Specify Multiple ROI W/ xy coordinates

Posted by dparrell on Sep 18, 2015; 2:38am
URL: http://imagej.273.s1.nabble.com/Specify-Multiple-ROI-W-xy-coordinates-tp5014356.html

Hi Everyone! I have been looking for a bit and can't find a solution for part of my workflow yet. I would like to define several 3x3 pixel ROIs on an image in a similar way to the specify ROI plugin under Edit->selection, but in a more high throughput manner. I am using find maxima to identify many foci of interest in a time series stack I am using for stepwise photobleaching. I am using the macro at the end of this post to export the xy coordinates of these points to the data table.

I do not want to enter each ROI by hand if I don't need to, since there will be quite a few of them. Can anyone conceive of a way to use these xy coordinates, perhaps from an exported .csv file, to specify several ROI at once with set dimensions  i.e.. 3x3, 5x5? I guess a brute force approach would get this done in only a couple hours by hand, but I figured it is worth asking for some assistance.  Thank you for any ideas!
Daniel
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After finding maxima I export the XY coordinates from each point with this macro. I would like to use these coordinates to place each ROI (about 50-100 per image series).

getSelectionCoordinates(xCoordinates, yCoordinates);
for(i=0; i<lengthOf(xCoordinates); i++) {
setResult("X", i, xCoordinates[i]);
setResult("Y", i, yCoordinates[i]);
}
updateResults();