[ome-users] Importing legacy .mdb Zeiss databases

[Alexandre Cunha]

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.
>      >
>      >
>      >
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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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