Import ROI from NIS Elements to ImageJ


I have a question regarding importing nd2 files to ImageJ.
I have made ROI’s in NIS Elements, which are saved with the image in a nd2 file. When you import the nd2 file into ImageJ with the Bio-Format tool, you can choose to show the ROI’s (second column, under “metadata-viewing”). But this doesn’t work. I have tried to make separate tiiff’s of the ROI’s in NIS, but ImageJ doesn’t accept these. Does someone have experience with this, or knows a trick to get around this?

I use nd2 files in my confocal studies. I usually save my trimmed z-stack as an nd2 file. Then open the nd2 file using Biofomats plugin (loci.jar). Select a region of interest in image j and duplicate it using Ctrl+Shift+D. You now have options to save it per channel and per slice of z-stack. Select and you can make measurements as required.
Hope this helps.

Thanks jeskuruvilla,

Just so I understand it correctly: do you already have ROI’s in your nd2 file or do you draw them in ImageJ?


In my case I draw ROIs in image J. I don’t think the ROI is saved when importing an ND2 file to Image J

Ah okay, thanks for your response anyway!

Someone else with experience on my issue?

Can you share one of the NIS files? One that includes the ROIs in the metadata as you described.

No experience with this, but maybe if the ROIs are described in the metadata they can be transferred to IJ in a script.

On dropbox/google drive/your preferred cloud

Thanks for helping out!

Here is a link to a test image. As you can see, the PNG file shows the 3 ROIs drawn (rectagular, polygonal and circular respectively). Nikon themselves have a script to extract the rectangular but not the polygonal ROI (which I am interested in).

Hope you can bring me a step further!

I can only see a png image at the link you posted, but in order to help solving your issue, the original nd2 would be much more helpful, as we might cooperatively be able to figure out how to read the contained ROI metadata…

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Excuse me, wrong link! This should work: