Hi Alex,<br><br><div class="gmail_quote"><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">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.<br></blockquote></div><br>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.<br>
<br>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.<br>
<br>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.<br>
<br>-Curtis<br><br><div class="gmail_quote">On Fri, Feb 6, 2009 at 8:31 PM, Alexandre Cunha <span dir="ltr"><<a href="mailto:cunha@caltech.edu">cunha@caltech.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Dear Curtis and Brian,<br>
<br>
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.<br>
<br>
Cheers,<br>
- Alex.<br>
<br>
Curtis Rueden wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="Ih2E3d">
Hi Alex & Frans,<br>
<br>
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.<br>
<br>
-Curtis<br>
<br></div><div><div></div><div class="Wj3C7c">
On Thu, Feb 5, 2009 at 4:58 PM, Brian Loranger <<a href="mailto:brian.loranger@lifesci.dundee.ac.uk" target="_blank">brian.loranger@lifesci.dundee.ac.uk</a> <mailto:<a href="mailto:brian.loranger@lifesci.dundee.ac.uk" target="_blank">brian.loranger@lifesci.dundee.ac.uk</a>>> wrote:<br>
<br>
Hi Alexandre,<br>
<br>
Alas, we have done no testing with .mdb files in the Importer<br>
(although the good news is that its supported by the underlying bio-<br>
formats package).<br>
<br>
Most likely if we turned that format on there would be some issues<br>
importing. I can switch it on and and see how things look and let you<br>
know a time estimate - if we're lucky it will just be a matter of<br>
turning the format on (although more then likely that won't be the<br>
case). We are less then 2 weeks away from our next release, *knocks on<br>
wood*, so I doubt we will be able to get that working before then,<br>
but I would be hopeful we can get something for you after that.<br>
<br>
Cheers,<br>
<br>
Brian<br>
<br>
<br>
On 5 Feb 2009, at 09:26, Alexandre Cunha wrote:<br>
<br>
> Hello,<br>
><br>
> I have sent the following question to the Bio-formats folks and<br>
> thought to also<br>
> seek help here.<br>
><br>
> We are starting to move diverse proprietary databases (mainly Zeiss)<br>
> from one<br>
> of the Biology labs here on campus to OMERO. A typical lab user has<br>
> a directory<br>
> per project and a .mdb database file in that directory that I<br>
> believe refers to<br>
> the many .lsm image files in that same directory.<br>
><br>
> My question is: is there a way in OMERO to directly read the<br>
> many .mdb files<br>
> and save each as a OMERO database (or project) ? We would like to<br>
> avoid<br>
> rebuilding each database and if possible store legacy databases<br>
> seamlessly in<br>
> OMERO.<br>
><br>
> I appreciate receiving your suggestions.<br>
> Many thanks,<br>
> - Alex.<br>
><br>
><br>
><br>
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<br>
Brian Loranger<br>
Software Developer, Open Microscopy Environment<br>
Division of Gene Regulation and Expression<br>
University of Dundee<br>
(The University of Dundee is a registered Scottish charity, No:<br>
SC015096)<br>
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