Dear ImageJ users,
I come from the field of Computer Graphics, not quit familiar with Material science. I was asked to measure the curvature of irregularly shaped porosities in a particle. Could anyone tell me the definition of curvature in this context, and how I can calculate it? Thanks in advance Xiaoxiong -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Xiaoxiong,
I'm afraid it may be difficult to give much of a definition of curvature, without some more details. You may for example be referring to the outline of a pore, or perhaps the curvature of the depression (sounds as if this is the more likely question). You don't say where you are in the process, but the first step is to get some sort of image that can be measured. There are 2 types that immediately come to mind. * Cross section. May be difficult if the particles are small and especially if you are interested in the depression. * Height map. Can be acquired via a few different methods (not necessarily an exhaustive list): * Confocal microscope * Interference microscope (e.g., Scanning White Light Interference) * Atomic Force Microscope * Optical or Electron Microscope images taken at different angles, and using "stereoscopic" transformations to calculate the height map. Once you have some data, there are different ways to characterize the curvature. You could simply fit a cross section to a circle, and report the "radius of curvature", or you could move up in complexity. Coincidentally, there was a recent discussion on another list, with the subject "Surface Curvature from Range Images (or Depth Maps)" [1]. Hope this gets you started. Jim [1] https://groups.google.com/d/topic/scikit-image/PWdHI-Jy3rA/discussion On Wed, Dec 4, 2013 at 7:06 PM, Xiaoxiong Xing <[hidden email]>wrote: > Dear ImageJ users, > > I come from the field of Computer Graphics, not quit familiar with Material > science. I was asked to measure the curvature of irregularly shaped > porosities in a particle. Could anyone tell me the definition of curvature > in this context, and how I can calculate it? > > Thanks in advance > > Xiaoxiong > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > *-- Jim Passmore* Research Associate Sealed Air Corporation -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Thanks, Jim.
I now have an image stack taken by phase-contrast tomography. I read the "Surface Curvature from Range Images", it assumes a surface defined as a function of two coordinates. Do you know ff there is a plugin that can fit triangle mesh for the porosities and can export the mesh data, so that I can do the curvature calculation offline? Thanks, Xiaoxiong 2013/12/5 Jim Passmore <[hidden email]> > Xiaoxiong, > I'm afraid it may be difficult to give much of a definition of curvature, > without some more details. You may for example be referring to the outline > of a pore, or perhaps the curvature of the depression (sounds as if this is > the more likely question). You don't say where you are in the process, but > the first step is to get some sort of image that can be measured. There > are 2 types that immediately come to mind. > * Cross section. May be difficult if the particles are small and > especially if you are interested in the depression. > * Height map. Can be acquired via a few different methods (not necessarily > an exhaustive list): > * Confocal microscope > * Interference microscope (e.g., Scanning White Light Interference) > * Atomic Force Microscope > * Optical or Electron Microscope images taken at different angles, and > using "stereoscopic" transformations to calculate the height map. > > Once you have some data, there are different ways to characterize the > curvature. You could simply fit a cross section to a circle, and report > the "radius of curvature", or you could move up in complexity. > Coincidentally, there was a recent discussion on another list, with the > subject "Surface Curvature from Range Images (or Depth Maps)" [1]. > > Hope this gets you started. > > Jim > > [1] https://groups.google.com/d/topic/scikit-image/PWdHI-Jy3rA/discussion > > > > > On Wed, Dec 4, 2013 at 7:06 PM, Xiaoxiong Xing <[hidden email] > >wrote: > > > Dear ImageJ users, > > > > I come from the field of Computer Graphics, not quit familiar with > Material > > science. I was asked to measure the curvature of irregularly shaped > > porosities in a particle. Could anyone tell me the definition of > curvature > > in this context, and how I can calculate it? > > > > Thanks in advance > > > > Xiaoxiong > > > > -- > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > > > > > > > *-- Jim Passmore* > Research Associate > Sealed Air Corporation > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
On Thu, Dec 5, 2013 at 2:33 PM, Xiaoxiong Xing <[hidden email]>wrote:
> I now have an image stack taken by phase-contrast tomography. > Sounds as if you already have an image that ImageJ can open. That's good! > I read > the "Surface > Curvature from Range Images", it assumes a surface defined as a function of > two coordinates. > > Do you know ff there is a plugin that can fit triangle mesh for the > porosities and can export the mesh data, so that I can do the curvature > calculation offline? > I'm familiar with the concept of a "triangle mesh", but don't have any experience working with one. There are at least a couple of possibilities, maybe more. * The 3D Viewer plugin [1, 2] will render a stack to a surface, and export to several formats. I imported a stack, displayed as a surface, and was able to export an STL file that looks like a list of vertices to me. This plugin can also be used as a library for your own code, so some of the lower-level methods may be useful. * The TrackEM2 plugin [3] also does some 3D operations, although I've never used it myself, so I can't comment extensively. There is a page [4] describing scripting this plugin that includes code to create a triangle mesh. Note that I usually use the Fiji distribution of ImageJ, that includes both these plugins out of the box. You may have to install them if you install from the ImageJ website... Jim [1] http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2896381/ [2] http://3dviewer.neurofly.de/ [3] http://www.ini.uzh.ch/~acardona/trakem2.html [4] http://fiji.sc/TrakEM2_Scripting#Generate_3D_meshes *-- Jim Passmore* Research Associate Sealed Air Corporation -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Hi Jim,
> Note that I usually use the Fiji distribution of ImageJ, that includes > both these plugins out of the box. You may have to install them if > you install from the ImageJ website... For those curious: Fiji was actually invented, originally, to serve as a distribution mechanism for TrakEM2, because installing that plugin into ImageJ was otherwise very complex. So I would advise against trying to somehow get TrakEM2 working in a "vanilla" ImageJ installation... 3D Viewer, on the other hand, comes bundled with vanilla ImageJ, too. Regards, Curtis On Fri, Dec 6, 2013 at 10:25 AM, Jim Passmore <[hidden email]> wrote: > On Thu, Dec 5, 2013 at 2:33 PM, Xiaoxiong Xing <[hidden email] > >wrote: > > > I now have an image stack taken by phase-contrast tomography. > > > Sounds as if you already have an image that ImageJ can open. That's good! > > > > I read > > the "Surface > > Curvature from Range Images", it assumes a surface defined as a function > of > > two coordinates. > > > > Do you know ff there is a plugin that can fit triangle mesh for the > > porosities and can export the mesh data, so that I can do the curvature > > calculation offline? > > > > I'm familiar with the concept of a "triangle mesh", but don't have any > experience working with one. There are at least a couple of possibilities, > maybe more. > * The 3D Viewer plugin [1, 2] will render a stack to a surface, and export > to several formats. I imported a stack, displayed as a surface, and was > able to export an STL file that looks like a list of vertices to me. This > plugin can also be used as a library for your own code, so some of the > lower-level methods may be useful. > * The TrackEM2 plugin [3] also does some 3D operations, although I've never > used it myself, so I can't comment extensively. There is a page [4] > describing scripting this plugin that includes code to create a triangle > mesh. > > Note that I usually use the Fiji distribution of ImageJ, that includes both > these plugins out of the box. You may have to install them if you install > from the ImageJ website... > > Jim > > > [1] http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2896381/ > [2] http://3dviewer.neurofly.de/ > [3] http://www.ini.uzh.ch/~acardona/trakem2.html > [4] http://fiji.sc/TrakEM2_Scripting#Generate_3D_meshes > > > > *-- Jim Passmore* > Research Associate > Sealed Air Corporation > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Free forum by Nabble | Edit this page |