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This documentation is for OMERO 5.2. This version is now in maintenance mode and will only be updated in the event of critical bugs or security concerns. OMERO 5.3 is expected in the first quarter of 2017.

OMERO.server installation on OS X with Homebrew


This walk-through demonstrates how to install OMERO on a clean Mac OS X system (10.9 or later) using Homebrew. Note that this demonstrates how to install OMERO.server from the source code via Homebrew, in addition to all its prerequisites.

These instructions are implemented in a series of automated scripts which install OMERO via Homebrew from a fresh configuration.



Homebrew requires the latest version of Xcode. Install Xcode and the Command Line Tools for Xcode from the App Store. If you have already installed it, make sure all the latest updates are installed.


Oracle Java may be downloaded from the Oracle website.

After installing JDK 7 or JDK 8, check your installation works by running:

$ java -version
java version "1.8.0_31"
Java(TM) SE Runtime Environment (build 1.8.0_31-b13)
Java HotSpot(TM) 64-Bit Server VM (build 25.31-b07, mixed mode)

$ javac -version
javac 1.8.0_31


All the requirements for OMERO will be installed under /usr/local. See also: Installation instructions on the Homebrew wiki.

Install Homebrew and make sure /usr/local/bin is prepended to your PATH:

$ ruby -e "$(curl -fsSL"
$ export PATH=/usr/local/bin:$PATH

Update Homebrew and run ‘brew doctor’ to fix potential issues beforehand:

$ brew update
$ brew doctor

Install git if not already present:

$ brew list | grep "\bgit\b" || brew install git

Install PostgreSQL database server:

$ export LANG=${LANG:-en_US.UTF-8}
$ export LANGUAGE=${LANGUAGE:-en_US:en}
$ brew install postgresql

You should install OMERO using Python 2.7 provided by Homebrew since it makes using Homebrew-provided modules simpler, for example the Ice python bindings needed by OMERO. For a more thorough description of the Homebrew solution, see the Homebrew and Python page. Note that the automated script linked above tests the OMERO installation using the Homebrew Python.

To install the Python provided by Homebrew:

$ brew install python

Check that Python is working and is version 2.7:

$ which python
$ python --version
Python 2.7.9

The installation of OMERO via Homebrew depends upon two alternate repositories containing extra formulae: for the HDF5 formula and for all the OME-provided formulae and older versions of Ice. To add these, run:

$ brew tap homebrew/science
$ brew tap ome/alt


The Homebrew formulae used below provide Python bindings. As described in Homebrew and Python, you should not be in an active virtual environment when you brew install them.

See the script for the steps described above.

OMERO installation

OMERO 5.2.8 server

To install and deploy the 5.2.8 release of OMERO.server, run:

$ brew install omero52 --with-nginx --with-cpp
$ export PYTHONPATH=$(brew --prefix omero52)/lib/python
$ export ICE_CONFIG=$(brew --prefix omero52)/etc/ice.config

This will install the OMERO server to /usr/local/Cellar/omero, which means you will find the log files in /usr/local/Cellar/omero/|release|/var/log. The binaries will be linked to /usr/local/bin:

$ which omero

Install OMERO python dependencies:

$ pip install -r $(brew --prefix omero52)/share/web/requirements-py27-nginx.txt
$ cd /usr/local
$ bash bin/omero_python_deps

Start database server:

$ pg_ctl -D /usr/local/var/postgres -l /usr/local/var/postgres/server.log -w start

Create database and user:

$ createuser -w -D -R -S db_user
$ createdb -E UTF8 -O db_user omero_database
$ psql -h localhost -U db_user -l

Set database parameters in OMERO:

$ omero config set omero_database
$ omero config set omero.db.user db_user
$ omero config set omero.db.pass db_password

Create and run script to initialize the OMERO database:

$ omero db script --password $ROOT_PASSWORD -f $PSQL_SCRIPT_NAME
$ psql -h localhost -U db_user omero_database < $PSQL_SCRIPT_NAME

Set up OMERO data directory:

$ mkdir -p $OMERO_DATA_DIR
$ omero config set $OMERO_DATA_DIR

See the OMERO installation script

Development server

If you wish to build OMERO.server from source for development purposes, using the git repository, first use Homebrew to install the OMERO dependencies:

$ brew install --only-dependencies omero

The default version of Ice installed by the OMERO formula is currently Ice 3.5.

Prepare a place for your OMERO code to live, e.g.:

$ mkdir -p ~/code/projects
$ cd ~/code/projects

If you installed Ice 3.5, you will need to set SLICEPATH to be able to build the server, i.e. export SLICEPATH=/usr/local/share/Ice-3.5/slice.

If you want the development version of OMERO.server, you can clone the source code from the project’s GitHub account to build locally:

$ git clone --recursive git://
$ cd openmicroscopy && ./


If you have a GitHub account and you plan to develop code for OMERO, you should make a fork into your own account and then clone this fork to your local development machine, e.g.

$ git remote add  git://
$ cd openmicroscopy && ./

See also

Installing OMERO from source
Developer documentation page on how to check out to source code
Build System
Developer documentation page on how to build the OMERO.server

Then prepend the development bin directory to your PATH to pick the right executbale:

$ export PATH=~/code/projects/openmicroscopy/dist/bin:$PATH

and follow the steps for setting up the database and OMERO data directory as mentioned in the previous section.


Basic setup for OMERO using Nginx:

$ export HTTPPORT=${HTTPPORT:-8080}
$ omero web config nginx-development --http $HTTPPORT > $(brew --prefix omero52)/etc/nginx.conf

See installation script

For detailed instructions on how to deploy OMERO.web in a production environment such as Apache or Nginx please see OMERO.web deployment.


The internal Django webserver can be used for evaluation and development. In this case please follow the instructions under OMERO.web deployment for developers.


If necessary start PostgreSQL database server:

$ pg_ctl -D /usr/local/var/postgres -l /usr/local/var/postgres/server.log -w start

Start OMERO:

$ omero admin start

Start OMERO.web:

$ omero web start
$ nginx -c $(brew --prefix omero52)/etc/nginx.conf

Now connect to your OMERO.server using OMERO.insight or OMERO.web with the following credentials:

U: root
P: omero

Stop OMERO.web:

$ nginx -c $(brew --prefix omero52)/etc/nginx.conf -s stop
$ omero web stop


$ omero admin stop

See example script for a basic functionality test:

Common issues

General considerations

If you run into problems with Homebrew, you can always run:

$ brew update
$ brew doctor

Also, please check the Homebrew Bug Fixing Checklist.

Below is a non-exhaustive list of errors/warnings specific to the OMERO installation. Some if not all of them could possibly be avoided by removing any previous OMERO installation artifacts from your system.


Check to make sure the database has been created and ‘UTF8’ encoding is used

$ psql -h localhost -U db_user -l

This command should give similar output to the following:

                        List of databases

   Name         | Owner   | Encoding |  Collation  |    Ctype    | Access privileges
 omero_database | db_user | UTF8     | en_GB.UTF-8 | en_GB.UTF-8 |
 postgres       | ome     | UTF8     | en_GB.UTF-8 | en_GB.UTF-8 |
 template0      | ome     | UTF8     | en_GB.UTF-8 | en_GB.UTF-8 | =c/ome           +
                |         |          |             |             | ome=CTc/ome
 template1      | ome     | UTF8     | en_GB.UTF-8 | en_GB.UTF-8 | =c/ome           +
                |         |          |             |             | ome=CTc/ome
(4 rows)


Warning: It appears you have MacPorts or Fink installed.

Follow uninstall instructions from the Macports guide.


If you encounter this error during installation of PostgreSQL:

Error: You must ``brew link ossp-uuid' before postgresql can be installed


$ brew cleanup
$ brew link ossp-uuid


If you encounter an MD5 mismatch error similar to this:

==> Installing hdf5 dependency: szip
==> Downloading
Already downloaded: /Library/Caches/Homebrew/szip-2.1.tar.gz
Error: MD5 mismatch
Expected: 902f831bcefb69c6b635374424acbead
Got: 0d6a55bb7787f9ff8b9d608f23ef5be0
Archive: /Library/Caches/Homebrew/szip-2.1.tar.gz
(To retry an incomplete download, remove the file above.)

then manually remove the archived version located under /Library/Caches/Homebrew, since the maintainer may have updated the file.

numexpr (and other Python packages)

If you encounter an issue related to numexpr complaining about NumPy having too low a version number, verify that you have not previously installed any Python packages using pip. In the case where pip has been installed before Homebrew, uninstall it:

$ sudo pip uninstall pip

and then try running again. That should install pip via Homebrew and put the Python packages in correct locations.