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

Overview

Journal ACS Omega

Publisher American Chemical Society

Specialty Chemistry

Date 2021 Feb 8

PMID 33553865

Citations 4

Authors

Irene de Cesare

Criseida G Zamora-Chimal

Lorena Postiglione

Mahmoud Khazim

Elisa Pedone

Barbara Shannon

Gianfranco Fiore

Giansimone Perrino

Sara Napolitano

Diego di Bernardo

Nigel J Savery

Claire Grierson

Mario di Bernardo

Lucia Marucci

Affiliations

Soon will be listed here.

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.

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