Automated assessment of human engineered heart tissues using deep learning and template matching for segmentation and tracking

José M. Rivera-Arbeláez, Danjel Keekstra, Carla Cofiño-Fabres, Tom Boonen, Milica Dostanic, Simone A. ten Den, Kim Vermeul, Massimo Mastrangeli, Albert van den Berg, Loes I. Segerink, Marcelo C. Ribeiro, Nicola Strisciuglio, Robert Passier*

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

1 Citation (Scopus)
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The high rate of drug withdrawal from the market due to cardiovascular toxicity or lack of efficacy, the economic burden, and extremely long time before a compound reaches the market, have increased the relevance of human in vitro models like human (patient-derived) pluripotent stem cell (hPSC)-derived engineered heart tissues (EHTs) for the evaluation of the efficacy and toxicity of compounds at the early phase in the drug development pipeline. Consequently, the EHT contractile properties are highly relevant parameters for the analysis of cardiotoxicity, disease phenotype, and longitudinal measurements of cardiac function over time. In this study, we developed and validated the software HAARTA (Highly Accurate, Automatic and Robust Tracking Algorithm), which automatically analyzes contractile properties of EHTs by segmenting and tracking brightfield videos, using deep learning and template matching with sub-pixel precision. We demonstrate the robustness, accuracy, and computational efficiency of the software by comparing it to the state-of-the-art method (MUSCLEMOTION), and by testing it with a data set of EHTs from three different hPSC lines. HAARTA will facilitate standardized analysis of contractile properties of EHTs, which will be beneficial for in vitro drug screening and longitudinal measurements of cardiac function.

Original languageEnglish
Article numbere10513
Number of pages15
JournalBioengineering and Translational Medicine
Issue number3
Early online date18 Apr 2023
Publication statusPublished - May 2023


  • automated tracking
  • cardiac performance
  • contractile force
  • deep learning
  • engineered heart tissues
  • segmentation
  • sub-pixel interpolation
  • template matching


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