Medial axis skeletonization length
Dear all, I have a question I use the medial axis skeletonization implementation of scikit-image. Is it possible to get the length of the medial axis and the number of branches growing from the medial axis? Thank you very much in advance Stefanie
I tried this : https://dip4fish.blogspot.com/2014/05/construct-graph-from-skeleton-image-of... Le mer. 28 nov. 2018 à 19:59, Stefanie Lück <luecks@gmail.com> a écrit :
Dear all,
I have a question I use the medial axis skeletonization implementation of scikit-image. Is it possible to get the length of the medial axis and the number of branches growing from the medial axis?
Thank you very much in advance Stefanie
_______________________________________________ scikit-image mailing list -- scikit-image@python.org To unsubscribe send an email to scikit-image-leave@python.org
-- http://dip4fish.blogspot.fr/ Dedicated to Digital Image Processing for FISH, QFISH and other things about the telomeres.
Hi Stefanie, Jean-Patrick, et al, I invite you to look at my Skan (skeleton analysis) package. Docs here: https://jni.github.io/skan/ <https://jni.github.io/skan/> Paper here: https://peerj.com/articles/4312/ <https://peerj.com/articles/4312/> (the supplemental info mentions some of the edge cases we’ve taken care of.) Skan is installable with "pip install skan" or "conda install -c conda-forge skan”. I’m working on a new higher level Skeleton class, but it’s a WIP and you’ll need to install from source: https://github.com/jni/skan/blob/5c0d23e5b1eab2fb06b25ff599e98eaa11d621e6/sk... <https://github.com/jni/skan/blob/5c0d23e5b1eab2fb06b25ff599e98eaa11d621e6/sk...> (Not that that’s a big deal since the lib is pure Python.) Comments, suggestions, and contributions are all welcome! Juan.
On 29 Nov 2018, at 8:37 am, Jean-Patrick Pommier <jeanpatrick.pommier@gmail.com> wrote:
I tried this : https://dip4fish.blogspot.com/2014/05/construct-graph-from-skeleton-image-of... <https://dip4fish.blogspot.com/2014/05/construct-graph-from-skeleton-image-of...>
Le mer. 28 nov. 2018 à 19:59, Stefanie Lück <luecks@gmail.com <mailto:luecks@gmail.com>> a écrit : Dear all,
I have a question I use the medial axis skeletonization implementation of scikit-image. Is it possible to get the length of the medial axis and the number of branches growing from the medial axis?
Thank you very much in advance Stefanie
_______________________________________________ scikit-image mailing list -- scikit-image@python.org <mailto:scikit-image@python.org> To unsubscribe send an email to scikit-image-leave@python.org <mailto:scikit-image-leave@python.org>
-- http://dip4fish.blogspot.fr/ <http://dip4fish.blogspot.fr/> Dedicated to Digital Image Processing for FISH, QFISH and other things about the telomeres. _______________________________________________ scikit-image mailing list -- scikit-image@python.org To unsubscribe send an email to scikit-image-leave@python.org
hi tried installing skan, successful install, but getting error while using : --------------------------------------------------------------- from skan import csr Traceback (most recent call last): File "<input>", line 1, in <module> File "/home/etu/.eclipse/org.eclipse.platform_3.8_155965261/plugins/org.python.pydev_4.5.5.201603221110/pysrc/_pydev_bundle/pydev_import_hook.py", line 21, in do_import module = self._system_import(name, *args, **kwargs) File "/usr/local/lib/python2.7/dist-packages/skan/__init__.py", line 1, in <module> from .csr import skeleton_to_csgraph, branch_statistics, summarise File "/home/etu/.eclipse/org.eclipse.platform_3.8_155965261/plugins/org.python.pydev_4.5.5.201603221110/pysrc/_pydev_bundle/pydev_import_hook.py", line 21, in do_import module = self._system_import(name, *args, **kwargs) File "/usr/local/lib/python2.7/dist-packages/skan/csr.py", line 164 junction_centroids, *, spacing=1): ^ SyntaxError: invalid syntax On Thu, Nov 29, 2018 at 6:20 AM Juan Nunez-Iglesias <jni@fastmail.com> wrote:
Hi Stefanie, Jean-Patrick, et al,
I invite you to look at my Skan (skeleton analysis) package. Docs here: https://jni.github.io/skan/ Paper here: https://peerj.com/articles/4312/ (the supplemental info mentions some of the edge cases we’ve taken care of.)
Skan is installable with "pip install skan" or "conda install -c conda-forge skan”.
I’m working on a new higher level Skeleton class, but it’s a WIP and you’ll need to install from source:
https://github.com/jni/skan/blob/5c0d23e5b1eab2fb06b25ff599e98eaa11d621e6/sk... (Not that that’s a big deal since the lib is pure Python.)
Comments, suggestions, and contributions are all welcome!
Juan.
On 29 Nov 2018, at 8:37 am, Jean-Patrick Pommier < jeanpatrick.pommier@gmail.com> wrote:
I tried this : https://dip4fish.blogspot.com/2014/05/construct-graph-from-skeleton-image-of...
Le mer. 28 nov. 2018 à 19:59, Stefanie Lück <luecks@gmail.com> a écrit :
Dear all,
I have a question I use the medial axis skeletonization implementation of scikit-image. Is it possible to get the length of the medial axis and the number of branches growing from the medial axis?
Thank you very much in advance Stefanie
_______________________________________________ scikit-image mailing list -- scikit-image@python.org To unsubscribe send an email to scikit-image-leave@python.org
-- http://dip4fish.blogspot.fr/ Dedicated to Digital Image Processing for FISH, QFISH and other things about the telomeres. _______________________________________________ scikit-image mailing list -- scikit-image@python.org To unsubscribe send an email to scikit-image-leave@python.org
_______________________________________________ scikit-image mailing list -- scikit-image@python.org To unsubscribe send an email to scikit-image-leave@python.org
participants (5)
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Jean-Patrick Pommier -
Juan Nunez-Iglesias -
Leena Chourey -
Stefan van der Walt -
Stefanie Lück