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Binary Repository

OMERO.server Binary Repository


The OMERO.server binary data repository is a fundamental piece of server-side functionality. It provides optimized and indexed storage of original file, pixel and thumbnail data, attachments and full text indexes. Its structure is based on OMEIS.


The repository is internally laid out as follows:

/OMERO/Pixels      <--- Pixel data
/OMERO/Files       <--- Original file data
/OMERO/Thumbnails  <--- Thumbnail data
/OMERO/FullText    <--- Lucene full text search index


Your repository should be owned by the same user that is starting your OMERO.server instance. This is often either yourself (find this out by executing whoami) or a seperate omero (or similar) user who is dedicated to running OMERO.server. For example:

$ whoami
$ ls -al /OMERO
total 24
drwxr-xr-x  5 omero  omero   128 Dec 12  2006 .
drwxr-xr-x  7 root    root   160 Nov  5 15:24 ..
drwxr-xr-x  2 omero  omero  1656 Dec 18 14:31 Files
drwxr-xr-x 25 omero  omero 23256 Dec 10 19:06 Pixels
drwxr-xr-x  2 omero  omero    48 Dec  8  2006 Thumbnails

Your repository is not

  • The "database"
  • The directory where your OMERO.server binaries are
  • The directory where your OMERO.client (OMERO.insight, OMERO.editor or OMERO.importer) binaries are
  • Your PostgreSQL data directory
  • A place to store moldy sandwiches

Changing your repository location

Your repository location can be changed from it's /OMERO or C:\OMERO default by modifying your OMERO.server configuration as follows (remembering that Windows C:\ style paths must have backslashes escaped):

cd omero-Beta4.0.0
bin/omero config set /mnt/really_big_disk/OMERO

cd C:\omero-Beta4.0.0
bin\omero config set D:\\OMERO

The suggested procedure is to shut down your OMERO.server instance, move your repository, change your and then start the instance back up. For example:

cd omero-Beta4.0.0
bin/omero admin stop
mv /OMERO /mnt/really_big_disk
bin/omero config set /mnt/really_big_disk/OMERO
bin/omero admin start

cd C:\omero-Beta4.0.0
bin\omero admin stop
move C:\OMERO D:\
bin\omero config set D:\\OMERO
bin/omero admin start

NOTE: It is strongly recommended that you make all changes to your OMERO binary repository with the server shut down. Changing the configuration does not move the repository for you, you must do this yourself.

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