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 deepgrow


Interactive 3D Segmentation for Primary Gross Tumor Volume in Oropharyngeal Cancer

Saukkoriipi, Mikko, Sahlsten, Jaakko, Jaskari, Joel, Orasmaa, Lotta, Kangas, Jari, Rasouli, Nastaran, Raisamo, Roope, Hirvonen, Jussi, Mehtonen, Helena, Järnstedt, Jorma, Mäkitie, Antti, Naser, Mohamed, Fuller, Clifton, Kann, Benjamin, Kaski, Kimmo

arXiv.org Artificial Intelligence

The main treatment modality for oropharyngeal cancer (OPC) is radiotherapy, where accurate segmentation of the primary gross tumor volume (GTVp) is essential. However, accurate GTVp segmentation is challenging due to significant interobserver variability and the time-consuming nature of manual annotation, while fully automated methods can occasionally fail. An interactive deep learning (DL) model offers the advantage of automatic high-performance segmentation with the flexibility for user correction when necessary. In this study, we examine interactive DL for GTVp segmentation in OPC. We implement state-of-the-art algorithms and propose a novel two-stage Interactive Click Refinement (2S-ICR) framework. Using the 2021 HEad and neCK TumOR (HECKTOR) dataset for development and an external dataset from The University of Texas MD Anderson Cancer Center for evaluation, the 2S-ICR framework achieves a Dice similarity coefficient of 0.713 $\pm$ 0.152 without user interaction and 0.824 $\pm$ 0.099 after five interactions, outperforming existing methods in both cases.


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

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

arXiv.org Artificial Intelligence

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