[ome-users] Importing legacy .mdb Zeiss databases

[Alexandre Cunha]

Hi Curtis,

Thanks for the update and info about the conversion tool.
I will try bfconvert while we wait the batch mode importer to be in place.

Cheers,
- Alex.

Curtis Rueden wrote:
> 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 
> <mailto: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>
>         <mailto: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.
>             >
>             >
>             >
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> 
>            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)
> 
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