microscopemetrics-omero

microscopemetrics-omero is a python package for using OMERO as a data management solution for microscope-metrics

microscopemetrcis-omero provides a set of functions to store and retrieve data from OMERO as defined by the microscopemetrics-schema

It also provides a number of scripts to run microscope-metrics either in OMERO's scripting service or from outside of the OMERO server but using OMERO as a data management solution.

Documentation

Documentation is still scarce. You may find it at Documentation pages.

For the time being please refer to the tests directory to find some example code

Installation

Install microscopemetrics-omero with pip

  pip install microscopemetrics-omero

You may want to do that in the virtual environment of your OMERO instance and then install the scripts in ./tests/omero-server/microscope_metrics in the OMERO server's script directory.

For development, we use poetry After installing poetry, you can install microscope-metrics running the following command in the root directory of the project

  poetry install

Running Tests

To run tests, you need to install docker-compose and create an OMERO instance using the docker-compose.yaml in the tests directory.

  cd tests
  docker-compose up -d

Then run pytest in the root directory of the project to run the tests.

  pytest