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
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)
- 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 when using the OMERO web client interface:
- Images cannot be imported using OMERO.web
- Tags cannot be created in OMERO.web
Logging in with OMERO.insight (desktop client)
Setup the software on your computer
- The ACS server is running OMERO.server 5.6.3. In order to connect to that server, you need to first install the compatible Windows, Mac, or Linux client. Please download the file appropriate for your computer, install the client, and follow these installation instructions.
- 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.
Third-party image processing software
OMERO is compatible with a variety of third-party image processing software packages. You can import images from OMERO to your software such as Fiji or Python, and then process and analyze them. You can then export any results or preprocessed images back to OMERO.
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.
MATLAB
You can install packages to connect to OMERO with MATLAB. These packages include functions for connecting to the OMERO server and reading and exporting data. OMERO’s online documentation for analyzing OMERO data using MATLAB can be found here.
QuPath
Developed at the University of Edinburgh, QuPath is a comprehensive free open source desktop software application designed specifically to analyze whole slide images. Its primary use is biomarker analysis and immunohistochemical quantification, but it has also been used for tumor analysis on H&E. You can find online documentation on installing and viewing images on the QuPath website.