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ChipSeg: An Automatic Tool to Segment Bacterial and Mammalian Cells Cultured in Microfluidic Devices

de Cesare, Irene; Zamora-Chimal, Criseida G.; Postiglione, Lorena; Khazim, Mahmoud; Pedone, Elisa; Shannon, Barbara; Fiore, Gianfranco; Perrino, Giansimone; Napolitano, Sara; di Bernardo, Diego; ...
Open Access
Abstract
<p><strong>Abstract</strong></p> <p>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 that segments 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 us to segment individual cells in high cell density microfluidic devices, to quantify fluorescent protein expression over a tim...
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Funded by
EC| COSY-BIO
Project
COSY-BIO
Control Engineering of Biological Systems for Reliable Synthetic Biology Applications
  • Funder: European Commission (EC)
  • Project Code: 766840
  • Funding stream: H2020
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