Instructions

This document provides detailed instructions for using the OMERO system via the web interface and desktop application, including data organization, user management, and essential platform functionalities. The OMERO web interface allows users to view, organize, and analyze data, while the desktop application offers the same functionalities with the additional ability to upload images.

1. User Registration

To use the OMERO system, you must first register a user account. Follow these steps to register:

  1. Open the OMERO web interface and click on “Don’t have an account?” on the login page.
  2. Fill in the registration form with the following details:
    • Full name
    • Email address
    • Affiliated institution
  3. After completing the required fields, click “Create account”.
  4. Upon successful registration, you will receive a username and a temporary password.
  5. For security reasons, it is recommended to change the temporary password after the first login.

Forgotten Password?

  • If you forget your password, click on “Forgot your password?” on the login page.
  • Follow the instructions to reset your password via email.

Access Permissions After Registration

After registration, the user is automatically assigned to the “pending_users” group, where they cannot view or create images. To gain full access to OMERO and its tools, the user must request to be moved to the “contributors” group.

To request access, the user must contact the administrator via email at: ivan.stajduhar@riteh.uniri.hr.

2. Basic Navigation and Using the OMERO Interface

Once logged into the OMERO web interface, users can manage their data through an intuitive interface. Below are the key elements for navigation and using the OMERO system.

2.1 Selecting a Group for Viewing Data

If a user belongs to multiple groups, they can choose which group’s data to view by following these steps:

  1. Click on the currently active group in the top right corner of the interface.
  2. A dropdown menu will appear with a list of all groups the user belongs to.
  3. Clicking on a group updates the data display, showing only the data within that group.

After selecting a group, the user will see only those projects, datasets, and images that are available within that group, depending on the assigned permissions.

2.2 Creating New Projects, Datasets, and Screens

OMERO uses a hierarchical structure for data organization. The primary organizational elements are:

Screen – Used for high-throughput experiments.

Project – The highest level of organization, containing datasets.

Dataset – A collection of images within a project.

How to Create a New Object?

  1. Click “Create New” at the top of the interface.
  2. Select Project, Dataset, or Screen.
  3. Enter a name and an optional description.
  4. Click “OK”.

Notes:

  • All data is organized hierarchically, so when adding new images, ensure they are placed in the correct dataset.
  • Images cannot be added directly to a project – they must be stored within a dataset.
  • If you are in a Read-Write group, all members can collaborate on the same projects and datasets.
  • If you belong to multiple groups, make sure you have selected the correct group before adding data.

3. Uploading Images to OMERO

Images can only be uploaded using the OMERO desktop application, which can be downloaded from the official website: OMERO Downloads. Of course, all functionalities available in the OMERO web interface can also be used through the OMERO desktop application.

3.1 Logging In

  1. Open the OMERO desktop application.
  2. Select “Enter the server’s address”.
  3. In the server address field, enter: optiderm.riteh.hr.
  4. Enter your username and password.
  5. Click “Login” to access the system.

3.2 Uploading an Image

  1. In the top-right corner of the application, click “Open the Importer”.
  2. Locate the desired image on your computer and select it.
  3. Click the arrow “Add the selected files to the queue”.
  4. In the next window, select the project and dataset where the image will be stored.
  5. Click “Import” to start the upload process.
  6. After the upload is complete, click “Close”.

4. Administrators and Group Owners

In the OMERO system, administrators and group owners have special privileges for managing users and group settings.

4.1 Administrators

Administrators are members of the “system” group and have full control over users and groups. They can also transfer ownership of projects or datasets if necessary, enabling data reallocation between users.

How to Access Administrator Options?

  • Administrators must click on “Admin” in the navigation bar to manage users and groups.

Administrator Privileges:

  • Add new users and manage existing accounts.
  • Move users from one group to another or assign them to multiple groups.
  • Create new groups and define their permissions.
  • Assign group owners.

4.2 Group Owners

Each group can have an owner, designated by an administrator.

How to Access Group Settings?

  • The group owner must open “User settings” to manage members and permissions within their group.

Group Owner Privileges:

  • Add and remove members within their group.
  • Change group permissions (Read-Only, Read-Annotate, Read-Write).

Notes:

  • Group owners cannot create new groups or manage users outside their group.
  • Administrators can change the group owner if necessary.

5. Group Permissions in OMERO

Each group in the OMERO system has specific permissions that define what members can do with the data. The appropriate permission level depends on the required level of collaboration within the group. There are four permission levels:

Private

  • Only the owner can view and edit their data.
  • Other group members cannot access the data.

Read-Only

  • All group members can view data, but cannot modify it.
  • Only the owner can edit and delete their data.

Read-Annotate

  • All members can view data and add annotations (comments, tags).
  • Only the owner can edit and delete their data.

Read-Write

  • All group members can view, edit, and delete data within the group.
  • Ideal for teamwork, where everyone needs full control over the data.
  • Group owners cannot create new groups or manage users outside their group.
  • Administrators can change the group owner if necessary.

Additional Information and Support

For additional information and technical support, please contact the administrator at ivan.stajduhar@riteh.uniri.hr or refer to the official OMERO documentation: OMERO documentation.

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