OMERO

OMERO type access

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OMERO is an image data management tool that makes it easy to view, annotate, analyze, share data, and prepare figures for publications or posters.

More information can be found here.

Initialization

For information on how to use the Initialization parameter, please refer to the Initialization - Bash script and Initialization - pip packages section of the documentation.

OMERO Services

When started, the application launches several services, including Redis and PostgreSQL.

PostgreSQL database

A PostgreSQL database server is started automatically. By default, a database directory named postgresql is created in the /work directory.

A pre-existing PostgreSQL database directory can be used instead, via the option Database folder. The default database configuration is as follows:

  • Username: db_user

  • Password: db_password

  • Database name: omero_database

Start OMERO App

When opening the OMERO web interface, users are prompted to enter the required information. By default:

  • Username: root

  • Password: omero

The root account serves as Administrator account.

The Administrator has unrestricted access to the entire instance and all activities within it. For example, they can create groups, add new users, and manage user permissions.

Note

  • All users are registered on the server with an email address. However, since no email server is configured in the backend, the application cannot send emails to users through the web interface.

  • New members can be added and collaborate on the project only if the application is deployed with a public link.

OMERO Data Directory

By default, the folder where OMERO data are stored is named OMERO. However, it is possible to select a pre-existing folder using the optional parameter Omero data dir.

Note

A pre-existing OMERO data folder must be associated with the correct PostgreSQL database, which needs to be selected via the Database folder parameter .

Import Images

To import images from a UCloud folder into the OMERO instance, the folder containing the images must first be mounted using the Select folders to use parameter.

Once the job has started, the following command can be executed in the terminal of the job progress view:

$ omero import -s localhost -u USER -w PASSWORD /work/image-folder

where image-folder is the name of the UCloud folder has been mounted.

For the root (Administrator) user, the command is:

$ omero import -s localhost -u root -w omero /work/image-folder

More details on the OMERO import command are shown by writing in the terminal:

$ omero import --help

Add OMERO tools

The app is deployed with several tools, including:

  • omero-figure

  • omero-fpbioimage

  • omero-parade

  • omero-mapr

  • omero-gallery

Additional tools can be added by using the Initialization parameter.

MAPR

OMERO.mapr is an OMERO.web app that enables browsing of data through attributes linked to images in the form of map annotations. Details on how to configure and use MAPR can be found here.

Map annotations

Namespaces and keys must be configured to define the attributes that can be searched.

For example, to allow searching for Primary Antibody or Secondary Antibody, the following configuration can be applied:

$ omero config append omero.web.mapr.config '{"menu": "antibody", "config":{"default":["Primary Antibody"], "all":["Primary Antibody", "Secondary Antibody"], "ns":["openmicroscopy.org/omero/client/mapAnnotation"], "label":"Antibody"}}'

A link can also be added to the top of the webclient page. In this example, an "Antibodies" link is added, redirecting to the Antibodies search page:

$ omero config append omero.web.ui.top_links '["Antibodies", {"viewname": "maprindex_antibody"}, {"title": "Find Antibody values"}]'

To ensure these changes take effect when the application interface is opened, the configuration lines must be included in a bash script and passed through the Initialization parameter.

Example script for the Antibodies configuration:

#!/bin/bash

omero config append omero.web.mapr.config '{"menu": "antibody", "config":{"default":["Primary Antibody"], "all":["Primary Antibody", "Secondary Antibody"], "ns":["openmicroscopy.org/omero/client/mapAnnotation"], "label":"Antibody"}}'

omero config append omero.web.ui.top_links '["Antibodies", {"viewname": "maprindex_antibody"}, {"title": "Find Antibody values"}]'