Residual encoder and convolutional decoder neural network for glioma segmentation

Kamlesh Pawar, Zhaolin Chen, N. Jon Shah, Gary Egan

Research output: Chapter in Book/Report/Conference proceedingConference PaperResearchpeer-review

11 Citations (Scopus)


A deep learning approach to glioma segmentation is presented. An encoder and decoder pair deep learning network is designed which takes T1, T2, T1-CE (contrast enhanced) and T2-Flair (fluid attenuation inversion recovery) images as input and outputs the segmented labels. The encoder is a 49 layer deep residual learning architecture that encodes the 240 × 240 × 4 input images into 8 × 8 × 2048 feature maps. The decoder network takes these feature maps and extract the segmented labels. The decoder network is fully convolutional network consisting of convolutional and upsampling layers. Additionally, the input images are downsampled using bilinear interpolation and are inserted into the decoder network through concatenation. This concatenation step provides spatial information of the tumor to the decoder, which was lost due to pooling/downlsampling during encoding. The network is trained on the BRATS-17 training dataset and validated on the validation dataset. The dice score, sensitivity and specificity of the segmented whole tumor, core tumor and enhancing tumor is computed on validation dataset. The mean dice score for whole tumor, core tumor and enhancing tumor for validation dataset were 0.824, 0.627 and 0.575, respectively.
Original languageEnglish
Title of host publicationBrainlesion
Subtitle of host publicationGlioma, Multiple Sclerosis, Stroke and Traumatic Brain Injuries - 3rd International Workshop, BrainLes 2017, Held in Conjunction with MICCAI 2017, Revised Selected Papers
Place of PublicationSwitzerland
Number of pages11
ISBN (Electronic)9783319752389
ISBN (Print)9783319752372
Publication statusPublished - 1 Jan 2018
EventInternational MICCAI Brain Lesion Workshop 2017 - Quebec City, Canada
Duration: 14 Sept 201714 Sept 2017
Conference number: 3rd (Proceedings)

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume10670 LNCS
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349


WorkshopInternational MICCAI Brain Lesion Workshop 2017
Abbreviated titleBrainLes 2017
CityQuebec City
OtherHeld in conjunction with the Medical Image Computing for Computer Assisted Intervention, MICCAI 2017
Internet address


  • CNN
  • Computer vision
  • Deep learning
  • Image segmentation

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