Re: 3D reconstruction of sections

Posted by Albert Cardona-2 on Jan 12, 2011; 2:16pm
URL: http://imagej.273.s1.nabble.com/3D-reconstruction-of-sections-tp3686011p3686012.html

2011/1/12 Xiaowei Li <[hidden email]>:

> Hi ImageJ users and developers,
>
>     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.

Dear Xiaowei,

It would help if you described "real 3D".

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".

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?

Albert

--
http://albert.rierol.net