Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
Serra,
I suspect there is no simple answer to your question. "Colocalization studies" is a catch-all term that can mean a variety of things, and there are many ways to measure colocalization, depending on the specific question you are trying to address... ImageJ has several plugins for colocalization, some of which work on stacks (e.g .image correlator plus), and some that work on single images only (e.g. colocalization finder). If you have time points, you can process each time point individually, or you can load all time points into a single stack, and process the whole stack if you are using a tool or plugin that works on stacks. If you are doing other types of colocalization analysis that work only on individulal images (or pairs of images), you could find or write a macro to process an entire folder of images automatically. If you are collecting z-stacks, maybe you want to model your data in 3-D and look at colocalization of your 3-D objects, rather than comparing images pixel by pixel... doing this with imagej may not be that easy and/or convenient, unless you find a suitable plugin or macro, or you have some programming skills yourself.. We typically do this type of analysis with commercial software such as Volocity or Imaris that is designed to handle 3D/4D data. These are just a few tips... you probably will need to define your question more precisely, and/or take some time to explore the various imagej analysis functions and plugins to see which ones work for you, which ones will work on stacks, and/or which ones you can automate with macros. If you want to do colocalization of 3-D objects, you may need a different software, or find someone who can help you with imagej...
--
Julio Vazquez
Fred Hutchinson Cancer Research Center
Seattle, WA 98109-1024
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On Dec 25, 2007, at 2:00 PM, Serra Akinturk wrote:
Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocalDear members,
My confocal LSM images are both in z-stacks and time series. Unfortunately i couldnt manage to do colocalization analysis by using image j with those 4D images.
Is there anyone who does colocalization quantification in image J with images that include z-stacks and time series?
I will look forward to read your suggestions.
Merry Christmas and Happy New Year!
Warmest regards,
S.Serra Akinturk
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