Analyzing a grid of ROIs

Posted by Audrey O'Neill on May 07, 2013; 6:18pm
URL: http://imagej.273.s1.nabble.com/Analyzing-a-grid-of-ROIs-tp5002945.html

Hello -

Does anyone have experience with anaylzing a grid of square ROIs according to mean gray values?

Basically, I am trying to quantify how sorted or patchy a given field of cells (half of which are stained for GFP) is, using nearest-neighbor analysis.

The method is described in more detail in this paper (http://www.ncbi.nlm.nih.gov/pubmed/9520108?dopt=Abstract), but basically what we want to do is:

1. divide the image into a grid of squares with height and width approximately equal to cell diameter
2. find the mean gray value of the whole image and set it as the threshold
3. count each square as above or below the threshold
4. count how many of each "above threshold" square's nearest neighbor squares (above, below, left, and right) are above threshold

I can do step (1) using a variant of the macro found here (http://imagej.1557.x6.nabble.com/How-to-create-a-regular-grid-of-rectangular-ROI-s-td3685056.html), and step (2) is fairly trivial, but I am totally lost when it comes to steps (3) and (4).

Thanks very much!

Audrey
Postdoc, Bush lab
Cell and Tissue Biology
UCSF School of Dentistry

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