Leena,

You should use Python 3.6 or later. Skan does not support Python 2.7.

As mentioned by Stéfan, at this point, if you have further questions, we should probably move away from the scikit-image mailing list and to the skan issue tracker. github.com/jni/skan

On Fri, Nov 30, 2018, at 1:53 PM, imagepy@sina.com wrote:

you can also try sknw

----- 原始邮件 -----
发件人: Leena Chourey<leenagour@gmail.com>
收件人: Mailing list for scikit-image (http://scikit-image.org)<scikit-image@python.org>
主题: [scikit-image] Re: Medial axis skeletonization length
日期: 2018-11-30 09:10

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/skan/csr.py#L234-L425
(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.html

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

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Dedicated to Digital Image Processing for FISH, QFISH and other things about the telomeres.

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