Colleagues,
Here's an interesting challenge. As I understand it, both the 3D Viewer or the 3D rotation utility built into ImageJ work on some form of an algorithm in which the relative positions of the slices in a stack are shifted relative to each other, and then a Maximum projection is generated, creating a new view through the shifted stack. We have been looking at the DIC stacks that are generated either with confocal or manual DIC systems, which also have optical slices. However, when we try a standard Max projection, the resultant is a mess, since the criteria for inclusion are not intensity, but contrast. On the other hand, we have been able to use the Stack Focuser plugin to create "flattened" images of these stacks so that all components remain in focus. I am wondering if it is possible to use an image shift algorithm similar to the one for transparent fluorescent objects to generate a rotating, or at least a simple stereo view of such DIC samples. -- Joel B. Sheffield, Ph.D Department of Biology Temple University Philadelphia, PA 19122 Voice: 215 204 8839 e-mail: [hidden email] URL: http://astro.temple.edu/~jbs |
Do you mean you want to use something like stack focuser on the rotated
stack? Mikhail Umorin, Ph.D. On Thu, Apr 21, 2011 at 7:28 PM, Mikhail Umorin <[hidden email]> wrote: > Do you mean you want to use something like stack focuser on the rotated > stack? > > Mikhail Umorin, Ph.D. > > > On Thu, Apr 21, 2011 at 2:23 PM, JOEL B. SHEFFIELD <[hidden email]> wrote: > >> Colleagues, >> >> Here's an interesting challenge. As I understand it, both the 3D Viewer >> or >> the 3D rotation utility built into ImageJ work on some form of an >> algorithm >> in which the relative positions of the slices in a stack are shifted >> relative to each other, and then a Maximum projection is generated, >> creating >> a new view through the shifted stack. We have been looking at the DIC >> stacks that are generated either with confocal or manual DIC systems, >> which >> also have optical slices. However, when we try a standard Max projection, >> the resultant is a mess, since the criteria for inclusion are not >> intensity, >> but contrast. On the other hand, we have been able to use the Stack >> Focuser plugin to create "flattened" images of these stacks so that all >> components remain in focus. I am wondering if it is possible to use an >> image shift algorithm similar to the one for transparent fluorescent >> objects >> to generate a rotating, or at least a simple stereo view of such DIC >> samples. >> >> -- >> >> >> Joel B. Sheffield, Ph.D >> Department of Biology >> Temple University >> Philadelphia, PA 19122 >> Voice: 215 204 8839 >> e-mail: [hidden email] >> URL: http://astro.temple.edu/~jbs >> > > |
No. I want to create a rotating image from a DIC stack, so I can see some
depth. On Thu, Apr 21, 2011 at 8:44 PM, Mikhail Umorin <[hidden email]> wrote: > Do you mean you want to use something like stack focuser on the rotated > stack? > > Mikhail Umorin, Ph.D. > > On Thu, Apr 21, 2011 at 7:28 PM, Mikhail Umorin <[hidden email]> wrote: > > > Do you mean you want to use something like stack focuser on the rotated > > stack? > > > > Mikhail Umorin, Ph.D. > > > > > > On Thu, Apr 21, 2011 at 2:23 PM, JOEL B. SHEFFIELD <[hidden email]> > wrote: > > > >> Colleagues, > >> > >> Here's an interesting challenge. As I understand it, both the 3D Viewer > >> or > >> the 3D rotation utility built into ImageJ work on some form of an > >> algorithm > >> in which the relative positions of the slices in a stack are shifted > >> relative to each other, and then a Maximum projection is generated, > >> creating > >> a new view through the shifted stack. We have been looking at the DIC > >> stacks that are generated either with confocal or manual DIC systems, > >> which > >> also have optical slices. However, when we try a standard Max > projection, > >> the resultant is a mess, since the criteria for inclusion are not > >> intensity, > >> but contrast. On the other hand, we have been able to use the Stack > >> Focuser plugin to create "flattened" images of these stacks so that all > >> components remain in focus. I am wondering if it is possible to use an > >> image shift algorithm similar to the one for transparent fluorescent > >> objects > >> to generate a rotating, or at least a simple stereo view of such DIC > >> samples. > >> > >> -- > >> > >> > >> Joel B. Sheffield, Ph.D > >> Department of Biology > >> Temple University > >> Philadelphia, PA 19122 > >> Voice: 215 204 8839 > >> e-mail: [hidden email] > >> URL: http://astro.temple.edu/~jbs > >> > > > > > -- Joel B. Sheffield, Ph.D Department of Biology Temple University Philadelphia, PA 19122 Voice: 215 204 8839 e-mail: [hidden email] URL: http://astro.temple.edu/~jbs |
On Friday 22 Apr 2011, JOEL B. SHEFFIELD wrote:
> No. I want to create a rotating image from a DIC stack, so I can see some > depth. Joel, Can you post a smallish stack as an example to work with? Regards Gabriel |
In reply to this post by Joel Sheffield
Hi Joel,
On Apr 22, 2011, at 6:03 AM, IMAGEJ automatic digest system wrote: > Date: Thu, 21 Apr 2011 15:23:20 -0400 > From: "JOEL B. SHEFFIELD" <[hidden email]> > Subject: 3D using Stack Focusser? > > Colleagues, > > Here's an interesting challenge. As I understand it, both the 3D Viewer or > the 3D rotation utility built into ImageJ work on some form of an algorithm > in which the relative positions of the slices in a stack are shifted > relative to each other, and then a Maximum projection is generated, 3D viewer is not using a max projection i think.... its more like an average or sum projection through the volume in a given direction/line... but maybe thats not so important here... > creating > a new view through the shifted stack. We have been looking at the DIC > stacks that are generated either with confocal or manual DIC systems, which > also have optical slices. However, when we try a standard Max projection, > the resultant is a mess, since the criteria for inclusion are not intensity, > but contrast. Yes, this is expected to be the case... the intensity in a DIC image is a complicated function of the local refractive index gradient, and the direction of that gradient with respect to the angle the polarizers and prisms are set at. I have seen no good way to convert this kind of image into something that will give an intuitively sensible looking 3D volume rendered result... but it would be neat. > On the other hand, we have been able to use the Stack > Focuser plugin to create "flattened" images of these stacks so that all > components remain in focus. I am wondering if it is possible to use an > image shift algorithm similar to the one for transparent fluorescent objects > to generate a rotating, or at least a simple stereo view of such DIC > samples. > the problem here is that, (unlike fluorescence) the same object looks very different in DIC depending on its orientation, so when you move to a new view point in 3d space... well, things just dont add up or make sense... Perhaps this might help: Interesting features in DIC are usually where there is a steep intensity grdient in the image. So, you can take a DIC image z stack, compute its gradient image per slice, and use that for 3D rendering. I dont have a DIC z stack handy... but i imagine the above trick might give something useful? Maybe? ? D > -- > > > Joel B. Sheffield, Ph.D > Department of Biology > Temple University > Philadelphia, PA 19122 > Voice: 215 204 8839 > e-mail: [hidden email] > URL: http://astro.temple.edu/~jbs Dr. Daniel James White BSc. (Hons.) PhD Senior Microscopist / Image Processing and Analysis Light Microscopy Facility Max Planck Institute of Molecular Cell Biology and Genetics Pfotenhauerstrasse 108 01307 DRESDEN Germany +49 (0)15114966933 (German Mobile) +49 (0)351 210 2627 (Work phone at MPI-CBG) +49 (0)351 210 1078 (Fax MPI-CBG LMF) http://www.bioimagexd.net BioImageXD http://pacific.mpi-cbg.de Fiji (is just ImageJ - batteries included) http://www.chalkie.org.uk [hidden email] ( [hidden email] ) |
Free forum by Nabble | Edit this page |