10.1021/acsomega.0c03906
https://zenodo.org/records/4822255
oai:zenodo.org:4822255
de Cesare, Irene
Irene
de Cesare
Department of Engineering Mathematics, University of Bristol, Woodland Road, Bristol BS8 1UB, U.K.
Zamora-Chimal, Criseida G.
Criseida G.
Zamora-Chimal
Department of Engineering Mathematics, University of Bristol, Woodland Road, Bristol BS8 1UB, U.K. - BrisSynBio, Life Sciences Building, University of Bristol, Tyndall Avenue, Bristol BS8 1TQ, U.K.
Postiglione, Lorena
Lorena
Postiglione
Department of Engineering Mathematics, University of Bristol, Woodland Road, Bristol BS8 1UB, U.K.
Khazim, Mahmoud
Mahmoud
Khazim
Department of Engineering Mathematics, University of Bristol, Woodland Road, Bristol BS8 1UB, U.K. - School of Cellular and Molecular Medicine, University of Bristol, University Walk, Bristol BS8 1TD, U.K.
Pedone, Elisa
Elisa
Pedone
Department of Engineering Mathematics, University of Bristol, Woodland Road, Bristol BS8 1UB, U.K. - School of Cellular and Molecular Medicine, University of Bristol, University Walk, Bristol BS8 1TD, U.K.
Shannon, Barbara
Barbara
Shannon
BrisSynBio, Life Sciences Building, University of Bristol, Tyndall Avenue, Bristol BS8 1TQ, U.K. - School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, U.K.
Fiore, Gianfranco
Gianfranco
Fiore
Department of Engineering Mathematics, University of Bristol, Woodland Road, Bristol BS8 1UB, U.K. - BrisSynBio, Life Sciences Building, University of Bristol, Tyndall Avenue, Bristol BS8 1TQ, U.K.
Perrino, Giansimone
Giansimone
Perrino
Telethon Institute of Genetic and Medicine Via Campi Flegrei 34, 80078 Pozzuoli, Italy
Napolitano, Sara
Sara
Napolitano
Telethon Institute of Genetic and Medicine Via Campi Flegrei 34, 80078 Pozzuoli, Italy
di Bernardo, Diego
Diego
di Bernardo
0000-0002-1911-7407
Telethon Institute of Genetic and Medicine Via Campi Flegrei 34, 80078 Pozzuoli, Italy - Department of Chemical, Materials and Industrial Production Engineering, University of Naples Federico II, 80125 Naples, Italy
Savery, Nigel J.
Nigel J.
Savery
0000-0002-0803-4075
BrisSynBio, Life Sciences Building, University of Bristol, Tyndall Avenue, Bristol BS8 1TQ, U.K. - School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, U.K.
Grierson, Claire
Claire
Grierson
0000-0002-4000-0975
BrisSynBio, Life Sciences Building, University of Bristol, Tyndall Avenue, Bristol BS8 1TQ, U.K. - School of Biological Sciences, University of Bristol, Tyndall Avenue, Bristol BS8 1TQ, U.K.
di Bernardo, Mario
Mario
di Bernardo
0000-0002-2171-4745
Department of Engineering Mathematics, University of Bristol, Woodland Road, Bristol BS8 1UB, U.K. - BrisSynBio, Life Sciences Building, University of Bristol, Tyndall Avenue, Bristol BS8 1TQ, U.K. - Department of EE and ICT, University of Naples Federico II, Via Claudio 21, 80125 Naples, Italy
Marucci, Lucia
Lucia
Marucci
0000-0002-7553-6358
Department of Engineering Mathematics, University of Bristol, Woodland Road, Bristol BS8 1UB, U.K. - BrisSynBio, Life Sciences Building, University of Bristol, Tyndall Avenue, Bristol BS8 1TQ, U.K. - School of Cellular and Molecular Medicine, University of Bristol, University Walk, Bristol BS8 1TD, U.K.
ChipSeg: An Automatic Tool to Segment Bacterial and Mammalian Cells Cultured in Microfluidic Devices
Zenodo
2021
2021-01-18
https://zenodo.org/communities/cosy-bio
https://zenodo.org/communities/eu
Creative Commons Attribution 4.0 International
Abstract
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 time-lapse experiment, and to track individual mammalian cells. ChipSeg enables robust segmentation in external feedback control experiments and can be easily customized for other experimental settings and research aims.
European Commission
10.13039/501100000780
766840
Control Engineering of Biological Systems for Reliable Synthetic Biology Applications