"Save XY Coordinates" for multiple ROIs?


I would like to collect the XY coordinates and RGB values for about 50 ROIs per image, for a lot of images. Is there a way to export the data for all 50 at once (ideally with identifying numbers)? I can highlight as many as I like in the ROI manager, but only the data for the first one is exported. Cut and paste is getting old.



Hello :slight_smile:

I think this thread could be of help to you (outlines of multiple bubbles (ROIs) in a foam z-stack):

Or this thread (xy locations of multiple points in series of images):

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Thanks. I saw those, but don’t see how to apply them. Still hoping someone may have solved the “Save XY Coordinates” case specifically.

@bmacgreg : If you can export one roi, you apply that in the loop Herbie wrote down; it shows you how to select each roi in the roi manager. Then for each selected roi, rather than rather call “outline2results”, you insert the proper command to export the data and your given your remark “but only the data for the first one is exported”, you already know how.
Otherwise check this forum entry.

Hmm. Thanks, but I confess I don’t understand a word of that, as far as ending up with a single file… Well, some day I’ll figure it out.


I had developed a plugin (CellDetection) that is maybe useful for your analysis.
The plugin was developed to measure multiple ROIs detected in high intensity out line (like cell edge).
But, this plugin can use manual selected ROI position and shape.
And it can record multiple ROIs in each image of Hyper stack image.
And it can measure these ROIs with one click.
And it can save recorded ROIs position and shape data as tsv file.

If you are interested in this plugin, please download it and try it.
*note : A manual.txt is included in the zip file, but it is written by Japanese…and English web pages is not written yet.


Thank you, I will give it a try!

New address (old email still works)

Barbara MacGregor
Dept. of Earth Sciences
University of Minnesota
John T. Tate Hall, Rm. 452
116 Church St. SE
Minneapolis MN 55455

Email: macgregb@umn.edu
Cell: +1 (919) 260-6038

Hi I hope you found a way already, but just in case, here you are

  1. If you only need to store all the 50 ROIs, you can just click More–Save in the ROI manager.
  2. If you want to get both XY and measurements, you can do More—Multi-Measure in the ROI manager.