Open Microscopy Environment

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

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

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