ROI Manager Output

Posted by Serapio M. Baca on Aug 08, 2007; 9:55pm
URL: http://imagej.273.s1.nabble.com/ROI-Manager-Output-tp3698671.html

I would like to do the following and I am not sure what is the best  
way to go about it:

1. Run through an image stack with the ROI manager and outline every  
cell of interest.
2. Obtain a matrix of intensity per frame per ROI of all of the cells.
3. Save in a format that is readable by MATLAB or Determine how to  
graphically offset the Intensity-Over-Time plots to get a sense of  
the activity of the different cells over time.

Right now, I do (1) and then I have to reclick onto each ROI, do the  
intensity-over-time plot and then save the values and copy and paste  
to excel. Not that much of a hassle for a few cells, but in my field  
I can have as many as 100, which makes this hacked approach too slow.

Any advice, clever tricks, or pointers to preexisting solutions would  
be greatly appreciated.

Best Regards,

Serapio
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Serapio M. Baca, PhD
Postdoctoral Fellow
UCLA Neurobiology
Feldman Lab
[hidden email]