3D reconstruction of multiple, fluorescently labelled, sections

[Daniel James White]

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
*****

Hi Emma,
>
> Date:    Fri, 18 Nov 2011 08:39:57 -0600
> From:    Emma King <[hidden email]>
> Subject: 3D reconstruction of multiple, fluorescently labelled, sections
>
> We would like to take serial sections (20 microns thick) of rat spinal cord (up to 1cm long), label them with a bright and specific fluorescent label, acquire images (we can use either a widefield or confocal microscope) and then reconstruct the data in to one, 3D structure.

what do you mean by reconstruct? A z stack of xy images is a 3D image...
you can volume render it with ImageJs 3D viewer (bundles in the Fiji distribution of ImageJ
found at http://fiji.sc
or also in BioimageXD (www.bioimagexd.net) whaích uses VTK for fast high quality volume rendering
using the computer's 3D graphics card (GPU) or very nice fast ray cast rendering by the CPU (uses all cores of the CPUs)
Also you can do iso surface rendering of objects, or segment object however you like and surfce render those.

No need to buy expensive software for this unless you really need a special feature of one of those.

>
> We have the sectioning, staining and acquisition parameters/options=20
> under control, but don't have any software capable of reconstructing=20
> the resultant images. Does anyone have any suggestions as to what=20
> software to use and where to get it from?=20

Fiji from  fiji.sc
BioImageXD  from www.bioimagexd.net

>
> Any help much appreciated.=20

no worries, ask for help with the above if you struggle.

cheers

Dan

>
> Cheers,=20
> Emma=20
>
> Advanced Microscopy Unit=20
> School of Biomedical Sciences=20
> Univeristy of Nottingham

Dr. Daniel James White BSc. (Hons.) PhD

Leader - Image Processing Facility,
Senior Microscopist,
Light Microscopy Facility.

Max Planck Institute of Molecular Cell Biology and Genetics
Pfotenhauerstrasse 108
01307 DRESDEN
Germany

[phone] (German Mobile)
[phone] (Work phone at MPI-CBG)
[phone] (Fax MPI-CBG LMF)
chalkie666 Skype
http://www.bioimagexd.net  BioImageXD
http://fiji.sc                                        Fiji -  is just ImageJ (Batteries Included)
http://www.chalkie.org.uk                Dan's Homepages
https://ifn.mpi-cbg.de  Biopolis Dresden Imaging Platform (BioDIP)
dan (at) chalkie.org.uk
( white (at) mpi-cbg.de )