Cell Tracking


Phase Contrast Images

Wound Healing Assay

In cooperation with Biocenter Oulu we have developed a solution for analyzing dynamic behavior of cells in phase-contrast images. Our current cell tracking system can track individual cells and provide detailed spatio-temporal measurements of cell behaviors including cell count and migration speed together with direction.


To analyze cell migration characteristics in time-lapse movies, the MSER-based automatic cell detection was accompanied by a Kalman filter multiobject tracker. This allowed quantitative cell motion analysis resulting in accurate measurements of the migration magnitude and direction of individual cells, as well as characteristics of collective migration of cell groups.


Our results demonstrate that MSER accompanied by temporal data association is a powerful tool for accurate and reliable analysis of the dynamic behaviour of cells in phase-contrast image sequences. These techniques tolerate varying and nonoptimal imaging conditions and due to their relatively light computational requirements they should help to resolve problems in computationally demanding and often time-consuming large-scale dynamical analysis of cultured cells.

Segmentation (MSER):

MSER-based segmentation

MSER segmentation mask

Example of extracted cell trajectories in a woundhealing assay case:


In video below, motion of cells is illustrated with arrows and colors.



Kaakinen M, Huttunen S, Paavolainen L, Marjomäki V, Heikkilä J & Eklund L (2014)
Automatic detection and analysis of cell motility in phase-contrast time-lapse images using a combination of maximally stable extremal regions and Kalman filter approaches.
Journal of Microscopy, January, 253(1):65-78.



Last updated: 5.10.2015