ArticlePLoS computational biology2021
Sarc-Graph: Automated segmentation, tracking, and analysis of sarcomeres in hiPSC-derived cardiomyocytes.
Article in PLoS computational biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
18 citing papers in PubMed.
- Artificial Intelligence-Powered Histopathology in Stem Cell Research: Bridging Morphology, Function, and Omics.Current issues in molecular biology · 2026Review
- High-Throughput Methods for Variant Functional Assessment in Cardiac Disease.Circulation. Genomic and precision medicine · 2026Review
- Sarcomere analysis in human cardiomyocytes by computing radial frequency spectra.Biological chemistry · 2025Article
- Quantifying HiPSC-CM structural organization at scale with deep learning-enhanced SarcGraph.PLoS computational biology · 2025Article
- Developmental remodelling ofOpen biology · 2025Article
- Antisense-mediated regulation of exon usage in the elastic spring region of Titin modulates sarcomere function.Cardiovascular research · 2025Article
- Cell Architecture and Dynamics of Human Induced Pluripotent Stem Cell-Derived Cardiomyocytes (hiPSC-CMs) on Hydrogels with Spatially Patterned Laminin and N-Cadherin.ACS applied materials & interfaces · 2025Article
- SarcGraph for High-Throughput Regional Analysis of Sarcomere Organization and Contractile Function in 2D Cardiac Muscle Bundles.microPublication biology · 2025Article
- Induced pluripotent stem cell-derived cardiomyocyte in vitro models: benchmarking progress and ongoing challenges.Nature methods · 2025Review
- The Current State of Realistic Heart Models for Disease Modelling and Cardiotoxicity.International journal of molecular sciences · 2024Review
- Article
- PatternJ: an ImageJ toolset for the automated and quantitative analysis of regular spatial patterns found in sarcomeres, axons, somites, and more.Biology open · 2024Article
- A Systems Approach to Biomechanics, Mechanobiology, and Biotransport.Journal of biomechanical engineering · 2024Article
- MicroBundleCompute: Automated segmentation, tracking, and analysis of subdomain deformation in cardiac microbundles.PloS one · 2024Article
- Human engineered cardiac tissue model of hypertrophic cardiomyopathy recapitulates key hallmarks of the disease and the effect of chronic mavacamten treatment.Frontiers in bioengineering and biotechnology · 2023Article
- A comprehensive review of computational and image analysis techniques for quantitative evaluation of striated muscle tissue architecture.Biophysics reviews · 2022Review
- Monitoring the maturation of the sarcomere network: a super-resolution microscopy-based approach.Cellular and molecular life sciences : CMLS · 2022Article
- Asymmetric biphasic electric stimulation supports cardiac maturation and functionality.Journal of tissue engineeringArticle
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.