OMERO walkthrough for facility managers

In this document, we go through a common workflow that an imaging facility manager who facilitates OMERO usage for others might follow:

  • Create and manage Groups and Users.
  • Import data for others.
  • Import large or heterogeneous data for others.
  • Manage data for others.
  • Set up OMERO for publication of data.
  • Get users started.

Administrate Groups and Users

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Administrate Groups and Users

This chapter will show how to manage groups and users using the graphical interface in OMERO.web and the command-line interface. Most of the following tasks below can only be done by users with some administrator privileges. We will show:

  • How to manage groups, creating and editing a new/existing group.
  • How to manage users, creating and editing a new/existing user.
  • How to set up the OMERO server to be able to email all users.

Import for others using the Desktop application

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Import data using the Desktop Client

Second part of this import section will show how to import data for another user, using OMERO.insight. The user importing the data needs to have some admin or restricted-admin privileges. More information about restricted privileges can be found at https://docs.openmicroscopy.org/latest/omero/sysadmins/restricted-admins.html

The import for another user requires that the user doing the import has specific privileges. We will use the user importer1, this could be, for example, a facility manager.

We will show:

  • How to install the OMERO.insight desktop client on Windows, Mac and Linux.
  • How to import data for the user logged in using OMERO.insight.
  • How to select a target Project and Dataset or create a new ones in OMERO for the imports.
  • How to add Tags to imported images at the import stage, to facilitate the management of these images later in OMERO.server.
  • How to import data for other users in OMERO.insight.

Import large data using Command Line Interface

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Import data using the Command Line Interface (CLI)

Description

This chapter will show how to import data for another user, using Command Line Interface (CLI).

The user importing the data needs to have some admin (or restricted-admin) privileges. More information about restricted privileges can be found at https://docs.openmicroscopy.org/latest/omero/sysadmins/restricted-admins.html

The import for another user will be done only as demo since the user is required to have specific privileges. We will use a user with login name importer1, who could be in real life e.g. a facility manager.

We will show:

  • How to import data using the CLI for myself and for others into a remote OMERO.server
  • How to import data using the CLI “in-place”, which means not copying the imported data into OMERO. Instead, OMERO will point to the original location of “in-place” imported files, thus preventing data duplication.
  • How to deal with imports of large amounts of data in CLI, using the –bulk option and helper csv and yml files which define what is to be imported and how.

Manage data for others

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Data management and cooperation

In this document, we introduce the basic concepts of data management, such as browsing, navigating to others’ data, and changing the display of the images in OMERO. The example here uses OMERO.web, but majority of the features described here are also present in OMERO.insight.

Further, we show how to use the Command Line Interface (CLI) for data management, introducting mainly the features which are not present in the OMERO.web.

Description

We will show:

  • How to browse data in OMERO.web, navigating to yours and other users’ Images.
  • How to use the basic layout of OMERO.web for Images organized in Projects and Datasets.
  • How to use OMERO.web for viewing of High-Content Screening (HCS) data.
  • How to use the Preview panel.
  • How to adjust the rendering settings of your and other users’ images from the Preview panel.
  • How to organize Images in Projects and Datasets.
  • How to move the data between groups if you are data owner.
  • How to move the data between groups if you are an administrator working on behalf of others.
  • How to use Command Line for duplicating objects such as Images, Datasets or Projects.
  • How to use Command Line for changing the ownership of objects.

Set up OMERO for publication of data

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Prepare data for publication using OMERO

Users can publish Image data to the world using OMERO. Here we describe some steps to facilitate that. The steps are to be done by an administrator or restricted administrator in OMERO.

Description

We will show:

  • How to set up configurations in OMERO.web for establishing of a public user.
  • How to set up a public group.
  • How to get the data into the public group.
  • How to open the public group to the outer world.

Get users started

Here we describe how to get users started. This is a walkthrough for a facility manager in charge of introducing new users to OMERO.

Step-by-Step

  1. Create the new user in OMERO and add them to the appropriate group(s) in OMERO. Consult the user and group creation sections of Administrate Groups and Users. In case your OMERO.server is set up for synchronization of logins with your institutional login system (LDAP), look for Managing LDAP Users in Administrate Groups and Users.
  2. Explain to the user the basics of Group and User system in OMERO, drawing their attention to the importance of logging into the correct group when importing data. The user sets then their default group in OMERO correctly, as explained in Administrate Groups and Users, or you do it for the user.
  3. Point the new user to the section explaining how to install and import data into OMERO using a Desktop client Import data using the Desktop Client.
  4. Point the new user to the basic workflow example OMERO walkthrough example. This will give them hints about the basic steps usually done when working with OMERO and how to go through them.
  5. Explain to the user the data management and annotation possibilities in OMERO, as highlighted in Data management and cooperation and Annotate Data and Filter using Annotations.
  6. Consult with the user the analysis possibilities when using 3rd party tools with OMERO, as listed in External Software and OMERO.
  7. Mention OMERO.figure. This will help to raise the usage of OMERO in your institution.