Re: 3d Reconstruction from Stack

Posted by Joel Sheffield on Jul 06, 2011; 6:05pm
URL: http://imagej.273.s1.nabble.com/3d-Reconstruction-from-Stack-tp3684002p3684004.html

Another pair of thoughts.  There is a plugin (actually 2 of them) called
"Unwarp", that imposes a distortion on one image to match a second one.
Perhaps you can normalize your images with these.  You might have to write a
macro to process all images sequentially.  Additionally, StackReg is another
alternative that has a scaling function.

Joel


On Wed, Jul 6, 2011 at 1:09 PM, Johannes Schindelin <
[hidden email]> wrote:

> Hi Andrew,
>
> On Thu, 23 Jun 2011, Andrew E. Meyer wrote:
>
> > We have an application where we are taking a stack of pictures of a fuel
> > injector seat and spray orifices, and trying to reconstruct a
> > 3-Dimensional image for use in verifying that the hardware was made to
> > spec.  We are using a microscope with a short focal length, so that the
> > features in the stack appear to grow in size as we get closer to the
> > object.  (think of a star field animation, where the nearer stars go
> > racing to the edge of the picture as the spaceship goes through the star
> > field).
> >
> > First, is there a name for this "star field" effect by which I could
> > search for information?
> >
> > We have tried using stack focuser and EDF to create a three dimensional
> > map from our stack with very limited success-the images are very noisy
> > and don't correspond to the reality which we can measure, so we cannot
> > trust them for the stuff we cannot measure.  Maybe I'm just not using
> > these extensions properly?  I'm new to this, but it is my understanding
> > that these techniques determine position of each point based on how
> > sharp the focus for the point is, so moving features might be a problem
> > for them.
>
> I imagine the problem is that your stack slices are not really in and out
> of focus.
>
> So maybe you need something completely different: you could use SIFT
> features in every slice to generate robust landmarks, and then use a
> RANSAC to find the most likely 3D locations of the landmarks.
>
> The last step would be an inverse mapping from the recorded stack into a
> 3D height-field.
>
> Ciao,
> Johannes
>

--


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