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 algorithms. We describe ChipSeg, a computational tool that segments bacterial and mammalian cells cultured microfluidic devices imaged by microscopy, which can be also the context of control. The method based on thresholding uses same core functions for both cell types. It allows us segment individual high density devices, quantify fluorescent protein expression over experiment, track cells. ChipSeg enables robust experiments easily customized other experimental settings research aims.