Analyzing Movies of Beating hiPSC-Derived Cardiomyocytes
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Zoom Link: https://bostonu.zoom.us/j/93315594357pwd=eE4wQS9lZjA2aloyMkQ2dG5CS21kZz09
Meeting ID: 933 1559 4357 Passcode: 689715
Abstract: A better fundamental understanding of human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) has the potential to advance applications ranging from drug discovery to cardiac repair. Automated quantitative analysis of beating hiPSC-CMs is an important and fast developing component of the hiPSC-CM research pipeline. Here we introduce “Sarc-Graph,” a computational framework to segment, track, and analyze sarcomeres in fluorescently tagged hiPSC-CMs. Our framework includes functions to segment z-discs and sarcomeres, track z-discs and sarcomeres in beating cells, and perform automated spatiotemporal analysis and data visualization. In addition to reporting good performance for sarcomere segmentation and tracking with little to no parameter tuning and a short runtime, we introduce two novel analysis approaches. First, we construct spatial graphs where z-discs correspond to nodes and sarcomeres correspond to edges. This makes measuring the network distance between each sarcomere (i.e., the number of connecting sarcomeres separating each sarcomere pair) straightforward. Second, we treat tracked and segmented components as fiducial markers and use them to compute the approximate deformation gradient of the entire tracked population. This represents a new quantitative descriptor of hiPSC-CM function. We showcase and validate our approach with both synthetic and experimental movies of beating hiPSC-CMs. By publishing Sarc-Graph, we aim to make automated quantitative analysis of hiPSC-CM behavior more accessible to the broader research community.
More information is available here: https://arxiv.org/abs/2102.02412
And the relevant code is posted here: https://github.com/elejeune11/Sarc-Graph
Bio: Emma Lejeune is an Assistant Professor in the Mechanical Engineering Department at Boston University. She received her PhD from Stanford University in September 2018, and was a Peter O’Donnell, Jr. postdoctoral research fellow at the Oden Institute at the University of Texas at Austin until 2020 when she joined the faculty at BU. Current areas of research involve integrating data-driven and physics based computational models, and characterizing and predicting the mechanical behavior of heterogeneous materials and biological systems