Open Microscopy Environment

Hello,

My name is Gonzalo Ortega, I am student of Bioengineering, at Entre Ríos National University, Argentina. I'm doing my thesis, for which I use the OMERO system.

I would like to ask if there is an editor for ome.tiff file's metadata, because the OMERO.editor only attaches protocols. On the other hand, I have installed the 4.4.8 OMERO.server on my personal computer for doing some tests. I used the command line tool of BIOFORMAT. I looked for an example of the current scheme of OME and I utilized tiffcomment and xmlvalid commands to add and validate some files. Spite of they are successfully validated, the metadata do not appear at OMERO.insight, and all the commentaries I've added to the .ome.tiff file
appear like raw data under the Description tag. What's going on?

Sorry for my primitive english.
Thank you.
Greetings.

Hi Gonzalo,

Thank you for your interest in OMERO and OME-TIFF.

I would like to ask if there is an editor for ome.tiff file's metadata, because the OMERO.editor only attaches protocols. On the other hand, I have installed the 4.4.8 OMERO.server on my personal computer for doing some tests. I used the command line tool of BIOFORMAT. I looked for an example of the current scheme of OME and I utilized tiffcomment and xmlvalid commands to add and validate some files.

The 'tiffcomment' command is the easiest way to edit the metadata in an OME-TIFF file by hand, so it sounds like you're on the right path.

Spite of they are successfully validated, the metadata do not appear at OMERO.insight, and all the commentaries I've added to the .ome.tiff file
appear like raw data under the Description tag. What's going on?

Could you please post the XML displayed by 'tiffcomment' for the OME-TIFF file? Once we have that, we can better advise you on how to make Insight display the metadata.

Regards,
-Melissa

Hi Melissa,

Thanks for your help.
I attach a .zip where you can find the XML displayed by 'tiffcomment', and more details about our fails.

Regards,
Gonzalo

Hi Gonzalo,

Thank you for sending additional information.

There are two problems, both of which are easy to solve. The first is that the XML editor that you are using writes 3 extra bytes to the beginning of the XML file; these can be removed as described here:

http://sourceforge.net/p/xml-copy-edito ... /03797d2d/

The second problem is that both of the files listed here:

http://www.openmicroscopy.org/Schemas/S ... bhiswt-3D/

belong to the same dataset, and so both need to be in the same folder in order for them to import correctly into OMERO. You will need to download tubhiswt_C0.ome.tif and run 'tiffcomment' on it as well - the only difference between the XML for the two files should be the value of 'UUID' on the root 'OME' element. Only one of the files then needs to be imported into OMERO; the other one will be detected automatically.

If those two things don't solve the problem, please let us know.

Regards,
-Melissa

Hi Melissa.

I could solve only one of the two problems.
I removed the three bytes that my free XML editor wrote at the beginning of the XML file that I have extracted with 'tiffcomment'.

Then I put both images (tubhiswt_C0.ome.tif and tubhiswt_C1.ome.tif) in the same folder. I realized that their XML only have one difference: the value of 'UUID' on the root 'OME' element, as you said. Finally, I imported only one of the files (tubhiswt_C0.ome.tif), but the other one was not detected automatically. What is wrong?

Then I imported both files. I opened OMERO.insight and saw that the XML I had extracted appeared like raw data at the description tag (at General tab in the right pane). Is OMERO programmed to do that?
The information that appear at Acquisition tab (right pane), is written at the XML of the file? Or, where is it stored?


Regards,
Gonzalo

Hi Gonzalo,

Then I put both images (tubhiswt_C0.ome.tif and tubhiswt_C1.ome.tif) in the same folder. I realized that their XML only have one difference: the value of 'UUID' on the root 'OME' element, as you said. Finally, I imported only one of the files (tubhiswt_C0.ome.tif), but the other one was not detected automatically. What is wrong?

Then I imported both files. I opened OMERO.insight and saw that the XML I had extracted appeared like raw data at the description tag (at General tab in the right pane). Is OMERO programmed to do that?

No, OMERO is not meant to do that. It sounds like there is still a problem with the XML that prevents the files from being detected as OME-TIFFs. Could you please send the current output of 'tiffcomment' for both tubhiswt_C0.ome.tif and tubhiswt_C1.ome.tif?

The information that appear at Acquisition tab (right pane), is written at the XML of the file? Or, where is it stored?

Yes, the Acquisition tab is populated using the file's metadata, which in this case is the XML given by 'tiffcomment'.

Regards,
-Melissa

Hi Melissa,

I attach the current output of 'tiffcomment' for both tubhiswt_C0.ome.tif and tubhiswt_C1.ome.tif. The files are metadata_tubhiswt_C0.xml and metadata_tubhiswt_C1.xml respectively. I pasted them in a blank file at gedit.

I asked you how the Acquisition tab is populated, because there are some metadata that appear under this tab but there are not showed at the xml files (e.g. PhotometricInterpretation, PlanarConfiguration).

Regards,
-Gonzalo

Hi Gonzalo,

Sorry for not spotting this sooner - you will need to either upgrade your server and Insight to 5.0.0-beta1 (http://www.openmicroscopy.org/site/support/omero5/), or use these example files instead:

http://www.openmicroscopy.org/Schemas/S ... bhiswt-3D/

OMERO 4.4.8 only supports schema versions up to 2012-06; 5.0.0-beta1 is the first release to support OME-TIFF files that use the 2013-06 schema. If you choose to use the 2012-06 schema, the only things that would need to change in the metadata files are:

• all occurrences of "2013-06" should become "2012-06"
• the values of "CalibratedMagnification" and "NominalMagnification" should be "100" (instead of "100.0")

If neither of those options work, please let us know.

Regards,
-Melissa

Hi Melissa.
We continue with the same problem . We have updated our server to version OMERO.server 4.4.10 (the latest stable) and have loaded the file called tubhiswt_C0.ome.tif. Then we opened the OMERO.insight, the Microscope and Image's metadatas do not appear at Acquisition tab yet.
In short, could you send us a sample image in which the OMERO.insight display all metadata? This would allow us to have a more clear idea of the data model with working OMERO.insight.

Regards,
Gonzalo

Although not complete metadata, the sample images available at http://downloads.openmicroscopy.org/images/DV/ should give you a better idea of the data model.

Cheers,

Will.