Visualization and quantitative analyses for mouse embryonic stem cell tracking by manipulating hierarchical data structures using time-lapse confocal microscopy images

We present a cell tracking method for time-lapse confocal microscopy (3D) images that uses dynamic hierarchical data structures to assist cell and colony segmentation and tracking. During the segmentation, the cell and colony numbers and their geometric data are recorded for each 3D image set. In tracking, the colony correspondences between neighboring frames of time-lapse 3D images are first computed using the recorded colony centers. Then, cell correspondences in the correspondent colonies are computed using the recorded cell centers. The examples show the proposed cell tracking method can achieve high tracking accuracy for time-lapse 3D images of undifferentiated but self-renewing mouse embryonic stem (mES) cells where the number and mobility of ES cells in a cell colony may change suddenly by a colony merging or splitting, and cell proliferation or death. The geometric data in the hierarchical data structures also help the visualization and quantitation of the cell shapes and mobility.