Known limitations

Time zone

We do not recommend changing the time zone on your server. The server is currently set to use local time and changing time zones will result in a mismatch between the original data import times stored in the server and the way the clients report them.

Too many open file descriptors

Starting with OMERO 5, the server works directly from original files. At times, this requires a significant number of open file handles. If you are having problems with large or frequent imports, are seeing “Too many open file descriptors” or similar, you may need to increase the maximum number of open files per process. On Linux, this may be done by setting the nofile limit in /etc/security/limits.conf, for example:

omero  soft  nofile  10000
omero  hard  nofile  12000

This permits the omero user to have 10000 open files per process, which may be increased up to a maximum of 12000 by the user. The username and limits will need adjusting for the specifics of your installation and usage requirements. Note that these settings take effect only for new logins, so the server and the shell or environment the server is started from will require restarting. Run ulimit -a as the user running OMERO to verify that the changes have taken effect.

Changing group permissions

If a group contains a projection made by one member from data owned by another user, you cannot make the group into a private group.

File format support

Large images

When you import an image over a certain size, OMERO will generate a pyramid of lower resolution images if it doesn’t already exist in the file. The threshold size is configurable using omero.pixeldata.max_plane_height and omero.pixeldata.max_plane_width but set to 3192x3192 pixels by default. However, this process can be very resource-intensive, depending on the size of the image as well as the image format and any data compression used, for example see PixelData threads and pyramid generation issues.

The OMERO pyramid generation process should be considered as deprecated and instead it is recommended that users avoid these issues by converting their data to pyramidal OME-TIFF files before importing into OMERO. A number of suitable tools are available such as bioformats2raw & raw2ometiff, bfconvert, Kheops, tifffile, aicsimageio, libvips and QuPath.

Large images with floating-point pixel data

Pyramids of image tiles are currently not generated for images with floating-point pixel data, meaning the imported image will be scrambled if it is over the size threshold mentioned above. This primarily affects the following file formats:

This issue can be avoided by pre-generating pyramidal OME-TIFF images as described above.

Calculation of minima and maxima pixel values

If images are imported with one of the omero import --skip options skipping calculation of the global minima and maxima pixel values, OMERO clients will use the extrema of the pixel type range by default. Users can adjust the minima/maxima via the rendering settings. Recalculating minima and maxima pixel values after import is currently not supported.

Flex data in OMERO.tables

If you are using the advanced configuration setting FlexReaderServerMaps for importing Flex data split between multiple directories for use with OMERO.tables, you should not upgrade beyond 5.0.x. Neither the 5.1 line nor OMERO 5.2 support this functionality.


Enabling synchronization of LDAP on user login may override admin actions carried out in the clients, see Synchronizing LDAP on user login for details.