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