Thread Subject:

3D reconstruction from 2D slices

Hi there,
Here is my problem.
I have about 600 2D slices (.bmp files) from an spherical-looking
element.
They are consecutive slices, but with a small gap between them (~ 3
microns).
I would like to know how to reconstruct the 3D object from all the
slices, taking into account the spacing in the z direction.
Is there any function in Matlab, or in the image processing toolbox,
that can do this? How can I do it if not?
I would appreciate any help.
Thank you very much.
Regards

Daniel,

You may be intereseted in the case study that I present at Advanced
Image Processing seminars around the country. The case study invloves
automated alignment of planar slices and then visualization fo the solid
once reconstructed.

http://www.mathworks.com/matlabcentral/fileexchange/loadFile.do?objectId=1713&objectType=file

Doug

Daniel Barrera-Medrano wrote:

> Hi there,
> Here is my problem.
> I have about 600 2D slices (.bmp files) from an spherical-looking
> element.
> They are consecutive slices, but with a small gap between them (~ 3
> microns).
> I would like to know how to reconstruct the 3D object from all the
> slices, taking into account the spacing in the z direction.
> Is there any function in Matlab, or in the image processing toolbox,
> that can do this? How can I do it if not?
> I would appreciate any help.
> Thank you very much.
> Regards

here is a bit of m-file, that reads in slices and shows a 3D solid:
--------------------
I=zeros(500,500,600);


for i=1:600
    i
    filename=['slice' int2str(i) '.gif'];
    I(:,:,i)=imread(filename);
end
    whos
%J = smooth3(I);
p = patch(isosurface(I,1.5));
isonormals(I,p)
set(p,'FaceColor','red','EdgeColor','none');
daspect([1 1 1])
view(3); axis tight
camlight
lighting gouraud
hcap = patch(isocaps(I,1.5),'FaceColor','interp','EdgeColor','none');

Here is information I found useful and sufficient when 3D-reconstructing
stacks of 2D images:

http://www.mathworks.com/access/helpdesk/help/techdoc/visualize/intro_vi.shtml#visualization_techniques

HTH,
yuri

On Wed, 25 Jun 2003 10:20:58 -0400, "Daniel Barrera-Medrano"
<danibarrera@yahoo.com> wrote:

>Hi there,
>Here is my problem.
>I have about 600 2D slices (.bmp files) from an spherical-looking
>element.
>They are consecutive slices, but with a small gap between them (~ 3
>microns).
>I would like to know how to reconstruct the 3D object from all the
>slices, taking into account the spacing in the z direction.
>Is there any function in Matlab, or in the image processing toolbox,
>that can do this? How can I do it if not?

Look here:
http://www.mathworks.com/access/helpdesk/help/techdoc/visualize/chvolvi5.shtml#3371

There is also an MRI example on this page:
http://www.mathworks.com/products/image/demos.jsp

  Lars

Lars Gregersen
COMSOL A/S
http://www.comsol.dk

Hi all,

I have 50 slices in 2D and want to obtain 3D image from these slices.
The velow links from Lars have been broken :(

How to do 3D image reconstruction from 2D slices ?

Thanks

Lars Gregersen <larsg @ comsol . dk> wrote in message <r50kfvsgj7go94gcn32hpofgu3uki66vpa@4ax.com>...
> On Wed, 25 Jun 2003 10:20:58 -0400, "Daniel Barrera-Medrano"
> <danibarrera@yahoo.com> wrote:
>
> >Hi there,
> >Here is my problem.
> >I have about 600 2D slices (.bmp files) from an spherical-looking
> >element.
> >They are consecutive slices, but with a small gap between them (~ 3
> >microns).
> >I would like to know how to reconstruct the 3D object from all the
> >slices, taking into account the spacing in the z direction.
> >Is there any function in Matlab, or in the image processing toolbox,
> >that can do this? How can I do it if not?
>
> Look here:
> http://www.mathworks.com/access/helpdesk/help/techdoc/visualize/chvolvi5.shtml#3371
>
> There is also an MRI example on this page:
> http://www.mathworks.com/products/image/demos.jsp
>
> Lars
>
> Lars Gregersen
> COMSOL A/S
> http://www.comsol.dk