Open Microscopy Environment

I want to keep many ROIs stored in the Overlay of an image in ImageJ into an OME.TIF file.

The Bio-Formats Exporter has "Export ROIs" option in the dialog, so I thought this should do the job.

I used the boats.gif example image of ImageJ. Put a few TextRois into Overlay, and saved it in uncompressed OME.TIF with the "Export ROIs" option. To my surprise, I cannot find any ROIs either in Overlay or ROI manager from the saved OME.TIF file.

I also tried using Image > Overlay > To ROI Manager and then Save As.. > OME.TIF with "Export ROIs". This doesn't work either.

Now I really wonder if I can save ROIs at all with the OME.TIF format. Actually, I thought once I managed to do it. Please tell me if I'm doing something wrong.

BTW, I can save ROIs in Overlay with standard TIFF format.


The same question was posted in ImageJ forum as well: https://forum.image.sc/t/how-do-i-save-rois-into-an-ome-tiff-file/20619

It turned out that I needed to open OME.TIF file using Bio-Formats Importer, rather than drag and drop to ImageJ toolbar! Then I can choose whether I want ROIs in ROI manager (you can see all of them or only one) or in Overlay (you can see all of them).

Thanks for keeping us posted.
~Josh

Thanks for this post. It has helped me work OME.TIFF files.