Analyze OMERO timelapse images using the TrackMate User Interface

In this example we open in Fiji an image stored in an OMERO server and use TrackMate to analyze it.


In this section, we show how to use TrackMate via its User Interface. The manual steps are essential to determine the suitable parameters to analyze the images. Note that when using the TrackMate User Interface, the generated tracks cannot be saved as ROIs into OMERO.server.


  • Install Fiji on the local machine with the OMERO.insight-ij plugin. The installation instructions can be found in the Fiji guide.



  1. Launch Fiji.

  2. Go to Plugins > OMERO > Connect To OMERO. This will show a login screen where you can enter the name of the server to connect to, the username and password. The OMERO plugin will allow you to browse your data in a similar manner to OMERO.web.

  3. In the OMERO login dialog, click the wrench iconimage1 and then add the server address in the dialog. By default, only “localhost” is listed. Click on the plus icon to add a new line to the list and type into the line the server address.

  4. Click Apply.

  5. Enter your credentials and click Login.

  6. Browse the Dataset where your image to be tracked is located, e.g. artificial-trackmate.

  7. Double-click on the FakeTracks.tif Image to open it in Fiji.

    1. Make sure it is opened using the Hyperstack viewer. This option depends on what you did last time when using your Fiji.

    2. In case you are not sure, Open Plugins > Bio-Formats > Bio-Formats importer and then select any image on your local computer to open it in Fiji. In the popup dialog, in the top left dropdown menu.

    3. Select Hyperstack and click OK. Then, close and re-open the FakeTracks.tif Image from OMERO.

  8. Go to Plugins > Tracking > TrackMate.

  9. Click Next in the first dialog that pops up.

  10. A new dialog pops up indicating to select a detector. Select the DoG detector. Click Next.

    1. Set the Estimated blob diameter to 5.0

    2. Set the Threshold to 5.0

  11. Click the Preview button to find spots. 4 spots should be found.

  12. Click the Next button several times until you get to the Select a view dialog.

  13. Select the HyperStack Displayer view

  14. Click the Next button twice until you get to the Select a tracker window. Select the LAP Tracker.

  15. Click the Next button several times until a dialog with three tabs pops up

  16. Select the Tracks tab to display the Tracks.

  17. Click Next until you get to Select an action dialog.

    1. Select the option Capture overlay

    2. Click Execute.

  18. Click OK in the following dialog, leaving the defaults (the whole stack will be captured).

  19. New image appears. Select it. This new Image can then be imported as an OME-TIFF using Plugins > OMERO > Save Image(s) to OMERO. The tracks will be part of the generated OME-TIFF and the timepoints will be captured as z-sections.