Saving OME.TIFFS with ROIs in the ROI field using ImageJ

Hey so I’m pretty new to using Fiji/ImageJ but I was wondering what the steps are to saving ROIs (regions of interest) in polygon coordinates into a OME.TIFF file.

In essence how do I add this using ImageJ/FIJI’s gui to do this. Is it through the ROI manager?

Hi @TeddyZ95

To save the ROI, add the ROI to the ROI manager.
You can use the Bio-Formats exporter plugin: Plugins > Bio-Formats > Bio-Formats exporter. In one of the dialog that will pop up, make sure that the checkbox Export ROIs is selected.




I’ve been using the plugin imagej 3d suite and they have a 3D Roi manager and i’ve tried doing that but it doesn’t seem to work.

Can the normal Roi manger handle 3D images and labeling? For instance can it differentiate between different stacks? I also am interested in saving them as polygons.

The Bio-Formats plugin will read ROIs only from the main ROI manager. I have not found a way in the UI to send the ROI from ImageJ 3d to the normal ROI manager but I am not an ImageJ expert.
This is probably achievable via a script.