Open Microscopy Environment

Hi there,

I was trying to do in-place import of INCell data-set and ,unfortunately, it has failed.

Source of files to be imported 'in-place' is on a mounted network share, running OMERO. Command issued in putty was:
/usr/local/omero.server/bin/omero import -- --transfer=ln_s /data/share/filepath/140218_Screen_R1_P1_1.xdce

I have attached a zip file with the log from putty.

OMERO server version is 5.0.0
ice version is 3.4.2

Let me know if you need any additional information to troubleshoot the problem.

Would be happy to hear any ideas/suggestions.

Thanks,
Misha

Hi Misha,

Thanks for taking the time to get in contact.

This may be a problem with the data reader in Bio-Formats.

Would you be able to send us some sample data in the same format as the files which you are trying to import?

You can upload data at http://qa.openmicroscopy.org.uk/qa/upload/ - Probably best if you zip up your dataset into a single zip file for upload.

Many thanks,

Kenny

Hi Kenny,

thanks for a quick reply!

I'm not sure how feasible it would be to upload the entire data-set since it's ~500Gb. Import was succesfull for 28 out of 96 wells. So I wonder what part of the data-set would make sense for your internal tests?

Cheers,
Misha

Hi Misha,

Having consulted the expert here, "The .xdce file plus the output of 'ls -l' on the directory should be sufficient. Based on the exception, [we] don't think there's a need for all of the pixel data."

Many thanks,

Kenny

Hi Kenny,

I have uploaded directory content together with the xdce file as 'failed INCell upload.zip'

Thanks for looking into it!

Cheers,
Misha

Thanks Misha,

Files received!

We'll try to look into it later tonight.

Best,

Kenny

Hi Misha,

Thank you again for uploading the relevant files. We are reviewing a fix for this now:

https://github.com/openmicroscopy/bioformats/pull/988

I would expect that to be included in the upcoming 5.0.1 release of OMERO.

Regards,
-Melissa

Hi Melissa,

thanks for an update!

So, I guess, I'll be patinetly waiting for 5.0.1 version OMERO.

Cheers,
Misha