[ome-users] Importing legacy .mdb Zeiss databases

[Curtis Rueden]

Hi Alex,

Thanks for your emails. I am glad to know we will be able to use Bio-Formats
> to import our .mdb files at some point. Meanwhile, I was wondering if you
> have a standalone application that I can call to transform the .mdb files to
> OMERO in a batch mode. I suppose we don't need the full blown OMERO.importer
> to do that and we will probably be better off using batch processing anyway.
>

Sorry for the delay in my reply. In answer to your question, there is no
direct batch uploader for OMERO at the moment, though a command line batch
upload tool is currently in development.

Another option, available now, is the bfconvert command line tool available
from the Bio-Formats web site. You can use bfconvert to convert from Zeiss
LSM & MDB formats into the OME-TIFF format en masse, then queue up all the
OME-TIFF files for import into OMERO using the OMERO.importer GUI.

Lastly, I believe the Dundee team is actively developing a tool, OMERO.fs,
that will allow you to manage imports similar to an iTunes music library,
automatically scanning a directory structure and importing the data without
needing to queue it up with the importer tool. But there are still a lot of
work to be done there.

-Curtis

On Fri, Feb 6, 2009 at 8:31 PM, Alexandre Cunha <cunha at caltech.edu> wrote:

> Dear Curtis and Brian,
>
> Thanks for your emails. I am glad to know we will be able to use
> Bio-Formats to import our .mdb files at some point. Meanwhile, I was
> wondering if you have a standalone application that I can call to transform
> the .mdb files to OMERO in a batch mode. I suppose we don't need the full
> blown OMERO.importer to do that and we will probably be better off using
> batch processing anyway.
>
> Cheers,
> - Alex.
>
> Curtis Rueden wrote:
>
>> Hi Alex & Frans,
>>
>> As Brian said, the core Bio-Formats library supports parsing information
>> from MDB, but it may be a while before the OMERO system supports it.
>> Fortunately, once it does it should be easy to retrieve the original MDB
>> file, as OMERO is capable of archiving the original data files. Lastly, I
>> believe OMERO has the ability to attach files as binary blobs to an image,
>> so for now you could simply archive the MDB files with the imported LSM
>> data.
>>
>> -Curtis
>>
>> On Thu, Feb 5, 2009 at 4:58 PM, Brian Loranger <
>> brian.loranger at lifesci.dundee.ac.uk <mailto:
>> brian.loranger at lifesci.dundee.ac.uk>> wrote:
>>
>>    Hi Alexandre,
>>
>>    Alas, we have done no testing with .mdb files in the Importer
>>    (although the good news is that its supported by the underlying bio-
>>    formats package).
>>
>>    Most likely if we turned that format on there would be some issues
>>    importing. I can switch it on and and see how things look  and let you
>>    know a time estimate - if we're lucky it will just be a matter of
>>    turning the format on (although more then likely that won't be the
>>    case). We are less then 2 weeks away from our next release, *knocks on
>>    wood*,  so I doubt we will be able to get that working before then,
>>    but I would be hopeful we can get something for you after that.
>>
>>    Cheers,
>>
>>    Brian
>>
>>
>>    On 5 Feb 2009, at 09:26, Alexandre Cunha wrote:
>>
>>     > Hello,
>>     >
>>     > I have sent the following question to the Bio-formats folks and
>>     > thought to also
>>     > seek help here.
>>     >
>>     > We are starting to move diverse proprietary databases (mainly Zeiss)
>>     > from one
>>     > of the Biology labs here on campus to OMERO. A typical lab user has
>>     > a directory
>>     > per project and a .mdb database file in that directory that I
>>     > believe refers to
>>     > the many .lsm image files in that same directory.
>>     >
>>     > My question is: is there a way in OMERO to directly read the
>>     > many .mdb files
>>     > and save each as a OMERO database (or project) ? We would like to
>>     > avoid
>>     > rebuilding each database and if possible store legacy databases
>>     > seamlessly in
>>     > OMERO.
>>     >
>>     > I appreciate receiving your suggestions.
>>     > Many thanks,
>>     > - Alex.
>>     >
>>     >
>>     >
>>     > _______________________________________________
>>     > ome-users mailing list
>>     > ome-users at lists.openmicroscopy.org.uk
>>    <mailto:ome-users at lists.openmicroscopy.org.uk>
>>     > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>
>>    Brian Loranger
>>    Software Developer, Open Microscopy Environment
>>    Division of Gene Regulation and Expression
>>    University of Dundee
>>    (The University of Dundee is a registered Scottish charity, No:
>>    SC015096)
>>
>>    _______________________________________________
>>    ome-users mailing list
>>    ome-users at lists.openmicroscopy.org.uk
>>    <mailto:ome-users at lists.openmicroscopy.org.uk>
>>    http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>
>>
>>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20090217/f1ef9e39/attachment.html>