Improving Deep Pancreas Segmentation in CT and MRI Images via Recurrent Neural Contextual Learning and Direct Loss Function

TL;DR

This paper introduces a novel recurrent neural network architecture with a direct loss function to improve the spatial consistency and accuracy of pancreas segmentation in CT and MRI images.

Contribution

It proposes a combined convolutional and LSTM-based network with a new Jaccard Loss for direct optimization of segmentation quality.

Findings

Outperforms state-of-the-art methods on CT pancreas segmentation

Achieves higher accuracy on MRI pancreas segmentation

Enhances segmentation consistency across slices

Abstract

Deep neural networks have demonstrated very promising performance on accurate segmentation of challenging organs (e.g., pancreas) in abdominal CT and MRI scans. The current deep learning approaches conduct pancreas segmentation by processing sequences of 2D image slices independently through deep, dense per-pixel masking for each image, without explicitly enforcing spatial consistency constraint on segmentation of successive slices. We propose a new convolutional/recurrent neural network architecture to address the contextual learning and segmentation consistency problem. A deep convolutional sub-network is first designed and pre-trained from scratch. The output layer of this network module is then connected to recurrent layers and can be fine-tuned for contextual learning, in an end-to-end manner. Our recurrent sub-network is a type of Long short-term memory (LSTM) network that performs segmentation on an image by integrating its neighboring slice segmentation predictions, in the form of a dependent sequence processing. Additionally, a novel segmentation-direct loss function (named Jaccard Loss) is proposed and deep networks are trained to optimize Jaccard Index (JI) directly. Extensive experiments are conducted to validate our proposed deep models, on quantitative pancreas segmentation using both CT and MRI scans. Our method outperforms the state-of-the-art work on CT [11] and MRI pancreas segmentation [1], respectively.