getting OMERO ROIs into imageJ/Fiji

[dsudar]

Hi,

The insight-ij package nicely supports getting ROIs generated in imagej/fiji into OMERO. Is there an equivalent facility to get ROIs generated in OMERO into imagej/fiji?

I have some folks who are interactively defining regions to be analyzed and then would like to run the Fiji-based analysis routine just on those defined areas. Maybe there's some example Fiji scripting code that extracts ROI image regions from OMERO you can point me to?

Thanks,
- Damir

[bramalingam]

Hi Damir,

Thank you for sharing your question.

We unfortunately do not have any example scripts on this front but I can point you at the source code on how the OMERO-IJ plugin extracts the ROI information.

It does it in two stages,

1. OmeroReader reads the OMERO ROI’s into the metadatastore,
https://github.com/openmicroscopy/openm ... .java#L462

example for reading an ellipse from OMERO into the metadata store:
https://github.com/openmicroscopy/openm ... .java#L636

Likewise all shapes are read from OMERO into the metadata store and then,

2. Bio-Formats reads the information from the metadatastore, using the ROIHandler class,
https://github.com/openmicroscopy/biofo ... .java#L146

and displays it in ImageJ.

Please let us know if you have any trouble, I can try and share an example snippet to fit your workflow.
Hope that helps for the time being.

Best,
Balaji

[dsudar]

Hi Balaji,

Thanks much for the pointers. I'll get some Java-expert help here to see if we can figure it out and will be in touch if we get stuck.

Cheers,
- Damir