importing OME.tiffs in Omero 5

[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.

[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.

[jburel]

Thanks Yuriy
This is an known issue we are currently working on
see http://trac.openmicroscopy.org.uk/ome/ticket/12056

Do you want to be cc'd on the ticket?

Regards

Jmarie

[yuriy_alexandrov]

yes certainly,

many thanks,
Y.

[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

[yuriy_alexandrov]

Many thanks Roger - I will check it out and let know soon.

Best wishes,
Y.

[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.

[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));


[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.

[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.