Exercise 2 - Tracking cancer cell migration in time-lapse movies

Cancer cell migration, image from Zenodo.

Download TIF file

• Open the above time-lapse sequence in Fiji and run the command: Plugins › Tracking › TrackMate

• You will be presented with a TrackMate window. Click Next.

• Select StarDist detector from the drop-down menu. Click Next.

  

  Segmentation detector

• You can now click on the Preview tab, to check how well StarDist is detecting the nuclei on the current slice. If detections look fine, click next to detect nuclei in the whole time-lapse sequence.
  

• Keep clicking Next button until you reach the Select a tracker window. Select Simple LAP tracker and click Next.
  Choose settings as in the image below and click Next.

  

  Simple LAP tracker

Tip

If you want to track splitting and/or merging events, then choose the LAP tracker, and tick the splitting/merging checkbox under settings.

• Keep clicking next until you reach the Display options window (see image below, left). Here, various display options for the tracks could be selected. Choose Show tracks backward in time. Play with different settings here and scroll through the stack to see the effect of these changes.

  Please explore the three tabs at the bottom - TrackScheme, Tracks and Spots. A lot of statistics is hidden there, such as the raw values for each nuclei in each frame of the time-lapse. All the statistics could be exported to a CSV file.
  

• Keep clicking next until you reach the last window called Select an action (see image below, right). Select Capture overlay and click Execute to generate a time-lapse movie with spots and tracks overlaid on top of the original data.
  

• A label time-lapse movie could also be generated by selecting Export label image from the drop-down list and clicking Execute.

  

  Display options

  

  Select an action

Final result:

Cell migration with tracks