SarcGraph for High-Throughput Regional Analysis of Sarcomere Organization and Contractile Function in 2D Cardiac Muscle Bundles

TL;DR

This paper introduces SarcGraph adaptations for automated, high-throughput analysis of sarcomere organization and contractile function in 2D cardiac muscle bundles derived from hiPSC-CMs, facilitating scalable cardiac tissue research.

Contribution

The paper presents novel modifications to SarcGraph enabling reliable, automated analysis of sarcomere dynamics in physiologically relevant 2D cardiac tissues.

Findings

Enhanced sarcomere detection accuracy in 2DMBs

Automated extraction of structural and functional metrics

Open-source dataset of 130 cardiac tissue videos

Abstract

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.