Deep learning–based retinal nerve fiber layer thickness measurement of murine eyes

Rui Ma, Yuan Liu, Yudong Tao, Karam A. Alawa, Mei Ling Shyu, Richard K. Lee

Research output: Contribution to journalArticlepeer-review


Purpose: To design a robust and automated estimation method for measuring the retinal nerve fiber layer (RNFL) thickness using spectral domain optical coherence tomography (SD-OCT). Methods: We developed a deep learning–based image segmentation network for automated segmentation of the RNFL in SD-OCT B-scans of mouse eyes. In total, 5500 SD-OCT B-scans (5200 B-scans were used as training data with the remaining 300 B-scans used as testing data) were used to develop this segmentation network. Postprocessing operations were then applied on the segmentation results to fill any discontinuities or remove any speckles in the RNFL. Subsequently, a three-dimensional retina thickness map was generated by z-stacking 100 segmentation processed thickness B-scan images together. Finally, the average absolute difference between algorithm predicted RNFL thickness compared to the ground truth manual human segmentation was calculated.Results: The proposed method achieves an average dice similarity coefficient of 0.929 in the SD-OCT segmentation task and an average absolute difference of 0.0009 mm in thickness estimation task on the basis of the testing dataset. We also evaluated our segmentation algorithm on another biological dataset with SD-OCT volumes for RNFL thickness after the optic nerve crush injury. Results were shown to be comparable between the predicted and manually measured retina thickness values. Conclusions: Experimental results demonstrate that our automated segmentation algorithm reliably predicts the RNFL thickness in SD-OCT volumes of mouse eyes compared to laborious and more subjective manual SD-OCT RNFL segmentation. Translational Relevance: Automated segmentation using a deep learning–based algorithm for murine eye OCT effectively and rapidly produced nerve fiber layer thicknesses comparable to manual segmentation.

Original languageEnglish (US)
Article number21
JournalTranslational Vision Science and Technology
Issue number8
StatePublished - Jul 2021


  • Artificial intelligence
  • Deep learning
  • Nerve fiber layer
  • Optical coherence tomography
  • Segmentation

ASJC Scopus subject areas

  • Biomedical Engineering
  • Ophthalmology


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