How to track the distance that cells travel using Icy?

I have a video with moving cells and my goal is to receive speed of each cell. So, first I use Spot Detector and then Track Manager to measure distance that cells travel, but for some reason program splits the trajectory of one cell into several fragments and considers that this is not the movement of one cell for a certain time, but the sequential movement of several cells.

On this image you can see the trajectories not as lines, but as set of points. Maybe I use wrong parameters for tracking but I’m new to use Icy so I’ll be grateful for any suggestions.

Dear Alina,

I am inviting @Stephane to join the discussion about tracking. Please be patient as Stephane is busy with our new Icy release and the preparation of the I2K2020 Conference (happening next week).
Maybe Thibault @lagache has also some ideas on this issue.

Best regards,

Dear Alina,
It seems that your cells are not properly tracked. This might be due to missing detections over a couple frames (>5 typically). In that case, the tracking algorithm (Spot tracking I imagine?) cannot close the gap for missing detections and will create 2 tracks: 1 before missing detections and one after…
To solve this issue, you can try to tune Spot detector (scale & threshold), or, if your cells are moving in the same direction use EMC2 algorithm that can help to close your gaps.
Hope that will help
Thibault Lagache


I increased average length of displacement between two frames to 30 and it helped me to get necessary tracks.


Thanks a lot,