OMERO Plug-in Advice

Dear OME team

You may have seen this issue which has arisen – OMERO Plugin to Fiji not working

Basically we’re looking at how best to create our ROIs, and using Fiji/ImageJ and OMERO as a plugin to do this.

I seem to have hit an insurmountable wall now, as I can’t work on any complete image bigger than about 200Mb using this method, and I can only “crop” 15,000 x 15,000 pixel sections from any larger images.

However I can open all images when using OMERO.insight, for example.

Can you explain what this limitation is with using OMERO as a plug-in to Fiji?
Are there any plans to allow larger images to be edited via this method?
Suggestions as to how we can work around this issue?

We are pursuing this option as people seem to be more “comfortable” editing images for their ROIs via a desktop application.

Many thanks
Mike W

1 Like

Dear Mike

How are you creating the ROIs?
If it is manually, you can do it using OMERO.insight. This was not demonstrated during the workshop.
We have not migrated that section to the omero-guides
but you can find a step-by-step under http://help.openmicroscopy.org/measurement-tool.html
You will find the same functionalities that the ones presented in OMERO.web i.e. https://omero-guides.readthedocs.io/en/latest/iviewer/docs/iviewer.html

If you have already ROIs created in Fiji and saved in OMERO, you can edit them in the measurement tool

Hope it helps

Jmarie