/morpho.py#L212

On Wed, May 20, 2015 at 7:00 AM, Daniel Bliss <daniel.p.bliss at gmail.com>
wrote:

> Hi all,
>
> I'm trying to implement the watershed algorithm described in this paper
> <http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.89.5268&rep=rep1&type=pdf>
> in Python.  Looking at the watershed function in skimage.morphology, it's
> not clear to me whether this function is an exact implementation of Vincent
> & Soille's method.  The docstring for morphology says, "Some ideas taken
> from . . ." and lists an older (by one year) paper by Soille.  "Some ideas"
> seems to suggest that the implementation is not exact, but where the
> differences are is not clear.  I've read through the morphology source
> code, as well as the C code it draws upon, but I'm getting tangled up
> trying to translate between Vincent and Soille's description and the
> C/Python code in skimage.  Can anyone provide a clear and complete
> explanation of what exactly skimage.morphology.watershed does relative to
> the Vincent and Soille 1991 method?
>
> Many thanks,
> Dan
>
> --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.python.org/pipermail/scikit-image/attachments/20150520/f530111d/attachment.html>