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How do I save ROIs into an OME.TIFF file?

Historical discussions about the Bio-Formats library. Please look for and ask new questions at https://forum.image.sc/tags/bio-formats
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Historical discussions about the Bio-Formats library. Please look for and ask new questions at https://forum.image.sc/tags/bio-formats

If you are having trouble with image files, there is information about reporting bugs in the Bio-Formats documentation. Please send us the data and let us know what version of Bio-Formats you are using. For issues with your code, please provide a link to a public repository, ideally GitHub.

How do I save ROIs into an OME.TIFF file?

Postby Kouichi_C_Nakamura » Wed Oct 31, 2018 1:20 pm

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
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Re: How do I save ROIs into an OME.TIFF file?

Postby Kouichi_C_Nakamura » Thu Nov 01, 2018 4:28 pm

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).
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Re: How do I save ROIs into an OME.TIFF file?

Postby jmoore » Thu Nov 01, 2018 4:50 pm

Thanks for keeping us posted.
~Josh
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Re: How do I save ROIs into an OME.TIFF file?

Postby radhikas » Fri Jan 18, 2019 10:04 am

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