[ome-devel] OMERO ImageJ tickets & priorities

[Curtis Rueden]

Hi Josh,

Thanks for following up on the OMERO ImageJ tickets. I am CCing ome-devel
with a better subject since the topic may be of interest to others.

> http://trac.openmicroscopy.org.uk/ome/ticket/4084
> Implement OMERO upload and download

Initial version of that project was completed before the September SAB
demo. I have now resolved the ticket as fixed, and linked over to the
relevant projects on GitHub.

Similarly, I also resolved as fixed:
http://trac.openmicroscopy.org.uk/ome/ticket/10645
OMERO-backed data in ImgLib2

> I don't know if Curtis has anything else he has open.

There was one other avenue of interoperability that J-M and I discussed
during my February Dundee visit: a suite of miscellaneous ImageJ commands
that provide OMERO-related features: e.g., uploading/downloading tabular
data. We made a list which I have saved, but those items are lower priority
than finishing the ImageJ2 parameterized scripting work [1], which will
enable OMERO to run ImageJ scripts server-side the same as single commands.
This will let people build up much more complex ImageJ workflows and then
run them on the server in a single shot.

We should also document the need for translating non-image data structures,
particular results tables and ROIs. I filed issues for those:

https://github.com/imagej/imagej-omero/issues/1
Support translation of ResultsTables to/from OMERO

https://github.com/imagej/imagej-omero/issues/2
Support translation of ROIs to/from OMERO

Anything else to discuss/decide right now regarding these tickets?

Regards,
Curtis

[1] Huge progress on ImageJ scripting (though still not 100%) over this
past long weekend:
https://github.com/imagej/imagej/commit/930324f82cc489154aa255ab9df87b403f99a3e1


On Fri, Nov 22, 2013 at 9:35 AM, Josh Moore <josh at glencoesoftware.com>wrote:

> Hi all,
>
> I had the task of digging through IJ2/OMERO tickets. That's mostly done
> now, I think. Here's how I see things:
>
>
> http://trac.openmicroscopy.org.uk/ome/ticket/918 - ImageJ in Scripting
> Engine
>
> is the main ticket that Curtis was looking at. It's a story that has 3
> open issues.
> All of those are on the OMERO side of things. I don't know if Curtis has
> anything else
> he has open.
>
>
> http://trac.openmicroscopy.org.uk/ome/ticket/10608 - ImageJ/OMERO
>
> is the parent requirement for that story. There are several other stories
> of interest
> in there, but I don't know what their status is. There are also some
> related loose
> tickets that I didn't know what to do with like
>
> http://trac.openmicroscopy.org.uk/ome/ticket/4084 - Implement OMERO
> upload and download
>
>
> Just FYI, 918 is also part of another requirement:
>
> http://trac.openmicroscopy.org.uk/ome/ticket/1856 - Scripting Improvements
>
> which contains most of the biggish script work. The next wave is most
> likely:
>
> http://trac.openmicroscopy.org.uk/ome/ticket/1860 - Scripting Cleanup
>
> with lots of bits and bobs. Input welcome. With the looming release of
> beta2,
> we haven't had time to get the IJ2 scripting set up for daily testing, so
> that's our next TODO.
>
> ~J.
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