Problem with LIF file format and meta-data

[toedling]

We are currently testing OMERO as a microscopy database solution for our institute. All of the microscopes will be from Leica and Leica is using the lif-file.
We imported several lif-files from confocal systems with different content, like normal images, z-stacks, time-series, tiled images.

In all cases the meta-data for the used excitation wavelengths show wrong values in the OMERO insight client. Additionally we also checked the meta-data in ImageJ and also there the the shown excitation wavelengths were wrong.

We are using LAS AF 2.4.1 (build 6384) on a SP5 and LAS AF 2.5.1.6757 on the LSI.
For OMERO, we have installed our own server (version 4.3), which seems to be running fine in all other aspects.

In the attached image, you can see a screenshot of OMERO Insight and the shown meta data, in red the wrong shown data, in blue the data which were right. In all experiments the same sample was used:
DAPI, blue, cell nucleus (excitation with laser 405)
Alexa488, green, phalloidin (actin) (excitation with laser 488)
Mitotracker, red (excitation with laser 561)

Has anyone encountered this problem before? Could it be an issue with the Leica file format or LOCI ?

Thanks,
Joern

[wmoore]

Hi Joern,

I just tried importing a LIFF and I see that the excitation wavelengths are wrong.

I've created a ticket for this: http://trac.openmicroscopy.org.uk/ome/ticket/6065

If you could send us one of your example files, then we can be sure we get the bug fixed.
You can upload files here: http://qa.openmicroscopy.org.uk/qa/upload/
Perhaps you can add the submission number in another post below?

Many thanks,

Will.

[toedling]

Hello,
I have uploaded one of the recent LIF files, using the upload link indicated. The assigned bug ID is 3859.
Cheers,
Joern

[wmoore]

Thanks Joern: - Received!

[toedling]

Hello,
did you have some time to look at the file and to figure out what's wrong?
Cheers,
Joern

[mlinkert]

Hi Joern,

Unfortunately, we haven't had a chance to thoroughly investigate this problem yet.

You can follow our progress here:

http://trac.openmicroscopy.org/ome/ticket/6189

If you would like to be automatically notified of our progress, please send a private message containing a valid email address; we can then CC you on the ticket, and you will receive an email each time we update it.

Otherwise, you can expect that the problem will be fixed in the 4.3.2 release of OMERO/Bio-Formats.

Regards,
-Melissa

[jburel]

Good morning
To be 100% sure, could you send either the file corresponding to the screenshot or the screenshot corresponding to the file already submitted.
Thanks

Jmarie

[wmoore]

Hi Joern,

Just an update: In OMERO 4.3.2 (just released) we have fixed the excitation wavelengths in LIF files, but unfortunately we ran out of time to fix emission filters. You will see that the emission filters that were on the microscope are saved under "Instrument" but they are not linked to the various channels.

So, now we are at least saving correct metadata, although it is incomplete.
Apologies for that, we'll keep working on it...

Will.