The visualization of the dynamic behavior of immune cells using time-lapse video microscopy plays an important role in modern immunology. To draw robust conclusions, quantification of such cell migration data is required. This is far from trivial because imaging experiments are associated with various artifacts that can affect the estimated positions of the immune cells under analysis. We develop methods to correct for these artifacts and employ the most robust measures for determining cell motility and directed migration. These methods are tested on spatially explicit models of T cell migration in lymph nodes (LNs). We show that several dynamical properties of T cells are a consequence of the densely packed LN environment. Because imaging is typically restricted to experiments lasting 1 h, and because T cell-DC conjugates frequently move into and out of the imaged volume, it is difficult to estimate the true duration of interactions from contact data. We propose a method to properly make such an estimate of the average of the contact durations. We also use these techniques to analyze the migration of antigen specific CD8 T cells in the skin after localized infection with herpes simplex virus. This provided evidence for directed migration towards the infection.
