Delineating the heterogeneity of embryo preimplantation development using automated and accurate morphokinetic annotation

Nir Zabari, Yoav Kan-Tor, Yuval Or, Zeev Shoham, Yoel Shufaro, Dganit Richter, Iris Har-Vardi, Assaf Ben-Meir, Naama Srebnik, Amnon Buxboim*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

3 Scopus citations


Purpose: Our objective was to design an automated deep learning model that extracts the morphokinetic events of embryos that were recorded by time-lapse incubators. Using automated annotation, we set out to characterize the temporal heterogeneity of preimplantation development across a large number of embryos. Methods: To perform a retrospective study, we used a dataset of video files of 67,707 embryos from four IVF clinics. A convolutional neural network (CNN) model was trained to assess the developmental states that appear in single frames from 20,253 manually-annotated embryos. Probability-weighted superposition of multiple predicted states was permitted, thus accounting for visual uncertainties. Superimposed embryo states were collapsed onto discrete series of morphokinetic events via monotonic regression of whole-embryo profiles. Unsupervised K-means clustering was applied to define subpopulations of embryos of distinctive morphokinetic profiles. Results: We perform automated assessment of single-frame embryo states with 97% accuracy and demonstrate whole-embryo morphokinetic annotation with R-square 0.994. High quality embryos that had been valid candidates for transfer were clustered into nine subpopulations, as characterized by distinctive developmental dynamics. Retrospective comparative analysis of transfer versus implantation rates reveals differences between embryo clusters as marked by poor synchronization of the third mitotic cell-cleavage cycle. Conclusions: By demonstrating fully automated, accurate, and standardized morphokinetic annotation of time-lapse embryo recordings from IVF clinics, we provide practical means to overcome current limitations that hinder the implementation of morphokinetic decision-support tools within clinical IVF settings due to inter-observer and intra-observer manual annotation variations and workload constrains. Furthermore, our work provides a platform to address embryo heterogeneity using dimensionality-reduced morphokinetic descriptions of preimplantation development.

Original languageAmerican English
Pages (from-to)1391-1406
Number of pages16
JournalJournal of Assisted Reproduction and Genetics
Issue number6
StatePublished - Jun 2023

Bibliographical note

Publisher Copyright:
© 2023, The Author(s).


  • Assisted reproductive technologies
  • Automated morphokinetic annotation
  • Embryo morphokinetic classification
  • IVF
  • Machine learning


Dive into the research topics of 'Delineating the heterogeneity of embryo preimplantation development using automated and accurate morphokinetic annotation'. Together they form a unique fingerprint.

Cite this