{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,20]],"date-time":"2026-03-20T15:26:18Z","timestamp":1774020378715,"version":"3.50.1"},"reference-count":39,"publisher":"Oxford University Press (OUP)","issue":"16","license":[{"start":{"date-parts":[[2022,6,25]],"date-time":"2022-06-25T00:00:00Z","timestamp":1656115200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Pentecost Family Foundation and Pentecost Family Myeloma Research Center (PMRC) at Moffitt Cancer Center"},{"name":"H. Lee Moffitt Cancer Center Physical Sciences in Oncology","award":["1U54CA193489-01A1"],"award-info":[{"award-number":["1U54CA193489-01A1"]}]},{"name":"Lee Moffitt Cancer Center\u2019s Team Science Grant"},{"name":"Miles for Moffitt Foundation"},{"name":"Cancer Center Support","award":["P30-CA076292"],"award-info":[{"award-number":["P30-CA076292"]}]},{"name":"Moffitt Cancer Center. Access to primary cells was made possible through the Total Cancer Care Protocol at the Moffitt Cancer Center"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,8,10]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Motivation<\/jats:title><jats:p>Time-lapse microscopy is a powerful technique that relies on images of live cells cultured ex vivo that are captured at regular intervals of time to describe and quantify their behavior under certain experimental conditions. This imaging method has great potential in advancing the field of precision oncology by quantifying the response of cancer cells to various therapies and identifying the most efficacious treatment for a given patient. Digital image processing algorithms developed so far require high-resolution images involving very few cells originating from homogeneous cell line populations. We propose a novel framework that tracks cancer cells to capture their behavior and quantify cell viability to inform clinical decisions in a high-throughput manner.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>The brightfield microscopy images a large number of patient-derived cells in an ex vivo reconstruction of the tumor microenvironment treated with 31 drugs for up to 6 days. We developed a robust and user-friendly pipeline CancerCellTracker that detects cells in co-culture, tracks these cells across time and identifies cell death events using changes in cell attributes. We validated our computational pipeline by comparing the timing of cell death estimates by CancerCellTracker from brightfield images and a fluorescent channel featuring ethidium homodimer. We benchmarked our results using a state-of-the-art algorithm implemented in ImageJ and previously published in the literature. We highlighted CancerCellTracker\u2019s efficiency in estimating the percentage of live cells in the presence of bone marrow stromal cells.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>https:\/\/github.com\/compbiolabucf\/CancerCellTracker.<\/jats:p><\/jats:sec><jats:sec><jats:title>Supplementary information<\/jats:title><jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac417","type":"journal-article","created":{"date-parts":[[2022,6,25]],"date-time":"2022-06-25T12:41:31Z","timestamp":1656160891000},"page":"4002-4010","source":"Crossref","is-referenced-by-count":8,"title":["CancerCellTracker: a brightfield time-lapse microscopy framework for cancer drug sensitivity estimation"],"prefix":"10.1093","volume":"38","author":[{"given":"Qibing","family":"Jiang","sequence":"first","affiliation":[{"name":"Department of Computer Science, University of Central Florida , Orlando, FL 32816, USA"}]},{"given":"Praneeth","family":"Sudalagunta","sequence":"additional","affiliation":[{"name":"Departments of Malignant Hematology and Chemical Biology and Molecular Medicine, H. Lee Moffitt Cancer Center and Research Institute , Tampa, FL 33612, USA"}]},{"given":"Maria C","family":"Silva","sequence":"additional","affiliation":[{"name":"Departments of Malignant Hematology and Chemical Biology and Molecular Medicine, H. Lee Moffitt Cancer Center and Research Institute , Tampa, FL 33612, USA"}]},{"given":"Rafael R","family":"Canevarolo","sequence":"additional","affiliation":[{"name":"Departments of Malignant Hematology and Chemical Biology and Molecular Medicine, H. Lee Moffitt Cancer Center and Research Institute , Tampa, FL 33612, USA"}]},{"given":"Xiaohong","family":"Zhao","sequence":"additional","affiliation":[{"name":"Departments of Malignant Hematology and Chemical Biology and Molecular Medicine, H. Lee Moffitt Cancer Center and Research Institute , Tampa, FL 33612, USA"}]},{"given":"Khandakar Tanvir","family":"Ahmed","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of Central Florida , Orlando, FL 32816, USA"}]},{"given":"Raghunandan Reddy","family":"Alugubelli","sequence":"additional","affiliation":[{"name":"Departments of Malignant Hematology and Chemical Biology and Molecular Medicine, H. Lee Moffitt Cancer Center and Research Institute , Tampa, FL 33612, USA"}]},{"given":"Gabriel","family":"DeAvila","sequence":"additional","affiliation":[{"name":"Departments of Malignant Hematology and Chemical Biology and Molecular Medicine, H. Lee Moffitt Cancer Center and Research Institute , Tampa, FL 33612, USA"}]},{"given":"Alexandre","family":"Tungesvik","sequence":"additional","affiliation":[{"name":"Departments of Malignant Hematology and Chemical Biology and Molecular Medicine, H. Lee Moffitt Cancer Center and Research Institute , Tampa, FL 33612, USA"}]},{"given":"Lia","family":"Perez","sequence":"additional","affiliation":[{"name":"Departments of Malignant Hematology and Chemical Biology and Molecular Medicine, H. Lee Moffitt Cancer Center and Research Institute , Tampa, FL 33612, USA"}]},{"given":"Robert A","family":"Gatenby","sequence":"additional","affiliation":[{"name":"Departments of Malignant Hematology and Chemical Biology and Molecular Medicine, H. Lee Moffitt Cancer Center and Research Institute , Tampa, FL 33612, USA"}]},{"given":"Robert J","family":"Gillies","sequence":"additional","affiliation":[{"name":"Departments of Malignant Hematology and Chemical Biology and Molecular Medicine, H. Lee Moffitt Cancer Center and Research Institute , Tampa, FL 33612, USA"}]},{"given":"Rachid","family":"Baz","sequence":"additional","affiliation":[{"name":"Departments of Malignant Hematology and Chemical Biology and Molecular Medicine, H. Lee Moffitt Cancer Center and Research Institute , Tampa, FL 33612, USA"}]},{"given":"Mark B","family":"Meads","sequence":"additional","affiliation":[{"name":"Departments of Malignant Hematology and Chemical Biology and Molecular Medicine, H. Lee Moffitt Cancer Center and Research Institute , Tampa, FL 33612, USA"}]},{"given":"Kenneth H","family":"Shain","sequence":"additional","affiliation":[{"name":"Departments of Malignant Hematology and Chemical Biology and Molecular Medicine, H. Lee Moffitt Cancer Center and Research Institute , Tampa, FL 33612, USA"}]},{"given":"Ariosto S","family":"Silva","sequence":"additional","affiliation":[{"name":"Departments of Malignant Hematology and Chemical Biology and Molecular Medicine, H. 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