[ome-devel] Next steps with ImageJ-OMERO

[Curtis Rueden]

Hi Jean-Marie,

> we decided to rewrite in Java some Matlab code he already had, to
> convert ImageJ ROI into OMERO ROI. This is currently in a standalone
> class, solely for training purpose and should be pushed to the
> relevant components when ready.

This is great. Please let me know when and where that work gets pushed, and
I'll be happy to take a look! One option would be to file it as PR of
imagej-omero, which we can discuss/enhance/merge together.

Also note that Melissa wrote some code in Bio-Formats that translates
between ImageJ and OME-XML ROIs. You can find it in the ROIHandler class:

https://github.com/openmicroscopy/bioformats/blob/v5.0.5/components/bio-formats-plugins/src/loci/plugins/util/ROIHandler.java

When combined with an OMEROMetadataStore, this should also allow reading
and writing ROIs to/from OMERO.

I added some notes to https://github.com/imagej/imagej-omero/issues/2
documenting all of this.

> * User opens an image in Fiji/ImageJ, draw some ROI and import the
>   image and save roi into OMERO
> * User opens an image in Fiji/ImageJ,
>   already stored in OMERO and save/read some ROI from the server

Good idea. I was planning to do this as part of the ROIs work, but there
was no issue filed for it. I have now filed one:

https://github.com/imagej/imagej-omero/issues/49

Regards,
Curtis

P.S. I CCed ome-devel to keep the community in the loop about our progress.


On Thu, Oct 2, 2014 at 7:12 AM, Jean-Marie Burel <j.burel at dundee.ac.uk>
wrote:

>   Hi Curtis
>
>
>  Thanks for the imagej-omero milestone updates.
>
> Graeme Ball whom you met in Paris has also organised some Fiji workshops
> in Dundee, so the local users base is growing.
>
> In every place we have run workshops in recent months (e.g. in Dundee,
> Montpellier), the users are very interested to be able to run some of the
> ImageJ plugins server side.
>
> Common workflow will be: Run a plugin on an image using ImageJ/Fiji as a
> Desktop application, then run the plugin server-side on a large number of
> images.
>
> Being able to click on a button to analyse a dataset while leaving the
> lab, and check the result when they arrive a home is very attractive for
> many scientists
>
>
>  Balaji is now learning some Java, so as part of his training we decided
> to rewrite in Java
>
> some Matlab code he already had, to convert ImageJ ROI into OMERO ROI.
>
> This is currently in a standalone class, solely for training purpose and
> should be pushed to
>
> the relevant components when ready.
>
> That work could potentially fit into one of your milestones. (
> https://github.com/imagej/imagej-omero/milestones/0.3.0)
>
>
>  We were also considering using that work for 2 client-side workflows we
> would like to cover as ImageJ plugins:
>
>  * User opens an image in Fiji/ImageJ, draw some ROI and import the image
> and save roi into OMERO
>
>  * User opens an image in Fiji/ImageJ, already stored in OMERO and
> save/read some ROI from the server
>
>
>
> This will complement the work that you are doing and satisfy the needs of
> the growing IJ user base here in Dundee.
>
>
>  Let me know if you can think of other areas that could benefit the
> interaction between Imagej and OMERO.
>
>
>  Cheers
>
> Jmarie
>
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