SarcGraph for High-Throughput Regional Analysis of Sarcomere Organization and Contractile Function in 2D Cardiac Muscle Bundles
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arXiv
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| Main Authors: | , , , , , |
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| Format: | Preprint |
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2025
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| _version_ | 1866914159056125952 |
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| author | Mohammadzadeh, Saeed Tsan, Yao-Chang Renberg, Aaron Kobeissi, Hiba Helms, Adam Lejeune, Emma |
| author_facet | Mohammadzadeh, Saeed Tsan, Yao-Chang Renberg, Aaron Kobeissi, Hiba Helms, Adam Lejeune, Emma |
| contents | Timelapse images of human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) provide rich information on cell structure and contractile function. However, it is challenging to reproducibly generate tissue samples and conduct scalable experiments with these cells. The two-dimensional cardiac muscle bundle (2DMB) platform helps address these limitations by standardizing tissue geometry, resulting in physiologic, uniaxial contractions of discrete tissues on an elastomeric substrate with stiffness similar to the heart. 2DMBs are highly conducive to sarcomere imaging using fluorescent reporters, but, due to their larger and more physiologic sarcomere displacements and velocities, prior sarcomere-tracking pipelines have been unreliable. Here, we present adaptations to SarcGraph, an open-source Python package for sarcomere detection and tracking, that enable automated analysis of high-frame-rate 2DMB recordings. Key modifications to the pipeline include: 1) switching to a frame-by-frame sarcomere detection approach and automating tissue segmentation with spatial partitioning, 2) performing Gaussian Process Regression for signal denoising, and 3) incorporating an automatic contractile phase detection pipeline. These enhancements enable the extraction of structural organization and functional contractility metrics for both the whole 2DMB tissue and distinct tissue regions, both in a fully automated manner. We complement this software release with a dataset of 130 example movies of baseline and drug-treated samples disseminated through the Harvard Dataverse. By providing open-source tools and datasets, we aim to enable high-throughput analysis of engineered cardiac tissues and advance collective progress within the hiPSC-CM research community. |
| format | Preprint |
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arxiv_https___arxiv_org_abs_2511_11913 |
| institution | arXiv |
| publishDate | 2025 |
| record_format | arxiv |
| spellingShingle | SarcGraph for High-Throughput Regional Analysis of Sarcomere Organization and Contractile Function in 2D Cardiac Muscle Bundles Mohammadzadeh, Saeed Tsan, Yao-Chang Renberg, Aaron Kobeissi, Hiba Helms, Adam Lejeune, Emma Quantitative Methods 92F05, 74A05 J.2; J.3 Timelapse images of human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) provide rich information on cell structure and contractile function. However, it is challenging to reproducibly generate tissue samples and conduct scalable experiments with these cells. The two-dimensional cardiac muscle bundle (2DMB) platform helps address these limitations by standardizing tissue geometry, resulting in physiologic, uniaxial contractions of discrete tissues on an elastomeric substrate with stiffness similar to the heart. 2DMBs are highly conducive to sarcomere imaging using fluorescent reporters, but, due to their larger and more physiologic sarcomere displacements and velocities, prior sarcomere-tracking pipelines have been unreliable. Here, we present adaptations to SarcGraph, an open-source Python package for sarcomere detection and tracking, that enable automated analysis of high-frame-rate 2DMB recordings. Key modifications to the pipeline include: 1) switching to a frame-by-frame sarcomere detection approach and automating tissue segmentation with spatial partitioning, 2) performing Gaussian Process Regression for signal denoising, and 3) incorporating an automatic contractile phase detection pipeline. These enhancements enable the extraction of structural organization and functional contractility metrics for both the whole 2DMB tissue and distinct tissue regions, both in a fully automated manner. We complement this software release with a dataset of 130 example movies of baseline and drug-treated samples disseminated through the Harvard Dataverse. By providing open-source tools and datasets, we aim to enable high-throughput analysis of engineered cardiac tissues and advance collective progress within the hiPSC-CM research community. |
| title | SarcGraph for High-Throughput Regional Analysis of Sarcomere Organization and Contractile Function in 2D Cardiac Muscle Bundles |
| topic | Quantitative Methods 92F05, 74A05 J.2; J.3 |
| url | https://arxiv.org/abs/2511.11913 |