Re: 3D reconstruction of sections

Posted by dscho on Jan 13, 2011; 12:13am
URL: http://imagej.273.s1.nabble.com/3D-reconstruction-of-sections-tp3686011p3686013.html

Hi,

On Wed, 12 Jan 2011, Albert Cardona wrote:

> 2011/1/12 Xiaowei Li <[hidden email]>:
>
> >   We are trying to reconstruct the 3D structure of a mice organ from
> > about 200 sections of about 1 um thickness. The sections were H&E
> > stained and imaged in bright field with 40x objective.  The obtained
> > images were stitched in order to get full images of all sections
> >
> >  The images were imported to Fiji as a stack and viewed in 3D viewer.
> > However, we are not happy about the presentation of the 3D structure.
> > The cells are filled with colors and are very difficult to see a real
> > 3D structure. We would like to know whether there is other plugins or
> > package that can make the reconstructed 3D look like a real 3D.
>
> It would help if you described "real 3D".

I agree.

> Have you tried selecting the object in the 3D Viewer, and then going to
> "Edit - Display as" and choosing Surface or Orthoslice?
>
> Have you tried changing the transparency, or the threshold for a 3D
> surface? In "Edit - Attributes".

Also, there is a function in Edit>Attributes called "Transfer function"
where you can modify the transparency (this is called "alpha" as is common
in image processing).

> Could you make the data available, even if in scaled down form, so that
> we can see what the issue is? Could you attach a screenshot of the 3D
> image that doesn't look like you expect, with a description of what is
> wrong with it?

I agree that it is very hard to give you a meaningful feedback if you do
not make example data available.

Ciao,
Johannes