Suggestive annotation: A deep active learning framework for biomedical image segmentation

Lin Yang, Yizhe Zhang, Jianxu Chen, Siyuan Zhang, Danny Z. Chen

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

238 Scopus citations

Abstract

Image segmentation is a fundamental problem in biomedical image analysis. Recent advances in deep learning have achieved promising results on many biomedical image segmentation benchmarks. However, due to large variations in biomedical images (different modalities, image settings, objects, noise, etc.), to utilize deep learning on a new application, it usually needs a new set of training data. This can incur a great deal of annotation effort and cost, because only biomedical experts can annotate effectively, and often there are too many instances in images (e.g., cells) to annotate. In this paper, we aim to address the following question: With limited effort (e.g., time) for annotation, what instances should be annotated in order to attain the best performance? We present a deep active learning framework that combines fully convolutional network (FCN) and active learning to significantly reduce annotation effort by making judicious suggestions on the most effective annotation areas. We utilize uncertainty and similarity information provided by FCN and formulate a generalized version of the maximum set cover problem to determine the most representative and uncertain areas for annotation. Extensive experiments using the 2015 MICCAI Gland Challenge dataset and a lymph node ultrasound image segmentation dataset show that, using annotation suggestions by our method, state-of-the-art segmentation performance can be achieved by using only 50% of training data.

Original languageEnglish (US)
Title of host publicationMedical Image Computing and Computer Assisted Intervention − MICCAI 2017 - 20th International Conference, Proceedings
EditorsLena Maier-Hein, Alfred Franz, Pierre Jannin, Simon Duchesne, Maxime Descoteaux, D. Louis Collins
PublisherSpringer Verlag
Pages399-407
Number of pages9
ISBN (Print)9783319661780
DOIs
StatePublished - 2017
Externally publishedYes
Event20th International Conference on Medical Image Computing and Computer-Assisted Intervention, MICCAI 2017 - Quebec City, Canada
Duration: Sep 11 2017Sep 13 2017

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume10435 LNCS
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Other

Other20th International Conference on Medical Image Computing and Computer-Assisted Intervention, MICCAI 2017
Country/TerritoryCanada
CityQuebec City
Period9/11/179/13/17

ASJC Scopus subject areas

  • Theoretical Computer Science
  • Computer Science(all)

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