Re: Colocalization on Z-stack images

Posted by phil laissue on
URL: http://confocal-microscopy-list.275.s1.nabble.com/Colocalization-on-Z-stack-images-tp7580319p7580323.html

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Hi Marjan,

more information would be needed to understand the problem, but I'm
pasting in a few references below. If you have a z-stack, the best
option is to do a 3D colocalisation analysis by including all focal
planes (hopefully you acquired using Nyquist-Shannon reconstruction
theorem).

(from an earlier post):
By no means a comprehensive list, but in my humble opinion some of the
most user-friendly discussions/approaches. Really depends on the
structures in question, there's not one single approach that works
best.

pixel-based:
http://www.ncbi.nlm.nih.gov/pubmed/23026999
diva-portal.org/smash/get/diva2:563664/FULLTEXT02
coloc2:
http://fiji.sc/Colocalization_Analysis
http://www.ncbi.nlm.nih.gov/pubmed/21209361
http://www.ncbi.nlm.nih.gov/pubmed/15189895
object-based:
http://www.ncbi.nlm.nih.gov/pubmed/20858446
http://crg.ubc.ca/moore/
http://www.ncbi.nlm.nih.gov/pubmed/19746416

http://www.ncbi.nlm.nih.gov/pubmed/23381680
(happy to send you reprint and matlab code)

Also worth checking out:
http://www.ncbi.nlm.nih.gov/pubmed/17210054
http://www.ncbi.nlm.nih.gov/pubmed/22086768

Hope this helps. Kind regards

Philippe

______________________________
Philippe Laissue, PhD, Bioimaging Manager
School of Biological Sciences, Room 4.17
University of Essex, Colchester CO4 3SQ, UK
(0044) 01206 872246 / (0044) 07842 676 456
[hidden email]
privatewww.essex.ac.uk/~plaissue

On Wed, May 8, 2013 at 5:44 PM, Marjan Gharagozloo <[hidden email]> wrote:

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>
> Dear All,
>
> I'd like to study colocalization of Draq5 and Cy3 in Nucleus.
> Actually, this topic is totally new to me and I've read many articles and
> manuals to find a way for quantifying colocalization. However, I don't
> know how I can analyze colocalization in my Zstack images. I know by
> changing focal plane, I'll get different results and quantities. It's
> kind of you if send me some information to do this analysis.
>
> Many thanks and best regards:
> Marjan
>
> --
> Best regards:
>
> Marjan Gharagozloo (PhD)
> Postdoctoral Fellow
> University of Waterloo
> School of Pharmacy, PHR3002
> 10 Victoria St S, N2G 2B2
> Kitchener, ON, Canada