Re: 3D reconstruction of sections

Posted by Joel Sheffield on Jan 12, 2011; 1:38pm
URL: http://imagej.273.s1.nabble.com/3D-reconstruction-of-sections-tp3686011p3686014.html

One trick that I have used is to invert the colors so that the nuclei become
bright objects, and then use the old 3D image routine in the stacks menu of
ImageJ to make a series of maximum projection images that rotate.  Then you
can invert the colors back and still see the stereo effect.

You might also consider using a subset of the images rather than all 200.

Best of luck.

Joel


On Wed, Jan 12, 2011 at 5:31 AM, Xiaowei Li <[hidden email]> wrote:

> 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.
>
> Thank you in advance.
>
> Best Regards,
>
> Xiaowei
>
>
>
>
>
> --
> Xiaowei Li, Ph.D
> Associate Professor
> Shanghai Centre for Systems Biomedicine
> Shanghai Jiao Tong University
> Office:86 21-34206632
> Fax:  [phone]
>

--


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