[ome-devel] Who's who in Pixels? (iRODS ideas...)

[Harri Jäälinoja]

Hi again,
I was just browsing the list archives looking for info about OMERO 
scripting, and my eye caught this:

http://lists.openmicroscopy.org.uk/pipermail/ome-users/2011-June/002652.html

"The OME Team is starting to see many requests for the kind of thing you 
are asking:  "... manage image data across multiple centers/institutes 
and research labs"."

This is also something that can be accomplished with iRODS. So I think 
if it is possible to achieve a working integration between the two 
systems, there is no need to implement the same functionality again in 
OMERO.

What I suggested earlier, the possibility register data into OMERO, 
would be one way to allow "image access" to iRODS. In this case, when I 
want to see my collaborators data in OMERO, I would first use iRODS to 
replicate it on a local storage resource (where OMERO can see it), and 
then register it to OMERO.

It might be possible to make this process easier to the end user, as 
there is a Java API to iRODS, but that would be more difficult, as we've 
discussed earlier :)
http://lists.openmicroscopy.org.uk/pipermail/ome-users/2010-October/002452.html

Cheers,
Harri

On 16/12/11 14:07, Harri Jäälinoja wrote:
>
> 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