Open Microscopy Environment

Dear all,

We recently acquired an Operetta microscope from PerkinElmer, and would like to use OMERO for data storage.

I wanted to ask if someone here has used OMERO with the Operetta before, and if so, what are the export options they used please?

It seems that the PerkinElmer format is not totally supported, does someone know exactly what data or metadata is lost during the import to OMERO?

PerkinElmer was telling me that the data exported from OMERO (OME.tif) could not be re-imported into Harmony (the PE software for image analysis that comes with the Operetta). Does anyone have experience with OMERO and Harmony?

Thank you very much for your help,

Best wishes,

David

Hi David,

It seems that the PerkinElmer format is not totally supported, does someone know exactly what data or metadata is lost during the import to OMERO?

We would certainly like to fix any problems that are present in importing Operetta data into OMERO. What sorts of problems have you encountered? Would you be willing to send a sample dataset that demonstrates the problems?

If the files fail to import, then you can report the errors directly from OMERO.importer or OMERO.insight; otherwise, you can upload the files to OMERO.qa:

http://qa.openmicroscopy.org.uk/qa/upload/

If that does not work, please let me know and I will privately send our SFTP server information so that you can send the files that way.

Regards,
-Melissa

We've also recently acquired an operetta and I'm trying to get data that has been exported from the Harmony database as "Columbus export (including images)" or "Index and images". Neither results in a dataset that can be imported in omero. Upon export I get a folder that has an xml file (index.idx.xml) with a lot of metadata, and all of the tiff files plus another folder that says "Assaylayout" . The files import into an omero project just fine, but most of the image specific metadata is gone, e.g. no channel information, pixel size is wrong, etc.
Because the images are tif files, they import using either the importer or insight directly. If I try to import them into a "Screen" the screen name appears, but the images end up as orphans.

I would happily contribute some datasets, but the qa only accepts image format files, and I think you need the xml file with the folder of images to make sense of the plate layout etc.

According to PE the naming scheme of the files in the folder is this:

r01c01f01p01rc1-ch1sk1fk1fl1.tiff where:

r=row, c=column, f=field, p=plane, rc=record, ch=channel, sk=timepoint (the remaining parts of the file name are currently not in use

, but they also say this:

Do not rely on image properties derived from image file names. The naming convention is subject to change without notice. Please see the meta information in the XML files for reliable data

Hi,

We've also recently acquired an operetta and I'm trying to get data that has been exported from the Harmony database as "Columbus export (including images)" or "Index and images". Neither results in a dataset that can be imported in omero. Upon export I get a folder that has an xml file (index.idx.xml) with a lot of metadata, and all of the tiff files plus another folder that says "Assaylayout" . The files import into an omero project just fine, but most of the image specific metadata is gone, e.g. no channel information, pixel size is wrong, etc.
Because the images are tif files, they import using either the importer or insight directly. If I try to import them into a "Screen" the screen name appears, but the images end up as orphans.

I would happily contribute some datasets, but the qa only accepts image format files, and I think you need the xml file with the folder of images to make sense of the plate layout etc.

You're right - we will need to see the XML file in addition to the TIFFs. I have sent you a private message that contains instructions on how to upload files to our SFTP server. Once we have a dataset or two, we can evaluate what it would take to import all of the metadata correctly.

Regards,
-Melissa

We've also recently acquired an operetta and I'm trying to get data that has been exported from the Harmony database as "Columbus export (including images)" or "Index and images". Neither results in a dataset that can be imported in omero. Upon export I get a folder that has an xml file (index.idx.xml) with a lot of metadata, and all of the tiff files plus another folder that says "Assaylayout" . The files import into an omero project just fine, but most of the image specific metadata is gone, e.g. no channel information, pixel size is wrong, etc.
Because the images are tif files, they import using either the importer or insight directly. If I try to import them into a "Screen" the screen name appears, but the images end up as orphans.

I would happily contribute some datasets, but the qa only accepts image format files, and I think you need the xml file with the folder of images to make sense of the plate layout etc.

You're right - we will need to see the XML file in addition to the TIFFs. I have sent you a private message that contains instructions on how to upload files to our SFTP server. Once we have a dataset or two, we can evaluate what it would take to import all of the metadata correctly.

Thank you very much for sending example datasets privately. There is now a ticket on our issue tracking system to add full support for this data:

http://trac.openmicroscopy.org.uk/ome/ticket/7254

If you would like to be automatically notified of updates to that ticket, please let me know and I will make sure that you are CC'd on the ticket.

Regards,
-Melissa

Dear all,

Thank you very much for creating a ticket on that issue. I am very interested in this feature, can you CC me on the ticket as well?

If you need any more information on the system, and/or images exported (there are multiple ways to do it from Harmony), let me know and I'll try to be of as much assistance as possible.

Thanks in advance,
David

Hi David,

Thank you very much for creating a ticket on that issue. I am very interested in this feature, can you CC me on the ticket as well?

You have now been CC'd on the ticket, and will receive an automated email with "[OME #7254]" in the subject line whenever we update the status of the ticket. Once the ticket has been closed ("resolution: => fixed" will appear in the body of the email), you can expect that the following stable release of OMERO will support these datasets.

Regards,
-Melissa