Kobeissi Hiba, Gao Xining, DePalma Samuel J, Ewoldt Jourdan K, Wang Miranda C, Das Shoshana L, Jilberto Javiera, Nordsletten David, Baker Brendon M, Chen Christopher S, Lejeune Emma
Department of Mechanical Engineering, Center for Multiscale and Translational Mechanobiology, Boston University, Boston, Massachusetts, United States.
Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States.
ArXiv. 2024 Aug 15:arXiv:2405.11096v2.
Movies of human induced pluripotent stem cell (hiPSC)-derived engineered cardiac tissue (microbundles) contain abundant information about structural and functional maturity. However, extracting these data in a reproducible and high-throughput manner remains a major challenge. Furthermore, it is not straightforward to make direct quantitative comparisons across the multiple in vitro experimental platforms employed to fabricate these tissues. Here, we present "MicroBundlePillarTrack," an open-source optical flow-based package developed in Python to track the deflection of pillars in cardiac microbundles grown on experimental platforms with two different pillar designs ("Type 1" and "Type 2" design). Our software is able to automatically segment the pillars, track their displacements, and output time-dependent metrics for contractility analysis, including beating amplitude and rate, contractile force, and tissue stress. Because this software is fully automated, it will allow for both faster and more reproducible analyses of larger datasets and it will enable more reliable cross-platform comparisons as compared to existing approaches that require manual steps and are tailored to a specific experimental platform. To complement this open-source software, we share a dataset of 1,540 brightfield example movies on which we have tested our software. Through sharing this data and software, our goal is to directly enable quantitative comparisons across labs, and facilitate future collective progress via the biomedical engineering open-source data and software ecosystem.
人类诱导多能干细胞（hiPSC）衍生的工程心脏组织（微束）的电影包含有关结构和功能成熟度的丰富信息。然而，以可重复和高通量的方式提取这些数据仍然是一项重大挑战。此外，在用于制造这些组织的多个体外实验平台之间进行直接定量比较并非易事。在这里，我们展示了“MicroBundlePillarTrack”，这是一个用Python开发的基于开源光流的软件包，用于跟踪在具有两种不同柱设计（“1型”和“2型”设计）的实验平台上生长的心脏微束中柱的偏转。我们的软件能够自动分割柱，跟踪它们的位移，并输出用于收缩性分析的时间相关指标，包括跳动幅度和速率、收缩力和组织应力。由于该软件是完全自动化的，与需要手动步骤且针对特定实验平台定制的现有方法相比，它将允许对更大的数据集进行更快、更可重复的分析，并且将实现更可靠的跨平台比较。为了补充这个开源软件，我们共享了一个包含1540个明场示例电影的数据集，我们在该数据集上测试了我们的软件。通过共享这些数据和软件，我们的目标是直接实现跨实验室的定量比较，并通过生物医学工程开源数据和软件生态系统促进未来的集体进步。
