Related Experiment Video
Updated: Jun 17, 2025
07:13
Isolation and Time-Lapse Imaging of Primary Mouse Embryonic Palatal Mesenchyme Cells to Analyze Collective Movement Attributes
Published on: February 13, 2021
2.2K
MicroBundlePillarTrack: A Python package for automated segmentation, tracking, and analysis of pillar deflection in
Hiba Kobeissi1, Xining Gao2,3,4, Samuel J DePalma5
1Department of Mechanical Engineering, Center for Multiscale and Translational Mechanobiology, Boston University, Boston, Massachusetts, United States.
Micropublication Biology
|August 8, 2024
Summary
We developed MicroBundlePillarTrack, an open-source software for analyzing human induced pluripotent stem cell-derived cardiac microbundles. This tool enables high-throughput, reproducible contractility analysis and cross-platform comparisons.
Area of Science:
- Biomedical Engineering
- Stem Cell Biology
- Cardiovascular Research
Background:
- Human induced pluripotent stem cell (hiPSC)-derived engineered cardiac tissues (microbundles) offer insights into structural and functional maturity.
- Extracting this data reproducibly and at high throughput is challenging.
- Quantitative comparisons across different in vitro experimental platforms are difficult.
Purpose of the Study:
- To present MicroBundlePillarTrack, an open-source Python package for automated analysis of cardiac microbundle contractility.
- To enable high-throughput and reproducible data extraction from hiPSC-derived cardiac tissues.
- To facilitate reliable quantitative comparisons across different experimental platforms.
Main Methods:
- Developed an open-source optical flow-based software package named MicroBundlePillarTrack.
- The software automatically segments pillars and tracks their displacements in microbundle movies.
- Outputs time-dependent metrics including beating amplitude, rate, contractile force, and tissue stress.
Main Results:
- The software successfully automates pillar segmentation and displacement tracking.
- Enables high-throughput analysis of large datasets, improving speed and reproducibility.
- Facilitates reliable cross-platform comparisons, overcoming limitations of manual methods.
Conclusions:
- MicroBundlePillarTrack provides a fully automated solution for cardiac microbundle contractility analysis.
- The open-source software and shared dataset promote quantitative comparisons across research labs.
- Aims to advance collective progress in the biomedical engineering open-source ecosystem.
