This project is financed by France BioImaging.

An OMERO webapp to follow microscope performance over time.

The following instructions are for Linux. Instructions for other OSs will be added soon.

Installation on your OMERO-web server instance

To be completed

Try OMERO-metrics using docker

Install docker and docker-compose on your computer following the instructions on the docker website.

Clone the repository:

$ git clone https://github.com/MontpellierRessourcesImagerie/OMERO-metrics.git
$ cd OMERO-metrics

Run the following command to start the server:

$ docker compose up -d

Wait for the server to start and then go to http://localhost:5080/ in your server.

Before trying anything, you need to generate users, and import some data, etc. If you wish, you can do that automatically. To do so you need to install the python environment and run a script that will generate some data for you.

$ python -m venv my_venv
$ source my_venv/bin/activate
$ pip install -e .
$ cd test/omero-server
$ python structure_generator.py

Go to http://localhost:5080/ and log in with the following credentials:

• Username: Asterix
• Password: abc123

Installation for development

Here we explain how to install OMERO-metrics using an OMERO-web server running locally. The main advantage is that you may edit the code and debug very easily.

Pre-requirements

You need to make sure that Python (version 3.9, 3.10 or 3.11) is installed in your computer.

Configuration

Clone the repository and create a virtual environment to run your server in

$ git clone https://github.com/MontpellierRessourcesImagerie/OMERO-metrics.git
$ cd OMERO-metrics
$ python -m venv my_venv
$ source my_venv/bin/activate
$ pip install -e .

We created a little bash script that is configuring the setup. You can run it by typing:

test /OMERO_metrics$ ./configuration_omero.sh /path/to/omeroweb /path/to/mydatabase

where /path/to/omeroweb is the path to the OMERO-web directory and /path/to/mydatabase is the path to the OMERO_metrics sqlite database.

export REACT_VERSION=18.2.0
export OMERODIR=$(pwd)
omero config set omero.web.server_list '[["localhost", 6064, "omero_server"]]'
omero web start

Some Useful Links To Download ZeroC-Ice

#zeroc-ice @ https://github.com/glencoesoftware/zeroc-ice-py-macos-universal2/releases/download/20240131/zeroc_ice-3.6.5-cp311-cp311-macosx_11_0_universal2.whl
#zeroc-ice @ https://github.com/glencoesoftware/zeroc-ice-py-linux-x86_64/releases/download/20240202/zeroc_ice-3.6.5-cp311-cp311-manylinux_2_28_x86_64.whl

Further Info

1. This app was derived from cookiecutter-omero-webapp.
2. For further info on deployment, see Deployment

License

This project, similar to many Open Microscopy Environment (OME) projects, is licensed under the terms of the AGPL v3.

Copyright

2024 CNRS