http://imagej.273.s1.nabble.com/measuring-grayscale-of-objects-in-a-plate-tp5004160p5004166.html
I am confused about what "your ROIs" means. Do you mean 1) the ROI set that I have saved, which has one ROI for each of the 48 wells, or 2) the ROIs that I get after I threshold/analyze particles/save to ROI manager?
If you mean (1), my saved ROI set has ROIs that includes each well in its entirety. However, since seeds take up only a fraction of the well, and since seeds can be in many different shapes and sizes and places within the well, my ROI set doesn't actually help very much in identifying the seeds themselves. In my original post, I suggested that if I could apply the threshold/analyze particle functions to only the ROI and not the entire image, then I could apply the process 48 times, one time for each ROI/well, which would then be in order, since my ROI set is already in order, and I do this in the order of my ROI set. However, I do not know how to apply the functions to only the ROI, so I can't use this method (unless you know how to do it).
If you mean (2), the seeds vary in position within each well. So even though in theory, if I tell the program to list in increasing y-coordinate values and then in increasing x-coordinate values, I should get the wells/seeds in order, this is not the case in practice. This is what I tried to explain in my previous post. Unless I am misunderstanding you, in which case you would have to explain your method in slightly more detail.
Thanks
JDing