VNet-T2 algorithm dataset

Published: 12 May 2022| Version 1 | DOI: 10.17632/25r9ccd7z2.1
Massimo Salvi, Bruno De Santi, Bianca Pop, Martino Bosco, Valentina Giannini, Daniele Regge, Filippo Molinari, Kristen Meiburger


This repository contains the scripts used to develop the VNet-T2 and the ASM model for prostate segmentation in MRI images: - Salvi M., De Santi B., Pop B., Bosco M., V. Giannini, D. Regge, Molinari F., and Meiburger K. M. , "Integration of deep learning and active shape models for more accurate prostate segmentation in 3D MR images", Journal of Imaging 2022 (DOI: 10.3390/jimaging8050133) Abstract: Magnetic resonance imaging (MRI) has a growing role in the clinical workup of prostate cancer. However, manual three-dimensional (3D) segmentation of the prostate is a laborious and time-consuming task. In this scenario, the use of automated algorithms for prostate segmentation allows us to bypass the huge workload of physicians. In this work, we propose a fully automated hybrid approach for prostate gland segmentation in MR images using an initial segmentation of prostate volumes using a custom-made 3D deep network (VNet-T2), followed by refinement using an Active Shape Model (ASM). While the deep network focuses on three-dimensional spatial coherence of the shape, the ASM relies on local image information and this joint effort allows for improved segmentation of the organ contours. Our method is developed and tested on a dataset composed of T2-weighted (T2w) MRI prostatic volumes of 60 male patients. In the test set, the proposed method shows excellent segmentation performance, achieving a mean dice score and Hausdorff distance of 0.851 and 7.55 mm, respectively. In the future, this algorithm could serve as an enabling technology for the development of computer-aided systems for prostate cancer characterization in MR imaging.



Medical Imaging, Magnetic Resonance Imaging, Biomedical Imaging, Deep Learning