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Re: importing OME.tiffs in Omero 5
Posted:
Thu Apr 24, 2014 2:41 pm
by yuriy_alexandrov
...
I checked again how Omero (talking about 5.0) Insight behaves when
1) importing generated OME-tiff
2) exporting it back form Omero to disk as OME-tiff, by using "Export as OME-tiff" option
As Will said, the uploading to Omero takes seconds (image is about 150M).
If one uses "Export as OME-tiff" on this imported image, the Description field is preserved in the resulting OME-tiff file - as needed.
However, this Description of imported image isn't displayed by Insight in the Description window (on the right).
The problem with new version of Bioformats is still there, - I generate OME-tiffs using old version of "loci_tools". The new one seemingly misses "getOMEXML" function.
Thanks,
Y.
Re: importing OME.tiffs in Omero 5
Posted:
Fri Apr 25, 2014 1:03 pm
by yuriy_alexandrov
Correction to the previous report -
If one uses "Export as OME-tiff" on the imported image, the Description of the resulting OME-tiff is not as expected - when creating original OME-tiff, the metadata were populated by "setUUIDFileName", and that was stored in Description as well as in metadata, however the Description of the exported OME-tiff contains some generated names for XY planes, so the original names are lost.
Best,
Y.
Re: importing OME.tiffs in Omero 5
Posted:
Fri Apr 25, 2014 1:54 pm
by jburel
Thanks Yuriy
This is an known issue we are currently working on
see
http://trac.openmicroscopy.org.uk/ome/ticket/12056Do you want to be cc'd on the ticket?
Regards
Jmarie
Re: importing OME.tiffs in Omero 5
Posted:
Fri Apr 25, 2014 2:33 pm
by yuriy_alexandrov
yes certainly,
many thanks,
Y.
Re: importing OME.tiffs in Omero 5
Posted:
Mon Apr 28, 2014 8:55 am
by rleigh
Hi Yuriy,
In 5.0 and later, getOMEXML is provided by the OMEXMLService. Example: components/formats-gpl/test/loci/formats/utests/xml/OMEXMLServiceTest.java and components/formats-bsd/src/loci/formats/out/OMETiffWriter.java.
Note that this was also the case in 4.4. MetadataTools.getOMEXMLService was just a compatibility wrapper, so if you change your code to use OMEXMLService.getOMEXML, it will still be compatible with 4.4.
Kind regards,
Roger
Re: importing OME.tiffs in Omero 5
Posted:
Mon Apr 28, 2014 4:47 pm
by yuriy_alexandrov
Many thanks Roger - I will check it out and let know soon.
Best wishes,
Y.
Re: importing OME.tiffs in Omero 5
Posted:
Tue Apr 29, 2014 10:13 am
by yuriy_alexandrov
Hi again,
I struggle to adjust syntax for getOMEXML call in 5
the working Matlab code was previously
- Code: Select all
img_description = char(loci.formats.MetadataTools.getOMEXML(metadata));
I changed it to this -
- Code: Select all
img_description = char(loci.formats.services.OMEXMLService.getOMEXML(metadata));
It results in error message
the class loci.formats.services.OMEXMLService has no property or method named getOMEXML
It looks like I'm (hopefully) doing something wrong, - in which case please show how to call it properly..
Best,
Y.
Re: importing OME.tiffs in Omero 5
Posted:
Tue Apr 29, 2014 10:51 pm
by mlinkert
getOMEXML is not a static method in loci.formats.services.OMEXMLService; you must construct an instance of OMEXMLService and call the method on that instance. The correct way to do this in Matlab is shown in
https://github.com/openmicroscopy/biofo ... ader.m#L82, so the following should do what you need:
- Code: Select all
service = loci.formats.services.OMEXMLServiceImpl();
img_description = char(service.getOMEXML(metadata));
Re: importing OME.tiffs in Omero 5
Posted:
Wed Apr 30, 2014 9:46 am
by yuriy_alexandrov
...
Thanks Melissa - this worked indeed!
Filling ImageDescription looks OK now.
The last question if I may?
We need to put ModuloAlong annotation into OME-tiff metadata - for gated FLIM images definitely, but for other data (raw OPT, etc.) as well.
So naturally, the same question arises about an example code for OME-tiff creation with ModuloAlong.
(If not Matlab, Java code would be helpful certainly.)
Many thanks again,
Y.
Re: importing OME.tiffs in Omero 5
Posted:
Wed Apr 30, 2014 11:06 am
by yuriy_alexandrov
some update on OME-tiff import.
I tried to import by Insight and it fails for OME-tiffs generated with 5.0 service, as well as with previous 4.0 loci_tools.jar library, and also 3rd party (LaVision FLIM) OME-tiffs also fail (that were imported previously without problems).
I wonder if is there any issues with OME-tiff import presently?
it might be something with server, as I'm unable to import neither sdt nor usual tiffs, as well.
I asked a colleague to try to import usual tiff by Insight on another computer - it fails there as well.
Best,
Y.