Open Microscopy Environment

Hi all,

I'm a beginner with OME and maybe I'm missing something trivial but it seems to be that there is a problem with exporting oif or oib files.
I have been uploading *.oif and *.oib files from an Olympus scope into OMERO and all is fine.
The problem occurs when exporting these files into OME-TIFF. The dimensions of Z and C always come out wrong.

The XML has "XYZCT" when it should have "XYCZT". Any file *.oif or *.oib that is exported into OME-TIFF has this problem.

This does not occur if I access the server directly via OMERO for Imajeg but importing a file with the Bio-formats importer into imagej has the same problem!

No other file type created the same problem.

The files are created with Fluoview FL1000.
Using the OMERO version 4.2.2 in server and clients.

Thanks,
Helio Roque

There are a couple bugs involved here. The first is where a bug during import sets incorrect dimension orders in your OMERO.server that are then exported incorrectly. This has been fixed, the ticket in question is here:

http://trac.openmicroscopy.org.uk/ome/ticket/3124

You can upgrade your OMERO.importer to a version that has these fixes by grabbing the latest build from the latest Beta-4.2 stable Hudson builds:

http://hudson.openmicroscopy.org.uk/vie ... O-Beta4.2/

The second is a problem with the way Bio-Formats importer for ImageJ attempts to correct badly exported OME-TIFFs coming from OMERO. This has also been fixed, the ticket in question is here:

http://trac.openmicroscopy.org.uk/ome/ticket/4076

You can upgrade to the latest Beta-4.2 stable Bio-Formats importer for ImageJ also by visiting Hudson:

http://hudson.openmicroscopy.org.uk/vie ... S-Beta4.2/

The only unfortunate problem this does not solve is fixing the actual exported OME-TIFF files and dimension orders within your OMERO.server. This can be done easily enough with a SQL UPDATE command executed against the OMERO database. What is the output of the following on your system:

Code: Select all

SELECT * FROM dimensionorder;


Thanks for the reply.

I'll get and install the latest stable versions of the clients.

The output in our system is:

id | permissions | value | external_id
----+-------------+-------+-------------
1 | -35 | XYZCT |
2 | -35 | XYZTC |
3 | -35 | XYCTZ |
4 | -35 | XYCZT |
5 | -35 | XYTCZ |
6 | -35 | XYTZC |
(6 rows)

Great.

You can fix all the dimension orders on your system (after running a database backup) by executing:

Code: Select all

UPDATE pixels SET dimensionorder = 1;


Thanks. This solved all my problems.