Thanks for your interest in subscribing to OMERO Plus Essentials. This guide contains all the information and links you’ll need to get started.
Using AWS
If this is your first time using AWS, follow Amazon’s instructions for creating your AWS account.
When configuring OMERO Plus Essentials, you’ll have the option to select the domain where OMERO Plus Essentials will be deployed. Register a domain name following these instructions.
Now you are ready to make your purchase via AWS Marketplace! Scroll down to our contact form below to receive the private offer.
Launching with CloudFormation
After purchasing the OMERO Plus Essentials subscription, follow these steps to launch with CloudFormation.
There are four steps within CloudFormation:
- Create stack: Keep all default options here.
- Specify stack details: Configure based on your preferences. Note the domain name instructions in the section above. Defaults and suggestions are provided where appropriate. Feel free to use these!
- Configure stack options: Keep all default options here, but be sure to acknowledge the checkbox under Capabilities at the bottom of this screen.
- Review and create: After reviewing, click Submit!
Understanding user and group permissions
Following the installation of OMERO Plus using CloudFormation, you should have received the login credentials for a user called root via the AWS SecretsManager. Using this login, other users can be created. It is not recommended to continue to log in as root nor to share these credentials widely.
OMERO Plus uses both Users and Groups to share data with others and manage permissions. Before creating new users, create one or more Groups and choose an appropriate permission level. When creating new users, choose from the available User types and add them to the appropriate group(s).
Importing data
There are two ways to import data into OMERO Essentials.
Here, you will find examples of different import scenarios.
Using the desktop client OMERO.insight, will be the most beginner friendly way to get your data imported. However, depending on your data type, size and volume, you may find the desktop client limiting and therefore require use of the CLI.
Using OMERO.web
Once you have data viewable, you will likely want to view others’ data (where you have permissions) and manage your projects.
Data Management
- Viewing others’ data, browsing folders, viewing HCS data
- Managing images in datasets and projects
- Moving data between groups
- Moving data between groups: owners of data
- Moving data between groups: administrators
- Change ownership of data
- Exporting and downloading data
Annotating, filtering and searching data
- Learn how to add tags, key-value pairs and attachments and use these to filter your results.
- Searching for data
Open Source Plugins
OMERO Plus Essentials is compatible with the OMERO ecosystem and therefore is compatible with open-source plugins. However, as these are open source and not maintained and tested by Glencoe Software, you will be required to install and troubleshoot these as per the plugin instructions. There is plentiful documentation on these open source plugins here.
Using PathViewer
PathViewer is a product exclusive to Glencoe Software that is available to you as part of OMERO Plus Essentials. PathViewer is an interactive visualization, analysis, and annotation tool specifically tailored for the digital pathology workflow.
The videos below will guide you through the basics of using PathViewer.
- Open images in PathViewer or in PathViewer GRID directly from OMERO.web.
- Navigating images (i.e., pan and zoom) in PathViewer and PathViewer GRID and making use of keyboard shortcuts for a fast, effective workflow.
- Annotating images in PathViewer
- Annotating serial sections in PathViewer GRID
Troubleshooting
If you are still stuck, you can contact our support team at essentials-support@glencoesoftware.com