Import ROI from NIS Elements to FIJI

Hi all,

I was wondering if anyone had successfully imported ROI from .nd2 files into FIJI. I have a user whose FRAP data was captured in NIS-Elements (Nikon). The .nd2 files, when opened in Elements, have the ROIs so I think they must be stored in the metadata somewhere but I can’t find any information about them.

This user has many images they want to analyse in FIJI now and I’m hoping to find an alternative to them opening every image in Elements and saving the ROIs for each one to use going forward.

An example .nd2 file should be available at this link:
https://uoe-my.sharepoint.com/:u:/g/personal/lmurphy5_ed_ac_uk/EcsTeeBF-PZAr95sZTOLiroBQe2Vabi2j529mvg77M3t3Q?e=0E15II

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When you open it in Fiji, do you see the ROIs?

No, and I’ve tried the different “import ROI” options that you can set for Bioformats import.

Well, I wasn’t able to find anything on the ND2 format itself. However, according to this version of the user’s manual, the program should be able to save the data in other formats. Have you tried saving as something else like a TIFF?

Hi Andrew,

Thanks for your input! It’s possible that saving as tiff might mean the ROIs are accessible but at this point the user has already saved a lot of data as .nd2 files. Going forward, if they are already having to resave each image it would be just as easy to save the ROIs as a mask at the same time so we can definitely use them in FIJI.

I think the answer is that Bio-Formats doesn’t currently pull the ROIs from the metadata which is the only thing that would really have saved the laborious task.

Laura

Well, that is unfortunate. Regrettably I don’t know much, if anything, about Bio-Formats since I have never had to use it. However, before we give up all hope, perhaps someone like @dgault might be able to give a more definitive answer.

Also, apologies for the late reply.

Hi @lmurphy, I have taken a look at the sample file you linked to. Currently when parsing the metadata for ND2 files, Bio-Formats will look for Text, HorizontalLine and VerticalLine and turn those into ROI’s. From your file I was expecting there to be reference to some other form of ROI, perhaps an ellipse which Bio-Formats currently doesn’t handle, however I was unable to see any properties that appeared relevant. Any unhandled properties will still be added to the global metadata so they should be maintained on the file.

From Image -> Show Info are there any properties that would correspond to the expected ROI’s? Or are there any metadata fields in Elements that would indicate the regions?

Hi David,

Yeah now I’ve completely trawled the metadata in both FIJI and NIS I really cannot see anything that indicates where these ROIs are stored at all!

I’ve attached a screenshot of them when the image is opened in NIS-Elements, they are circular but also have sort of target mark in them too. Also one them is specifically classed as a background ROI which seems to be different from a standard ROI in NIS.

For now, I’ve found you can colorize them in NIS which makes red, green and blue according to the order they were made. I needed this because I need to know which is which in regards to photobleached ROI, reference ROI and the background ROI. So I get the user to create an image of the colorized ROIs and then use that in the macro. It’s working fine and isn’t too arduous. Thanks for looking into it though.