Imaging Data Management with OMERO

Oct 22, 2020

OMERO is image management software that allows you to organize, view, annotate, analyze, and share your data from a single centralized repository. With OMERO, you and your collaborators can access your images from any computer without having to download the images directly to your machine. The following tutorial will cover importing and managing data with OMERO, organizing and annotating images, and incorporating OMERO with your current image analysis pipelines.

1. How OMERO Works

OMERO is client-server software. The OMERO server, which is hosted on the UVa HPC cluster Rivanna, manages your images and data. Using client software like the OMERO desktop app, OMERO web application, or third-party software such as Fiji/ImageJ, you can communicate with the OMERO server and have images delivered to your computer for viewing or processing and analysis. This allows you to keep all your data in one centralized storage location, with OMERO as a thin layer on top to manage and organize all your different images and metadata.

Integrating OMERO into your image analysis pipeline only requires minor additions to your existing workflow, as seen in the chart below. The main difference is that rather than managing the location of images and directly locating them yourself, you are allowing OMERO to manage the images and deliver them to your image processing software tools.

Common Imaging Analysis Workflow

Without OMERO With OMERO Integration
1. Acquire images into acquisition directory on microscope computer 1. Acquire images into acquisition directory on microscope computer
2. Copy acquisition directory to permanent storage (hard drive, Rivanna, lab workstation) 2. Copy acquisition directory to permanent storage (hard drive, Rivanna, lab workstation) and import images to OMERO database
3. Preprocess images 3. Preprocess images pulled from OMERO
4. Save preprocessed images to new directory 4. Import preprocessed images to OMERO
5. Analyze preprocessed images 5. Analyze preprocessed images pulled from OMERO
6. Save results to new file 6. Save results as annotations or attachments in OMERO



2. Getting Started

Requesting an UVA OMERO Account

OMERO accounts can be requested through this webform.

Optionally, you can also indicate the type of permissions you would like members of your group to have. By default, all group members will be able to view their own and others' data. Group members can make annotations on each other’s data, but cannot modify or delete another member’s data.

For details on obtaining more restrictive or flexible permissions for your group members, please read the Group/User Permissions section.


Logging into Your Account

Once you have an OMERO account you can log in and begin importing images. You can log into your OMERO account on your computer using the desktop app, OMERO.insight, or you can log into OMERO online and access your images in your web browser via OMERO.web.

Note: The OMERO web client is not capable of data import. To import images, use the desktop app OMERO.insight.

Logging in with OMERO.insight

  1. Download the OMERO.insight app and follow installation instructions: https://help.openmicroscopy.org/getting-started-5.html#installing

  2. Open OMERO.insight. You should see the following login screen.

  3. Click the wrench icon to open the Servers menu. You should see localhost 4064 listed under Server Address and Port.

  4. Click the + icon and enter omero.hpc.virginia.edu to add the UVa OMERO server. Click Apply.

  5. Enter your computing ID (e.g. mst3k) in the Username field. For password, enter the password emailed to you after your initial account request (you will be able to change this after logging in for the first time). Click Login.

Logging in with OMERO.web

  1. Go to omero.hpc.virginia.edu.

  2. Log in with your computing ID (e.g. mst3k) and the password that was emailed to you upon your initial account request.

    Important things to note when using OMERO.web:

    • OMERO.web cannot be used to import images

    • Tags cannot be created in OMERO.web

    • To use OMERO.web off-grounds, you must be connected to the UVa Anywhere VPN. Instructions for installing and using the VPN can be found on the UVa ITS Service Now page.


Managing Your Account

After logging into OMERO for the first time, it is highly recommended that you change your password. You can manage your account settings using either OMERO.insight or OMERO.web. If you cannot remember your Omero account password, email hpc-support@virginia.edu to have it reset.

Using OMERO.insight

  1. After logging into OMERO using the desktop app, click the Administration tab in the side menu.

  2. Click the arrow next to your lab/group account name, then click your own name to open the user account menu.

  3. Enter your new password in the New Password field and click the Change Password button.

    You can also change other settings in your account such as your default group account and email address.

Using OMERO.web

  1. After logging in to OMERO in your web browser, click your name in the top right corner of the screen and then click User settings.

  2. Click the Change Password button. Enter your current password and your desired new password. Click OK when complete.

3. Group/User Permissions

OMERO users can have one of two user roles, Group owner or Group member.

As a Group owner of a lab/group account, you can edit the permissions of other users in your group. This can be done from the desktop app OMERO.insight.

  1. In the Administration tab of the sidebar menu, click the name of your group. This will open the Group settings menu.

  2. Select your desired permissions and click Save.


There are several different permissions settings, which are described below. By default, all group permissions are set to Read-Annotate.

Permission Type Description Example
Private The Group owner can see all Group members and view their data, but cannot add annotations. Group members can only view and annotate their own data. This permissions setting does not allow for much collaboration. A PI is a Group owner with student Group members. The PI is able to see each student’s data, but the students are only able to see and annotate their own data.
Read-Only The Group owner can see all Group members' data and add annotations. Group members can see other members and their data. A PI as Group owner can view and annotate student Group members' data such as marking regions of interest to the images. Students are able to view each other’s data but not add annotations.
Read-Annotate The Group owner and Group members can view and annotate each other’s data. No one can overwrite or remove data. Several people are working together on data for a publication. As Group members, all are able to read and annotate each other’s data.
Read-Write The Group owner and Group members can view, annotate, modify, and delete each other’s data. A group is working on data for a publication in a way that requires them to be able to modify each other’s work.

4. Importing Images

Import Using the OMERO.insight

Images can be imported using the desktop app OMERO.insight. Images can be added to OMERO individually or in folders.

  1. Click the Importer tool icon in the top toolbar. This will open the OMERO Importer tool.

  2. In the left window pane of the Importer tool, navigate to the directory containing the images or folders of images that you want to import to the OMERO database.

  3. Click on the files or folders containing the images you want to import. To select multiple items, hold down the Ctrl (Windows) or Command (Mac) key while clicking. Once you are finished making your selections, click the “>” button. This will open the Import Location menu.

  4. In the Import Location menu, you can choose a Project, Dataset, or Screen* to import your images to, allowing you to organize your images before they are uploaded to the OMERO database. If your desired Project/Dataset/Screen doesn’t exist yet, you can click the New button to create a new one.

    Please visit the section on Organization Techniques to learn more about projects and screens.

  5. Once your data and locations are selected, click the Add to the Queue button. This will close the Import Location menu and return you to the Importer tool. Click the Import button in the bottom right corner of the Importer tool to begin uploading your images.

    You can monitor the progress of your import and begin viewing images in OMERO before the entire upload is complete.

    Once imported, you will see any new Projects or Datasets you created in the left window pane. If you expand the Datasets, thumbnail versions of your images will appear in the center window pane of the OMERO.insight app.

5. Viewing Images

OMERO is great for viewing images without having to download them or copy them locally to your machine. Viewing images using the desktop app and web app is largely similar; however, you can define regions of interest (ROIs) with OMERO.insight.

Viewing with OMERO.insight

As shown in the last step of the Importing Images section, thumbnail versions of your images will appear in the center window pane of the OMERO.insight app. Clicking on an image will select it, and will present the image’s metadata in the right window pane.

To view the full-size image, double-click the corresponding thumbnail or click the Full Viewer button under the General tab of the right window pane. This will open the Image Viewer.

Viewing with OMERO.web

Like with OMERO.insight, thumbnails of your images will display in the center window pane of OMERO.web when you select a Dataset. Click on an image to select it and display the image’s metadata.

You can view the full-size version of your image by double-clicking the image or by clicking the Full Viewer button under the General tab of the right window pane. This will open the Image Viewer in a new tab in your browser.

For more documentation on the OMERO image viewer, please visit: https://www.openmicroscopy.org/omero/iviewer/

6. Organization Techniques

Most researchers organize their data with some hierarchical structure. Often researchers use nested folders with descriptive names to indicate which experiment data belong to or to indicate when the data were collected. OMERO offers two schema for organizing your images in a similar fashion.

Organizing Data By Project

Data can be organized using the following hierarchy, from top to bottom:

  1. Project: The highest level organizational divider or “folder type” in OMERO. Projects can contain Datasets, but not individual images.

  2. Dataset: The next organizational level after Project. Datasets contain images. You can store a Dataset within a Project, or the Dataset can exist on its own outside of any Projects. Multiple Datasets can be stored within a project.


Organizing Data By Screens

Data can also be organized by Screens and Well Plates. The hierarchy for this organizational schema is (from highest to lowest level):

  1. Screens: The highest organizational level. This typically refers to some sort of phenotypic screening. Screens cannot contain images.

  2. Plate: The next level of organization. This typically refers to a microarray well plate. Plates can be stored under a Screen, or can exist outside of a Screen.

  3. Well: This usually refers to a single well from a well plate. Wells can only exist within a Plate (It is possible for wells to contain multiple images)

In order to import and organize data in this way, it is necessary to use Python and OMERO’s Python package. Advanced tutorials for writing your own Python scripts will be available on this workshop site in the near future!

7. Annotating Data

Documentation on annotating data can be found here: https://help.openmicroscopy.org/managing-data.html#annotating

8. Exporting Data

You can export data managed by OMERO to your local computer. You can export an image in its original file format or download it as a JPEG, PNG, TIFF, or OME-TIFF.

Documentation on exporting data can be found here: https://help.openmicroscopy.org/export.html

9. Image Analysis with OMERO

OMERO is compatible with a variety of third-party image processing software packages. Using these OMERO-software bindings, you can import images from OMERO to your software such as Fiji or Python, and then process and analyze them as usual. You can then export any results or preprocessed images back to OMERO.

Using OMERO to serve images to your analysis software has many benefits over more traditional methods of reading imaging data. With OMERO, there is no need to download the images directly to your local machine.

ImageJ/Fiji

Images managed by OMERO can be imported using the ImageJ/Fiji plugin for OMERO. Detailed instructions for installing and using the plugin can be found in OMERO’s online documentation at https://help.openmicroscopy.org/imagej.html or our Image Processing with Fiji and Omero workshop.

MATLAB and Python

You can install packages to connect to OMERO with MATLAB or Python. These packages include functions for connecting to the OMERO server and reading and exporting data.

OMERO’s online documentation for the OMERO MATLAB language bindings can be found at https://docs.openmicroscopy.org/omero/5.5.0/developers/Matlab.html

More information on the OMERO Python language bindings can be found at https://docs.openmicroscopy.org/omero/5.5.0/developers/Python.html.

More in-depth tutorials and sample scripts will be available on our workshop site soon!