From pe3ak at yahoo.com Tue Feb 9 18:37:34 2016 From: pe3ak at yahoo.com (Vova) Date: Tue, 9 Feb 2016 23:37:34 +0000 (UTC) Subject: [Tubetk-developers] tubes extraction from binary image References: <2001025347.1655207.1455061054573.JavaMail.yahoo.ref@mail.yahoo.com> Message-ID: <2001025347.1655207.1455061054573.JavaMail.yahoo@mail.yahoo.com> Hi I am seeking your advice/help on how to extract ?tubes/fibres from the binary image (in my case it is a 3D tomography dataset of the carbon paper). I am extensively using itk routines in c++ and would like to combine my code with a comprehensive tubetk library in c++ as well. However I could not find any documentation or example on how to extract the tubes using c++ code. Can someone please explain the necessary steps ? Thank you very much, Vlad. -------------- next part -------------- An HTML attachment was scrubbed... URL: From stephen.aylward at kitware.com Wed Feb 10 06:46:24 2016 From: stephen.aylward at kitware.com (Stephen Aylward) Date: Wed, 10 Feb 2016 06:46:24 -0500 Subject: [Tubetk-developers] tubes extraction from binary image In-Reply-To: <2001025347.1655207.1455061054573.JavaMail.yahoo@mail.yahoo.com> References: <2001025347.1655207.1455061054573.JavaMail.yahoo.ref@mail.yahoo.com> <2001025347.1655207.1455061054573.JavaMail.yahoo@mail.yahoo.com> Message-ID: Hi, I recommend 1) Convert the image to a distance map using ITK's Danielsson Distance measure filter. This will convert your binary image to an image that is bright along the center of your binary object 2) Use TubeTK's SegmentTubeUsingMinimalPath (which uses ITK's minimal path module) to compute the path down the center of your object, given the distance map and two end points. You will need to specify the two end points of the path, but hopefully that will be easy to due if your image acquisition protocol is somewhat constrained. The minimal path method will then return the path that connect those two endpoints along bright center of your distance map object. Hope this helps. s On Tue, Feb 9, 2016 at 6:37 PM, Vova via Tubetk-developers < tubetk-developers at public.kitware.com> wrote: > Hi > > I am seeking your advice/help on how to extract tubes/fibres from the > binary image (in my case it is a 3D tomography dataset of the carbon paper). > > I am extensively using itk routines in c++ and would like to combine my > code with a comprehensive tubetk library in c++ as well. > > However I could not find any documentation or example on how to extract > the tubes using c++ code. > > Can someone please explain the necessary steps ? > > Thank you very much, > > Vlad. > > _______________________________________________ > Tubetk-developers mailing list > Tubetk-developers at public.kitware.com > http://public.kitware.com/mailman/listinfo/tubetk-developers > > -- ==================================================== Stephen R. Aylward, Ph.D. Senior Director of Operations, North Carolina, Kitware, Inc. http://www.kitware.com and http://www.aylward.org (919) 969-6990 x300 ==================================================== -------------- next part -------------- An HTML attachment was scrubbed... URL: