Help wanted: implementation of 3D medial axis skeletonization
Hi all, I have been approached by a group that is interested in sponsoring the development of 3D skeletonization in scikit-image. One potential starting place would be: http://www.insight-journal.org/browse/publication/181 Is anyone interested in working on this? Please get in touch. Thanks! Stéfan
Hi Stéfan 3D skeletonization would be a great idea. I wonder if the algorithm you mention is the same as the one used in http://fiji.sc/Skeletonize3D (which is quite popular in the X-ray tomography community). There are so many 3D skeletonization algorithms that understanding which specs are required might be an important first step. Can you explain which kind of sponsoring it would be? Is it only available for people living in the US, or in other countries? For students only? Cheers Emma On Mon, Nov 02, 2015 at 02:26:46PM -0800, Stefan van der Walt wrote:
Hi all,
I have been approached by a group that is interested in sponsoring the development of 3D skeletonization in scikit-image. One potential starting place would be:
Is anyone interested in working on this? Please get in touch.
Thanks! Stéfan
Hi Emma On 2015-11-02 14:39:26, Emmanuelle Gouillart <emmanuelle.gouillart@nsup.org> wrote:
Can you explain which kind of sponsoring it would be? Is it only available for people living in the US, or in other countries? For students only?
I think there is a small amount of money available for anyone who is interested. And I agree, starting with a quick assessment of existing algorithms would be good! Stéfan
Should we use/apply this to a particular volumetric dataset while prototyping different methods, to ensure accurate comparisons? Should anisotropic, regularly sampled voxels be supported?
I can't work on this right now but I am very excited to see it happen... And it's the first example of a sponsored scikit-image project, right??? (Not counting GSoC.) Support for anisotropic voxels would be a definite plus, too. Don't forget that Fiji's code is mostly GPL, so don't try to copy it, at least not without first discussing dual licensing with the author(s). Juan.
I suggest the lobster, one of the bonsai, or the XMas tree datasets located here as excellent 'torture tests' for 3d skeletonization. http://www9.informatik.uni-erlangen.de/External/vollib/
Don't forget that Fiji's code is mostly GPL, so don't try to copy it, at least not without first discussing dual licensing with the author(s).
Excellent point. Actually I'm only using the Fiji page as a way to find the paper by Lee et al. again :-).
On Tue, Nov 3, 2015 at 12:55 PM, Josh Warner <silvertrumpet999@gmail.com> wrote:
Should we use/apply this to a particular volumetric dataset while prototyping different methods, to ensure accurate comparisons?
Should anisotropic, regularly sampled voxels be supported?
Hi, I don’t want to volunteer for this project, but I just wanted to mention that the 3D skeletonization from ITK is easily accessible to Python through SimpleITK, see example below for the lobster dataset. SimpleITK could be used for comparison or validation of the proposed scikit-image algorithm. Kind Regards, Kevin PS: is there another way to load those *.pvm datasets in Python without converting them to raw and hardcoding the image dimension and pixel type? An skimage.io.imread() plugin?
On 3 Nov 2015, at 21:18, Emmanuelle Gouillart <emmanuelle.gouillart@nsup.org> wrote:
Don't forget that Fiji's code is mostly GPL, so don't try to copy it, at least not without first discussing dual licensing with the author(s).
Excellent point. Actually I'm only using the Fiji page as a way to find the paper by Lee et al. again :-).
On Tue, Nov 3, 2015 at 12:55 PM, Josh Warner <silvertrumpet999@gmail.com> wrote:
Should we use/apply this to a particular volumetric dataset while prototyping different methods, to ensure accurate comparisons?
Should anisotropic, regularly sampled voxels be supported?
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Hi Kevin On 2015-11-07 09:46:17, 'Kevin Keraudren' via scikit-image <scikit-image@googlegroups.com> wrote:
I don’t want to volunteer for this project, but I just wanted to mention that the 3D skeletonization from ITK is easily accessible to Python through SimpleITK, see example below for the lobster dataset. SimpleITK could be used for comparison or validation of the proposed scikit-image algorithm.
Thanks for the pointer. In this case, one of the purposes of the exercise is to stay away from a heavy dependency such as ITK.
PS: is there another way to load those *.pvm datasets in Python without converting them to raw and hardcoding the image dimension and pixel type? An skimage.io.imread() plugin?
I have no idea about .pvm files, but perhaps we should start a set of plugin gists on the wiki somewhere? Stéfan
It looks like the lobster and bonsai can be downloaded directly as raw volumes (8 bit only, but will serve these purposes perfectly well) here: http://www.volvis.org/ This simple wrapper for np.fromfile will load them import numpy as np def loadraw(rawfile, shape=None, dtype=np.uint8): """ Load RAW volume to a NumPy array. Parameters ---------- rawfile : string Path to *.raw volume. shape : tuple Shape of the volume. If not provided, output will be a rank-1 stream which can be reshaped as desired. dtype : NumPy dtype Dtype of the raw image volume. """ vol = np.fromfile(rawfile, dtype=dtype) if shape is not None: vol = vol.reshape(shape) return vol For the lobster, use shape=(56, 324, 301) and recall the voxel spacing has a ratio of 1.4:1:1 For the bonsai, use shape=(256, 256, 256) and the volume is isotropic (1:1:1 spacing) On Monday, November 9, 2015 at 8:42:26 PM UTC-5, stefanv wrote: Hi Kevin
On 2015-11-07 09:46:17, 'Kevin Keraudren' via scikit-image < scikit-image@googlegroups.com> wrote:
I don’t want to volunteer for this project, but I just wanted to mention that the 3D skeletonization from ITK is easily accessible to Python through SimpleITK, see example below for the lobster dataset. SimpleITK could be used for comparison or validation of the proposed scikit-image algorithm.
Thanks for the pointer. In this case, one of the purposes of the exercise is to stay away from a heavy dependency such as ITK.
PS: is there another way to load those *.pvm datasets in Python without converting them to raw and hardcoding the image dimension and pixel type? An skimage.io.imread() plugin?
I have no idea about .pvm files, but perhaps we should start a set of plugin gists on the wiki somewhere?
Stéfan
participants (5)
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Emmanuelle Gouillart -
Josh Warner -
Juan Nunez-Iglesias -
Kevin Keraudren -
Stefan van der Walt