Known Limitations

Software limitations

Postgres 8.2 and earlier don't support "temp table ... dicard"

Postgres 8.2 and earlier don't support "temp table ... dicard". See #5861

now() in Postgres functions show time of db upgrade/install

now() in Postgres functions show time of db upgrade/install. See #5862

Switching between 'Shares' in web

Occasionally you may find that when switching from a 'share' login on the webclient back to your own user login, you get an error saying that you don't have permission to access your data. This is a mix-up between the different 'sessions' and can be resolved with a simple log-out and log-in.

OMERO.importer and number of files to import

It is preferable not to import more than 1000 image files in a single import.

OMERO.importer on Ubuntu

Under older Ubuntu installations the 'import folder' option currently does not work.

OMERO.importer and size of import

It is preferable not to import more than 1000 image files in a single import.

XML annotations and OMERO.importer

Certain implementations of XML annotations in OME-TIFF or OME-XML files can not be correctly imported into OMERO. You can find further details on ticket #3269.

Comment annotations and OMERO.clients

If you wish to add a large comment to an object (e.g. an Image), it is preferable to attach a file i.e. use file annotation.

Float pixels Type and OMERO

It is possible to import Float pixels Type files (e.g. some NIfTI files), but unfortunately it not always possible to visualise such images.

OMERO.insight History Feature

History feature in [OmeroInsightViewer Viewer] turned off since version 4.0.

OMERO.insight and Large Images

Currently it is only possible to view compressed version of large images (i.e. > 3kx3k)

OMERO.insight and Float Pixel Type Files

It is possible to import Float pixels Type files (e.g. some NIfTI files), but unfortunately it not always possible to visualise such images.

OMERO.insight and Changing Group Permissions

Changing of group permissions for very large groups can be very slow ticket #2872.

OMERO.insight and Moving Data

Data created/imported in a group cannot be moved to another group even if the user is a member of the 2 groups.

OMERO.insight and Metadata

If you wish to add very large comment, it is preferable to attach a file.

OMERO.web FastCGI and UNIX socket problems

Under certain circumstances when using UNIX sockets with OMERO.web FastCGI the workers do not seem to correctly initialize. You can find further details on ticket #3199.

Not finding certain pieces of data in wildcard searches

Sometimes data is missed when certain types of wildcard searches are performed. You can find further details on ticket #3164.

C++ compilation problems on Mac OS X 10.6 (Snow Leopard)

Under certain circumstances building OmeroCpp on Mac OS X 10.6 (Snow Leopard) can fail with "ld: symbol(s) not found". You can find further details, a potential solution and make any comments on your experience with the problem on ticket #3210.

Non-LDAP user password security

Encrypted login and communication, via SSL, has been available in OMERO for some time. However, under some circumstances it is possible for passwords to end up on the wire in the clear. Further details and status can be found on ticket #3232. Users who have their credentials stored in LDAP and who have OMERO configured to use their LDAP server are not affected by this issue.

Moving data between groups

In 4.2.0 we expanded the support for collaborative work using OMERO, this is detailed on the permissions page. When any data is imported it is currently assigned a group and currently that decision is final. This will change with future releases but we encourage users to be aware of their working group at all times, especially when importing.

Synchronization of lib/scripts

As described under OMERO.scripts, 4.2.0 includes a significantly improved scripting system. Several official scripts are shipped under lib/scripts in the deployment directory. If any of your users add their own "official scripts", they too will be stored under lib/scripts. When we release a new OMERO version, there will be some difficulties merging the two directories. We will address this issue as quickly as possible.

Import of reagents and screens

The import of some, complicated OME-XML files may not work with 4.2.0. Shortly before release, we tested a file with two entire screens, several plates, and many cross linked reagents which failed. This is a very unlikely scenario, and we know of no files that contain this level of data, but if you have issues getting screening data imported in the OME-XML format, please let us know.

Limited support for PostgreSQL 8.1

In order to reduce sporadic hangs, the 4.2 database introduced the use of the "pg_advisory_lock" method. This is not available on PostgreSQL 8.1, however. During db creation or upgraded the following message is printed:

        =====================================================================================
        pg_advisory_lock does not exist!

        You should consider upgrading to PostgreSQL 8.2 or above
        Until then, you may experience infrequent key constraint issues on insert.
        =====================================================================================

OMERO should continue to function normally, but in some cases an insert may throw an exception if two threads try to insert the same primary key.

Binary delete on Windows servers

On Windows servers not all binary files corresponding to a delete may be removed from the binary repository. See Delete: Binary Data for more details.