Hi Ian,
> I have been tasked with adding the ability to read OMERO tables to an
> existing imagej plugin.
That exact functionality is what Josh and I added to the ImageJ-OMERO
project in March of 2014. The only problem is: it still sits on a branch
[1]. We really need to get it merged.
> My preferred option would be to use the existing OMERO plugin in Fiji.
Be aware that there is more than one "existing OMERO plugin." There are
actually two:
* ImageJ-OMERO [2] - a flexible SciJava plugin suite for bidirectional
ImageJ+OMERO interoperability. This is what you get when you turn on the
OMERO-5.0 or OMERO-5.1 update site.
* OMERO.insight-ij [3] - a wrapper around OMERO.insight which runs within
ImageJ.
I would vastly prefer that all future work on ImageJ/OMERO interoperability
take place in the ImageJ-OMERO project, since it is written for the ImageJ2
platform.
> Is it possible to access methods in the OMERO plugin from a second
> plugin?
Yes, ImageJ-OMERO is a library fully intended for reuse from other
applications.
> Can I at least get a session and client?
You can [4], although for your use case you hopefully will not need to go
so low-level.
> Does anyone have any examples of passing data between plugins?
Unfortunately, there are no examples. You will be the second external
consumer of the API (after Alex Rigano of Omega fame). Perhaps we can flesh
out some tutorials/examples together.
> Plan b) is to use use java widget that I already have (basically
> JFileChooser for OMERO) This is easy to implement but I fear it might
> clash horribly with the existing OMERO plugin.
A widget is a separate thing from the code to read and write tables. Proper
separation of concerns and all that. Alex has some widgets he wrote too,
which he plans to contribute to ImageJ-OMERO [5]. If you want to migrate
your widget(s) into the project as well, that would be awesome.
Happy to text/audio/video chat any time you want to work through issues.
Regards,
Curtis
[1]
https://github.com/imagej/imagej-omero/compare/tables[2]
https://github.com/imagej/imagej-omero[3]
http://help.openmicroscopy.org/imagej.html[4]
https://github.com/imagej/imagej-omero/blob/imagej-omero-0.3.2/src/main/java/net/imagej/omero/OMEROSession.java[5] Actually, we may want to make an imagej-omero-swing component, to
separate out that stuff and avoid java.awt and javax.swing references from
the core imagej-omero component. But it's not too important in the short
term.
On Wed, Oct 7, 2015 at 3:47 AM, Munro, Ian <
[hidden email]> wrote:
> Hello all
>
> I wonder if anyone can help a newcomer to Imagej?
> I have been tasked with adding the ability to read OMERO tables to an
> existing imagej plugin.
>
> My preferred option would be to use the existing OMERO plugin in Fiji.
> Clearly this works well for image data but I’m unsure how to use non-image
> data from an OMERO table.
>
> Is it possible to access methods in the OMERO plugin from a second plugin?
> Can I at least get a session and client?
> Does anyone have any examples of passing data between plugins?
>
>
> Plan b) is to use use java widget that I already have (basically
> JFileChooser for OMERO)
> This is easy to implement but I fear it might clash horribly with the
> existing OMERO plugin.
>
> Any thoughts welcome.
>
> Many thanks.
>
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http://imagej.nih.gov/ij/list.html>
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