Overview
Slide scanning is an excellent way to share and archive slides, perform image analysis, and create publication quality images. The Research Histology Laboratory provides an efficient and high-quality solution for viewing brightfield whole slide histologic images or sharing them with someone across campus or across the world. Scanned images and associated metadata are accessible through a web-based UI.
| OMERO is a database and image management tool that handles all your images in a secure central repository. Animal Care Services hosts an OMERO database instance that facilitates viewing, sharing, and annotating images for your research team and invited collaborators. |
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Services detail
The laboratory is equipped with an Olympus VS120 virtual slide microscope system for preparing high quality brightfield whole slide image scans at 10x-100x magnification. Scanned slides may be viewed at any magnification up to the scanning resolution. Online access to your whole slide images is provided through the OMERO web-based interface and desktop app. This allows your research team to access your whole slide images on computer for viewing and capturing publication quality snapshots. You can optionally have multiple online accounts created to collaborate with co-investigators by sharing scanned slides and annotations securely. Slide images are quickly available on the server after scanning and assigning to your account.
Getting access
OMERO accounts can be requested by submitting an OMERO request form.
Request Access to OMERO
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.
Connecting to the OMERO database
Our OMERO platform is kept up-to-date to provide the best performance and security. We are currently running OMERO.server 5.6.16 and OMERO.web 5.29.1. Please ensure your client software is compatible with these versions.
Once you have an OMERO account, you can log in and begin viewing images. You can log into your OMERO account on your computer using the OMERO.insight desktop client, or you can use the OMERO web interface through your Internet browser.
Logging in with OMERO.web (Internet browser)
Modern web viewer
Your images can be explored using OMERO.iviewer, a powerful web tool for viewing large, multi-dimensional datasets directly in your browser. It allows for adjusting rendering settings, exploring different Z-planes and time-points, and creating high-quality figure snapshots.
- Visit omero.animalcare.ubc.ca.
- Log in with your user ID and the password that was emailed to you upon your initial account request. The OMERO database password is not the same as your CWL password.
Note on OMERO.web features
The latest version of OMERO.web offers a robust set of features directly in your browser. While bulk image imports are typically handled by the desktop client or command-line tools, you can now perform many daily tasks, including creating and managing tags, directly within the web interface.
Logging in with OMERO.insight (desktop client)
Setup the software on your computer
- The ACS server is running the latest stable version of OMERO.server (5.6.16). To connect to the server, you will need to install a compatible version of the OMERO.insight desktop client. Please ensure you download a client version that is compatible with OMERO.server 5.6.16 to ensure full functionality and a stable connection.
- Open OMERO.insight and follow the configuration instructions to setup the connection to the ACS OMERO server. Under step 3 of the instructions, enter omero.animalcare.ubc.ca as the server address. The port address needs to be set to 4064.
- To log in, enter your username 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). The OMERO database password is not the same as your CWL password.
Training and support
Official OMERO Guides
The Open Microscopy Environment team provides excellent, step-by-step guides and video tutorials for learning how to use OMERO's features effectively.
Community Help Forum
For technical questions or issues with analysis workflows, the image.sc Forum is the official community support channel for OMERO and many other scientific imaging tools. You can search for answers to previous questions or post your own.
Third-party image processing software
OMERO is designed to integrate with powerful, open-source image analysis tools. You can easily connect OMERO to your favourite software to pull image data for analysis and push results back to the server for storage and collaboration.
ImageJ/Fiji: The most popular image analysis platform in life sciences. Use the OMERO plugin to browse your data on the server and open images in Fiji for processing and analysis.
Python
Use the powerful omero-py library to interact with the OMERO server programmatically. This is ideal for building custom analysis pipelines, performing batch processing, and automating workflows.
QuPath
A leading tool for digital pathology and whole-slide image analysis. The QuPath OMERO extension allows you to read images directly from the OMERO server and save analysis results, such as annotations and detections, back to OMERO.
- Guide: Using OMERO with QuPath
Citing our service
If you use images processed or hosted by our lab in your publications, we would appreciate your acknowledgement. We suggest the following phrasing: "Histology services and/or image hosting were provided by the UBC Animal Care Services Research Histology Laboratory."
If a member of our staff has provided significant intellectual and technical contributions to your project, such as developing novel protocols, performing complex data analysis, or contributing to the interpretation of results, we ask that you consider co-authorship for that staff member.