[ome-devel] Who's who in Pixels?

[Harri Jäälinoja]

Hello all,

I am interested in finding out the true identities of the files in the 
/OMERO/Pixels directory, where the binary data goes. For example:

1 = image1.jpg
2 = /home/bob/Data/sample1/A1.tiff
3 = ...

Is there a way to query this from the OMERO database?

Are these identities permanent? For example, Pixels/1 will always be 
image1.jpg? Or if image1.jpg is deleted, can 1 later on point contain 
the pixels of image3.jpg, imported in the system later on?

What I am after is integration of OMERO with iRODS, which I was thinking 
about earlier on as well. The mailing list thread is here:
http://lists.openmicroscopy.org.uk/pipermail/ome-users/2010-October/002452.html

My latest idea is to have all OMERO data go in iRODS, by simply setting 
the OMERO binary repository be a folder where iRODS is mounted via FUSE. 
https://www.irods.org/index.php/iRODS_FUSE. I have tested with one image 
so far, so I cannot say much about performance or possible problems yet.

The original data (before OMERO import) are also in iRODS, and
OMERO import is made automatically via Dropbox:
http://wiki.helsinki.fi/display/LMUISA/iRODS+and+OMERO+integration. What 
I would like to achieve now is a sort of a link between the two. For 
example, I could add metadata to image1.jpg: 
CONVERTED_FILE_IN_OMERO="/Pixels/1". This way, if image1.jpg is 
archived, I could also find and archive Pixels/1, and thus free space on 
the resource where OMERO is running. This is still sketchy, and not the 
optimal situation (as pointed out by Josh in his reply on the mailing 
list) where one of the replicas of image1.jpg is known to OMERO. If 
OMERO were to understand image1.jpg as such, without the conversion to 
the internal format, I think we would have the optimal situation. And 
now that I think about it, maybe also programmatic access to OMERO will 
be useful here, not just snooping around in the repository.

Any comments?

Best regards,
Harri

-- 
__________________________________________________
Harri Jäälinoja
Light Microscopy Unit
Institute of Biotechnology, University of Helsinki
http://www.biocenter.helsinki.fi/bi/lmu/
+358 9 191 59370 fax +358 9 191 59366