ChipSeg: an automatic tool to segment bacterial and mammalian cells cultured in microfluidic devices

Extracting quantitative measurements from time-lapse images is necessary in external feedback control applications, where segmentation results are used to inform control algorithms. We describe ChipSeg, a computational tool to segment bacterial and mammalian cells cultured in microfluidic devices and imaged by time-lapse microscopy, which can be used also in the context of external feedback control. The method is based on thresholding and uses the same core functions for both cell types. It allows to segment individual cells in high cell-density microfluidic devices, to quantify fluorescence protein expression over a time-lapse experiment and to track individual mammalian cells. ChipSeg enables robust segmentation in external feedback control experiments and can be easily customised for other experimental settings and research aims.