Data management using OMERO
OMERO is an image data management tool which allows you to easily view, annotate, analyse, share your data and prepare figures for publications or posters.
Using the LCI OMERO server
You can use the LCI OMERO server for data management, sharing and much more.
- The KI OMERO server is located inside KI so it is safe to use. The server can be safely accessed online from anywhere. You can mark your best images with a star to be able to easily find them in a few months.
- You can attach a protocol, an article or a presentation to the images.
- Most importantly the images are in the original format delivered by the microscope, so all the metadata (details of the acquisition) is there. This way, you will always be able to tell which microscope you acquired the images and which laser power you used.
- You can tag the images so that you can later filter all the images you acquired on one microscope or using samples labelled with your favourite antibody. Tagging the images is easy and can be done in batches, when uploading the data.
- OMERO.figure is a fantastic tool to easily make figures for publication. All the channels images are zoomed in the same way and aligned automatically, including the name of the labelled molecules, the scale bar, etc.
How to get started
a. Create an account
Ask the LCI staff to create an account for you on the LCI OMERO server. We will send you an email with your credentials.
b. Download the OMERO.Insight software and connect to the server
Download the OMERO.Insight client software to your computer (for Windows users, download the .exe file).
The address of the LCI core facility OMERO server is: omero.ki.se. Follow the instructions in this video to install OMERO.Insight and connect to the LCI OMERO server.
If you get a message when downloading saying that ‘the developer has not been verified’, do the following:
- Open your System Preferences, you can do it if you click on Apple icon in top left of your Mac screen, see [1]
- Find the “Security and Privacy” icon and click onto it [2]
- Make sure you are on the “General” tab in the window which newly opens [3]
- Click “Open Anyway”
- In the new dialog, click “Open” [4]
- In rare cases you might also need to close the lock on the OMERO.Insight login page.
c. Change your password
Open your browser (NOT the OMERO.Insight software) and type omero.ki.se in the address bar. Login with your credentials. The first time you log in, change your password by clicking on your name at the top right and selecting User settings. It is best to use a password that is not the same as your KI password to avoid getting confused when you change your KI password.
How to use OMERO
Uploading data to the OMERO server
To upload data to the OMERO server, use the OMERO.insight software installed on your computer. Follow the instructions in the video or in the written text to upload all your images to the OMERO server. Only upload images in the original format delivered by your microscope.
Once the upload is finished, close OMERO.Insight as it is ONLY used to upload data, NOT to work on them. To work with your uploaded data, open omero.ki.se in your browser.
Work with your images and make figures/posters with OMERO.figure
Note that OMERO.figure and OMERO.iViewer are already installed on the LCI OMERO server. You do not need to download them.
Double click on an image to open the iViever. How to use OMERO.iViewer to work on images: video
OMERO.figure will allow you to:
- Use your images in the original format (no need to convert)
- Add a scale bar and any annotation you want (arrows, text, freehand form…)
- Adjust brightness and contrast
- Split the image to show the overlay in colour and each channel in black and white
- Change the name of the channels and place the name e.g. vertically or horizontally near each panel
- Include any segmentation that you have done in another software
- Show a full image as well as a zoomed in part of that image. You can move the zoomed in part around in the full image and display will automatically update everything
- All images can automatically be aligned just in one click
Creating OMERO.figures: video
Sharing data with KI or external collaborators
Ask the LCI to create an account for your boss or your collaborator. We will need the name, which group the collaborator should be associated with and the level of permissions (only viewing or able to download or to modify).
To share data, place it in the public group. The images are moved, not duplicated. There is a way to duplicate it first. Share the link from the public group.