HeartSeg

The medaka (Oryzias latipes) and the zebrafish (Danio rerio) are used as a model organism for a variety of subjects in biomedical research. The presented work aims to study the potential of automated ventricular dimension estimation through heart segmentation in medaka. For more on this, it's time for a closer look on our paper and the supplementary materials.

See our paper here: https://www.liebertpub.com/doi/10.1089/zeb.2019.1754

See demonstration of our algorithm and framework on the test set data: https://youtu.be/i5bX_XbwXq0

The raw data was provided by: Dr. Jakob Gierten

Affiliated with: Department of Pediatric Cardiology, University Hospital Heidelberg, Im Neuenheimer Feld 430, 69120 Heidelberg, Germany Centre for Organismal Studies, Heidelberg University, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany

Contributing

We hope this work sparks additional research in this direction. Either by contributing to this framework, deploying the framework, or reusing the annotated ground truth data. In any case feel free to reach out and make sure to reference this work.

Schutera, M., Just, S., Gierten, J., Mikut, R., Reischl, M., & Pylatiuk, C. (2019). Machine learning methods for automated quantification of ventricular dimensions. Zebrafish, 16(6), 542-545. Contact: mark.schutera@kit.edu and pylatiuk@kit.edu