[ome-devel] Integrating OMERO with DiGS

[James Perry]

Hi all,

Apologies if this is not the appropriate list for asking about this.

I am based at Edinburgh Parallel Computing Centre, working on the  
"Data Grid For Cell Biology" project. The project aims to adapt the  
Distributed Grid Storage (DiGS) software, which was originally  
developed for particle physics data, and use it for storing cell  
biology data. As part of this work we would like our software to  
integrate as well as possible with OMERO.

DiGS manages a "virtual file system" which distributes files  
transparently across storage at several sites, and replicates them so  
that there are multiple copies. It also manages a database of XML  
metadata describing the data files, and allows users to search this  
database.

At a minimum, we would like to use the same data formats as OMERO  
(OME-TIFF for image data, OME-XML for metadata), but ideally we would  
like a much closer integration. For example, data uploaded to OMERO by  
a user would automatically be replicated by DiGS and become available  
at another site (either through a DiGS client tool, yet to be written,  
or possibly even through another OMERO server). I have obtained the  
OMERO server and clients and have been studying them to find out how  
difficult this would be.

 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:

  - read images from an OMERO server (in their original format, or at  
least in a standard image format)
  - write images to an OMERO server
  - get image properties (for example, file size, upload time, owner)
  - enumerate images
  - access other files (for example, documents attached to images)
  - access the OME-XML metadata (read/write)

I have been looking at the OmeroApi pages on the Wiki but so far I  
can't tell for certain whether all these things are supported.

Any help or information would be greatly appreciated.

Thanks,
James Perry


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