measuring grayscale of objects in a plate

Posted by JDing on Jul 26, 2013; 7:10pm
URL: http://imagej.273.s1.nabble.com/measuring-grayscale-of-objects-in-a-plate-tp5004160.html

I have a 48 well plate (6x8) with a corn seed inside each well. I'm trying to get a "results" readout of the grayscale color of each seed, in order (so I want the grayscale for the seed in well A1, then for the seed in B1, ... , then in F8).

I already have some of it figured out. I use the threshold function to identify where the seeds are within a scan of the entire plate, then use "analyze particles" to put the outline of the seeds in the ROI manager, then revert to the original image (so that there's color) and use the ROI manager to measure each individual seed. The only problem is that the ROIs aren't in the correct order of the wells.

I have a saved ROI set that has an ROI corresponding to each well, in order. So if I could select each ROI/well one at a time, and threshold/analyze/measure only the space within that one cell, then revert back to the original image and repeat with the next ROI/well, then all the measurements would be in order at the end. This seems like a relatively simple solution. However, I can't find a way to do this with the functions in ImageJ. Is there a way to do it?

Hopefully I explained the problem clearly. If not, please let me know and I'll try to clarify. Thank you for your help!

JDing