Import a slide into OMERO

This page walks through importing one OME-TIFF slide from your Windows Documents folder into OMERO, filing it under a project named for the course and a dataset named for the topic. The worked example uses the project MedYear1 and the dataset GeneralHistology.

Imports run through OMERO.insight, the desktop client. The catalogue and OMERO.web cannot upload slide files themselves.

Before you start

• OMERO.insight installed on your PC, from the OMERO downloads page.
• Your OMERO username and password, and membership of the group the slides belong in.
• The slide saved locally at C:\Users\<your username>\Documents\. If Documents syncs to OneDrive, right-click the file and choose Always keep on this device first, so Insight reads a real file rather than a placeholder.
• Any companion files that came with the OME-TIFF kept in the same folder. A fileset split across folders will not import cleanly.
• Campus network or VPN, so the client can reach the server on port 4064.

Where the slide ends up

Keep to that shape across the archive: one project per course, one dataset per topic within it. It keeps the catalogue's links predictable and makes later duplication into teaching accounts far simpler.

Importing the slide

1. Sign in to OMERO.insight

   Open OMERO.insight. In the login window, click the spanner or gear beside the server name to check the server address and port, then enter your username and password and click Login.

   

2. Check you are in the right group

   The group selector sits at the top of the data browser. If you belong to more than one group, switch to the one that owns the teaching archive before creating anything — a project created in the wrong group has to be moved afterwards.

   

3. Create the project

   Right-click an empty part of the data tree and choose New → Project. Name it MedYear1, add a short description such as the course title and the academic session, and save.

   If the project already exists, skip to the next step. Do not create a second project with a variant spelling.

   

4. Create the dataset inside it

   Right-click MedYear1 and choose New → Dataset. Name it GeneralHistology. Creating it from the project this way links the two automatically; a dataset made at the top level has to be dragged into place later.

   

5. Open the importer

   Choose File → Import Data…, or click the import arrow on the toolbar. The importer opens in its own window: a file browser on the left, the import queue on the right.

   

6. Find the slide in Documents

   In the file browser, navigate to C:\Users\<your username>\Documents and select your .ome.tiff file. Click the arrow, or Add to the Queue, to move it across.

   Insight lists the file once even when the fileset is several files on disk. That is expected — it imports the set as a unit.

   

7. Set the destination

   In the import location panel, set the group, then pick MedYear1 as the project and GeneralHistology as the dataset. Check this panel every time: the importer remembers the last destination you used, which is the most common way slides end up in the wrong dataset.

   

   Note. Leave the file-naming and annotation options at their defaults unless you have a reason to change them. Tags are easier to add after import, once you can see the image.

8. Start the import

   Click Import. Each file shows a progress bar while it uploads, then reports that the server is processing it. Whole-slide images are large, so expect the upload to take a while and leave the window open until it finishes.

   

9. Check it arrived

   Back in the data browser, refresh the tree and expand MedYear1 → GeneralHistology. The slide should be listed with a thumbnail. Open it and confirm the whole slide is there and the magnification looks right.

   

   Note. A grey or missing thumbnail immediately after a large import usually means the server is still building the zoom pyramid. Give it a few minutes and refresh before assuming anything is wrong.

If something goes wrong

The client cannot reach the server

Check you are on the campus network or VPN, and that the port in the server settings is 4064. A connection that hangs rather than refusing is usually the firewall.

The file greys out in the browser, or Insight says it cannot read it

Most often a OneDrive placeholder that has not been downloaded, or a file still being written. Make it available offline, then reopen the importer.

The import fails part way through

Note the message shown against the file and try that single slide again on its own. If it fails a second time, send the message and the file name to the catalogue administrator rather than retrying repeatedly.

The slide imported into the wrong dataset

Nothing is lost. Drag the image to the correct dataset in the data tree, or use Move to from its right-click menu. Do not re-import it.

The image opens but looks blank or very low resolution

Wait for pyramid generation to finish, then reopen it. If it is still wrong, the source file may be incomplete — check it opens correctly on your PC before importing again.

Stuck on something not covered here? Contact the archive team.