Journal article Open Access

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; Savery, Nigel J.; Grierson, Claire; di Bernardo, Mario; Marucci, Lucia


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    "description": "<p><strong>Abstract</strong></p>\n\n<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 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.</p>", 
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    "title": "ChipSeg: An Automatic Tool to Segment Bacterial and Mammalian Cells Cultured in Microfluidic Devices", 
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      "pages": "2473\u20132476", 
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    "publication_date": "2021-01-18", 
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        "affiliation": "Department of Engineering Mathematics, University of Bristol, Woodland Road, Bristol BS8 1UB, U.K.", 
        "name": "de Cesare, Irene"
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        "affiliation": "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.", 
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        "affiliation": "Department of Engineering Mathematics, University of Bristol, Woodland Road, Bristol BS8 1UB, U.K.", 
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        "affiliation": "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.", 
        "name": "Khazim, Mahmoud"
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        "affiliation": "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.", 
        "name": "Pedone, Elisa"
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        "affiliation": "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.", 
        "name": "Shannon, Barbara"
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      {
        "affiliation": "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.", 
        "name": "Fiore, Gianfranco"
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        "affiliation": "Telethon Institute of Genetic and Medicine Via Campi Flegrei 34, 80078 Pozzuoli, Italy", 
        "name": "Perrino, Giansimone"
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        "affiliation": "Telethon Institute of Genetic and Medicine Via Campi Flegrei 34, 80078 Pozzuoli, Italy", 
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        "affiliation": "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", 
        "name": "di Bernardo, Diego"
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