DeepEdit: Deep Editable Learning for Interactive Segmentation of 3D Medical Images

• Published in: Data Augmentation, Labelling, and Imperfections pp. 11 - 21
• Main Authors: Diaz-Pinto, Andres, Mehta, Pritesh, Alle, Sachidanand, Asad, Muhammad, Brown, Richard, Nath, Vishwesh, Ihsani, Alvin, Antonelli, Michela, Palkovics, Daniel, Pinter, Csaba, Alkalay, Ron, Pieper, Steve, Roth, Holger R., Xu, Daguang, Dogra, Prerna, Vercauteren, Tom, Feng, Andrew, Quraini, Abood, Ourselin, Sebastien, Cardoso, M. Jorge
• Format: Book Chapter
• Language: English
• Published: Cham Springer Nature Switzerland 16.09.2022
• Series: Lecture Notes in Computer Science
• Subjects: CNNs; Deep learning; Interactive segmentation
• ISBN: 3031170261; 9783031170263
• ISSN: 0302-9743; 1611-3349
• DOI: 10.1007/978-3-031-17027-0_2

Automatic segmentation of medical images is a key step for diagnostic and interventional tasks. However, achieving this requires large amounts of annotated volumes, which can be tedious and time-consuming task for expert annotators. In this paper, we introduce DeepEdit, a deep learning-based method for volumetric medical image annotation, that allows automatic and semi-automatic segmentation, and click-based refinement. DeepEdit combines the power of two methods: a non-interactive (i.e. automatic segmentation using nnU-Net, UNET or UNETR) and an interactive segmentation method (i.e. DeepGrow), into a single deep learning model. It allows easy integration of uncertainty-based ranking strategies (i.e. aleatoric and epistemic uncertainty computation) and active learning. We propose and implement a method for training DeepEdit by using standard training combined with user interaction simulation. Once trained, DeepEdit allows clinicians to quickly segment their datasets by using the algorithm in auto segmentation mode or by providing clicks via a user interface (i.e. 3D Slicer, OHIF). We show the value of DeepEdit through evaluation on the PROSTATEx dataset for prostate/prostatic lesions and the Multi-Atlas Labeling Beyond the Cranial Vault (BTCV) dataset for abdominal CT segmentation, using state-of-the-art network architectures as baseline for comparison. DeepEdit could reduce the time and effort annotating 3D medical images compared to DeepGrow alone. Source code is available at https://github.com/Project-MONAI/MONAILabel.