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

[Harri Jäälinoja]

Hi Josh,

one more question/comment about the possibility to have OMERO use 
original images:

>> 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?
>
> There's been some recent work on making OMERO understand images without conversion, once that API is ready for general consumption, we'll contact the lists. It's possible that that'll be one of the 4.4 releases.
>

Do you think in this case it will be possible for OMERO to use the 
original images regardless of the directory where they are? In this way, 
it would for sure be possible to have one iRODS replica known by OMERO.

I guess what I am after is the possibility to register, as opposed to 
import, data into OMERO. I picked this up from the iRODS system which 
has this distinction. When data is imported, for example via a GUI, the 
original stays behind on the remote client machine. Registering can be 
used when the data is already on the server file system. The data can be 
registered into iRODS as long as it is readable by the iRODS server 
user, and from then on, iRODS will maintain metadata about it, just the 
same way as it does for data that resides in dedicated iRODS vault 
directories.

I can make a dedicated vault directory a Dropbox into OMERO. When new 
data arrives, OMERO will create another copy in its own binary storage, 
and forgets about the original copy. So this is still an import 
operation. Would it be possible for OMERO just to use the file in the 
Dropbox for all subsequent work? Or maybe add a command to the command 
line tool, something like:

bin/omero register --project="p1" --dataset "d1" 
/data/iRODS/Vault1/home/user1/Data/Screen1

What do you think? If this were possible, it would be easy to use iRODS 
for backing up the image data. This might be useful also if the OMERO 
server is used for image processing tasks and has a limited number of 
fast disk where it is not possible to store all data. Then to make room 
for active projects, we could simply remove the iRODS replicas on the 
fast disk for data that has not been accessed recently. Trying to access 
them in OMERO would result in an error, which would indicate to the user 
that s/he should ask the administrator to recover the data. This could 
be done in iRODS by making a fresh replica on the fast disk.

Cheers,
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