Automated Tracking of Mouse Embryogenesis from Large-scale Fluorescence Microscopy Data

dc.contributor.authorWang, Congchaoen
dc.contributor.committeechairYu, Guoqiangen
dc.contributor.committeememberWang, Yue J.en
dc.contributor.committeememberPark, Jung-Minen
dc.contributor.committeememberCao, Youngen
dc.contributor.committeememberGerdes, Ryan M.en
dc.contributor.departmentElectrical and Computer Engineeringen
dc.date.accessioned2021-06-04T08:00:23Zen
dc.date.available2021-06-04T08:00:23Zen
dc.date.issued2021-06-03en
dc.description.abstractRecent breakthroughs in microscopy techniques and fluorescence probes enable the recording of mouse embryogenesis at the cellular level for days, easily generating terabyte-level 3D time-lapse data. Since millions of cells are involved, this information-rich data brings a natural demand for an automated tool for its comprehensive analysis. This tool should automatically (1) detect and segment cells at each time point and (2) track cell migration across time. Most existing cell tracking methods cannot scale to the data with such large size and high complexity. For those purposely designed for embryo data analysis, the accuracy is heavily sacrificed. Here, we present a new computational framework for the mouse embryo data analysis with high accuracy and efficiency. Our framework detects and segments cells with a fully probability-principled method, which not only has high statistical power but also helps determine the desired cell territories and increase the segmentation accuracy. With the cells detected at each time point, our framework reconstructs cell traces with a new minimum-cost circulation-based paradigm, CINDA (CIrculation Network-based DataAssociation). Compared with the widely used minimum-cost flow-based methods, CINDA guarantees the global optimal solution with the best-of-known theoretical worst-case complexity and hundreds to thousands of times practical efficiency improvement. Since the information extracted from a single time point is limited, our framework iteratively refines cell detection and segmentation results based on the cell traces which contain more information from other time points. Results show that this dramatically improves the accuracy of cell detection, segmentation, and tracking. To make our work easy to use, we designed a standalone software, MIVAQ (Microscopic Image Visualization, Annotation, and Quantification), with our framework as the backbone and a user-friendly interface. With MIVAQ, users can easily analyze their data and visually check the results.en
dc.description.abstractgeneralMouse embryogenesis studies mouse embryos from fertilization to tissue and organ formation. The current microscope and fluorescent labeling technique enable the recording of the whole mouse embryo for a long time with high resolution. The generated data can be terabyte-level and contains more than one million cells. This information-rich data brings a natural demand for an automated tool for its comprehensive analysis. This tool should automatically (1) detect and segment cells at each time point to get the information of cell morphology and (2) track cell migration across time. However, the development of analytical tools lags far behind the capability of data generation. Existing tools either cannot scale to the data with such large size and high complexity or sacrifice accuracy heavily for efficiency. In this dissertation, we present a new computational framework for the mouse embryo data analysis with high accuracy and efficiency. To make our framework easy to use, we also designed a standalone software, MIVAQ, with a user-friendly interface. With MIVAQ, users can easily analyze their data and visually check the results.en
dc.description.degreeDoctor of Philosophyen
dc.format.mediumETDen
dc.identifier.othervt_gsexam:31051en
dc.identifier.urihttp://hdl.handle.net/10919/103595en
dc.publisherVirginia Techen
dc.rightsIn Copyrighten
dc.rights.urihttp://rightsstatements.org/vocab/InC/1.0/en
dc.subjectMouse embryoen
dc.subjectCell trackingen
dc.subjectOrder statisticsen
dc.subjectNetwork flowen
dc.titleAutomated Tracking of Mouse Embryogenesis from Large-scale Fluorescence Microscopy Dataen
dc.typeDissertationen
thesis.degree.disciplineComputer Engineeringen
thesis.degree.grantorVirginia Polytechnic Institute and State Universityen
thesis.degree.leveldoctoralen
thesis.degree.nameDoctor of Philosophyen
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