2D + Time Object Tracking Using Fiji and ilastik.

Tracking cells is one of the main challenges in biology, as it often requires time-consuming annotations and the images can have a low signal-to-noise ratio while containing a large number of cells. Here we present two methods for detecting and tracking cells using the open-source Fiji and ilastik frameworks. A straightforward approach is described using Fiji, consisting of a pre-processing and segmentation phase followed by a tracking phase, based on the overlapping of objects along the image sequence. Using ilastik, a classifier is trained through manual annotations to both detect cells over the background and be able to recognize false detections and merging cells. We describe these two methods in a step-by-step fashion, using as example a time-lapse microscopy movie of HeLa cells.