Uncertainty guided semi-supervised segmentation of retinal layers in OCT images

Suman Sedai, Bhavna Antony, Ravneet Rai, Katie Jones, Hiroshi Ishikawa, Joel Schuman, Wollstein Gadi, Rahil Garnavi

Research output: Chapter in Book/Report/Conference proceedingConference contribution


Deep convolutional neural networks have shown outstanding performance in medical image segmentation tasks. The usual problem when training supervised deep learning methods is the lack of labeled data which is time-consuming and costly to obtain. In this paper, we propose a novel uncertainty guided semi-supervised learning based on student-teacher approach for training the segmentation network using limited labeled samples and large number of unlabeled images. First, a teacher segmentation model is trained from the labeled samples using Bayesian deep learning. The trained model is used to generate soft segmentation labels and uncertainty map for the unlabeled set. The student model is then updated using the softly segmented samples and the corresponding pixel-wise confidence of the segmentation quality estimated from the uncertainty of the teacher model using a newly designed loss function. Experimental results on a retinal layer segmentation task show that the proposed method improves the segmentation performance in comparison to the fully supervised approach and is on par with the expert annotator. The proposed semi-supervised segmentation framework is a key contribution and applicable for biomedical image segmentation across various imaging modalities where access to annotated medical images is challenging.

Original languageEnglish (US)
Title of host publicationMedical Image Computing and Computer Assisted Intervention – MICCAI 2019 - 22nd International Conference, Proceedings
EditorsDinggang Shen, Pew-Thian Yap, Tianming Liu, Terry M. Peters, Ali Khan, Lawrence H. Staib, Caroline Essert, Sean Zhou
PublisherSpringer Science and Business Media Deutschland GmbH
Number of pages9
ISBN (Print)9783030322380
StatePublished - 2019
Event22nd International Conference on Medical Image Computing and Computer-Assisted Intervention, MICCAI 2019 - Shenzhen, China
Duration: Oct 13 2019Oct 17 2019

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume11764 LNCS
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349


Conference22nd International Conference on Medical Image Computing and Computer-Assisted Intervention, MICCAI 2019


  • Bayesian deep learning
  • OCT retinal imaging
  • Semi-supervised segmentation

ASJC Scopus subject areas

  • Theoretical Computer Science
  • General Computer Science


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