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On May 8, 2013, at 12:15 PM, Julio Vazquez Hutch <[log in to unmask]> wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
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> *****
> 
> Hi Marjan, 
> 
> It's a bit difficult to give you a pointed answer without knowing the specifics of your experiment, which software you have available, and/or how you are currently doing your analysis on single sections...
> 
> However, for starters, you could use imagej or fji (which you can download; just google "imagej or fiji imagej). 
> 
> Imagej has plugins for colocalization analysis. some of them, such as "Manders coefficients" work on stacks. Just go to the plugins section of th eIMageJ web site and rad about and/or try different plugins to see which one may work best for you
> 
> Another approach is to use thresholding to select the positive regions in each channel, convert to mask, perform image arithmetic between masks, and use the resulting mask(s) to analyze (Analyze > Measure) your images (obtain colocalized and non colocalized volumes and intensities for all channels). These operations also will work on stacks. You just may need to convert areas to volumes...
> 
> There is also software designed specifically for the analysis of 3-D microscopy data (we use primarily Volocity and Imaris, no commercial interest).  Such software would make it a bit easier to analyze stacks directly as volumes, and would allow you to process multiple stacks in a semi-automated fashion. Again, it all depends on what you have available and what you need to do, but you should be able to do quite a lot with ImageJ.
> 
> If there is a microscopy/image analysis department in your institution, it might be a good idea also to go check with them... much easier to learn such techniques this way. If there is nothing locally, there is an imaging department in Toronto, where you can probably get all the training and assistance you need, and possibly access to advanced software.
> 
> http://www.aomf.ca/coursesmain.html
> 
> You can also find expertise on ImageJ at the site below (also in Toronto, I think), including a detailed manual on how to perform various analyses with ImageJ:
> 
> http://www.uhnresearch.ca/facilities/wcif/download.php
> 
> 
> Hope this gives you some ideas... 
> 
> 
> Julio Vazquez
> Fred Hutchinson Cancer Research Center
> Seattle, WA 98109
> 
> http://www.fhcrc.org/en.html
> 
> ==
> 
> 
> 
> On May 8, 2013, at 8:44 AM, Marjan Gharagozloo wrote:
> 
>> *****
>> To join, leave or search the confocal microscopy listserv, go to:
>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
>> *****
>> 
>> 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