[ome-devel] Integrating OMERO with DiGS

[josh.moore at gmx.de]

James Perry writes:
 > Hi Josh,

Morning James,

 > Thank you for the very helpful response (and sorry for late reply,  
 > unexpected problems on another project have taken up a lot of my time  
 > this week).

No worries. Happens to all of us!

 > >  >  From what I have seen, I think it would be better for DiGS to go
 > >  > through the OMERO APIs to access image files rather than attempting to
 > >  > manipulate the OMERO data store directly. As I understand it, the data
 > >  > store is in an OMERO internal format which may change in different
 > >  > versions and may not be readable by other software. I was wondering if
 > >  > there are APIs to do things like the following:
 > >
 > > Definitely. What programming language are you looking to do this in?
 > > Currently, C++, Python, and Java are supported.
 > 
 > Our existing software is in C and Java, so it should be possible for  
 > us to use the Java API or link in C++ code if that seems more suitable.

That's strictly up to you. Of the three languages, there are the
fewest examples in C++, so starting with Java might make sense.

 > >  >   - access the OME-XML metadata (read/write)
 > >
 > > I'm not exactly sure what you mean, but in general all metadata that
 > > is imported is available through the API. Can you give a concrete example?
 > 
 > I was wondering whether the metadata is stored in the OME-XML format,  
 > and if so whether it is possible to access it in this format through  
 > the API. 

The data is not stored in OME-XML, and currently if it's not imported
in OME-XML, it's not accessible through the API. This export
functionality is slated for a later milestone.

 > This is because we have existing technology for building and  
 > running queries against XML metadata (for searching for data sets, for  
 > example) and we are wondering if this might be useful here. I will  
 > have a more detailed look at the APIs.
 > 
 > Thanks again for the detailed response. I intend to experiment with  
 > the OMERO APIs to see if we can do what we need to, but from what  
 > you've said it sounds hopeful.

Great! Let us know how it goes.

 > Regards,
 > James

Cheers,
~Josh.