3D cropping of stack

[Laura Lucia Prieto Godino]

Hi list,

I have confocal stack,and I would like to select a 3D volume and use  
subtract background and analize particles in only that volume, and  
discard the rest of the image. So ideally I need to do something  
similar to segmentation editor, but to crop the image to my selection  
in stead of just extracting the silhouette. Do you know if I can do  
such a thing with image j?
thank you so much!

Lucia



  Lucia Prieto Godino
PhD student.
Department of Zoology,
Downing street
University of Cambridge.
UK
http://www.neuroscience.cam.ac.uk/directory/profile.php?lauralucia

[Daniel James White]

Hi Lucia,

you can do that with the 3D viewer plugin in the Fiji imageJ  
distribution
http://pacific.mpi-cbg.de                Fiji -  is just ImageJ (Batteries Included)

see a movie of how to do it  here:
http://132.187.25.13/home/imagej/Viewer.avi

cheers

Dan


Begin forwarded message:

> Date:    Mon, 22 Mar 2010 16:43:16 +0000
> From:    Laura Lucia Prieto Godino <[hidden email]>
> Subject: 3D cropping of stack
>
> Hi list,
>
> I have confocal stack,and I would like to select a 3D volume and use
> subtract background and analize particles in only that volume, and
> discard the rest of the image. So ideally I need to do something
> similar to segmentation editor, but to crop the image to my selection
> in stead of just extracting the silhouette. Do you know if I can do
> such a thing with image j?
> thank you so much!
>
> Lucia
>
>
>
>  Lucia Prieto Godino
> PhD student.
> Department of Zoology,
> Downing street
> University of Cambridge.
> UK
> http://www.neuroscience.cam.ac.uk/directory/profile.php?lauralucia

Dr. Daniel James White BSc. (Hons.) PhD
Senior Microscopist / Image Visualisation, Processing and Analysis
Light Microscopy and Image Processing Facilities
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)

http://www.bioimagexd.net  BioImageXD
http://pacific.mpi-cbg.de                Fiji -  is just ImageJ (Batteries Included)
http://www.chalkie.org.uk                Dan's Homepages
https://ifn.mpi-cbg.de  Dresden Imaging Facility Network
dan (at) chalkie.org.uk
( white (at) mpi-cbg.de )