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Training Convolutional Networks for Prostate Segmentation With Limited Data

Multi-zonal segmentation is a critical component of computer-aided diagnostic systems for detecting and staging prostate cancer. Previously, convolutional neural networks such as the U-Net have been used to produce fully automatic multi-zonal prostate segmentation on magnetic resonance images (MRIs)...

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Autores principales: SAUNDERS, SARA L., LENG, ETHAN, SPILSETH, BENJAMIN, WASSERMAN, NEIL, METZGER, GREGORY J., BOLAN, PATRICK J.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8438764/
https://www.ncbi.nlm.nih.gov/pubmed/34527506
http://dx.doi.org/10.1109/access.2021.3100585
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author SAUNDERS, SARA L.
LENG, ETHAN
SPILSETH, BENJAMIN
WASSERMAN, NEIL
METZGER, GREGORY J.
BOLAN, PATRICK J.
author_facet SAUNDERS, SARA L.
LENG, ETHAN
SPILSETH, BENJAMIN
WASSERMAN, NEIL
METZGER, GREGORY J.
BOLAN, PATRICK J.
author_sort SAUNDERS, SARA L.
collection PubMed
description Multi-zonal segmentation is a critical component of computer-aided diagnostic systems for detecting and staging prostate cancer. Previously, convolutional neural networks such as the U-Net have been used to produce fully automatic multi-zonal prostate segmentation on magnetic resonance images (MRIs) with performance comparable to human experts, but these often require large amounts of manually segmented training data to produce acceptable results. For institutions that have limited amounts of labeled MRI exams, it is not clear how much data is needed to train a segmentation model, and which training strategy should be used to maximize the value of the available data. This work compares how the strategies of transfer learning and aggregated training using publicly available external data can improve segmentation performance on internal, site-specific prostate MR images, and evaluates how the performance varies with the amount of internal data used for training. Cross training experiments were performed to show that differences between internal and external data were impactful. Using a standard U-Net architecture, optimizations were performed to select between 2D and 3D variants, and to determine the depth of fine-tuning required for optimal transfer learning. With the optimized architecture, the performance of transfer learning and aggregated training were compared for a range of 5-40 internal datasets. The results show that both strategies consistently improve performance and produced segmentation results that are comparable to that of human experts with approximately 20 site-specific MRI datasets. These findings can help guide the development of site-specific prostate segmentation models for both clinical and research applications.
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spelling pubmed-84387642021-09-14 Training Convolutional Networks for Prostate Segmentation With Limited Data SAUNDERS, SARA L. LENG, ETHAN SPILSETH, BENJAMIN WASSERMAN, NEIL METZGER, GREGORY J. BOLAN, PATRICK J. IEEE Access Article Multi-zonal segmentation is a critical component of computer-aided diagnostic systems for detecting and staging prostate cancer. Previously, convolutional neural networks such as the U-Net have been used to produce fully automatic multi-zonal prostate segmentation on magnetic resonance images (MRIs) with performance comparable to human experts, but these often require large amounts of manually segmented training data to produce acceptable results. For institutions that have limited amounts of labeled MRI exams, it is not clear how much data is needed to train a segmentation model, and which training strategy should be used to maximize the value of the available data. This work compares how the strategies of transfer learning and aggregated training using publicly available external data can improve segmentation performance on internal, site-specific prostate MR images, and evaluates how the performance varies with the amount of internal data used for training. Cross training experiments were performed to show that differences between internal and external data were impactful. Using a standard U-Net architecture, optimizations were performed to select between 2D and 3D variants, and to determine the depth of fine-tuning required for optimal transfer learning. With the optimized architecture, the performance of transfer learning and aggregated training were compared for a range of 5-40 internal datasets. The results show that both strategies consistently improve performance and produced segmentation results that are comparable to that of human experts with approximately 20 site-specific MRI datasets. These findings can help guide the development of site-specific prostate segmentation models for both clinical and research applications. 2021-07-27 2021 /pmc/articles/PMC8438764/ /pubmed/34527506 http://dx.doi.org/10.1109/access.2021.3100585 Text en https://creativecommons.org/licenses/by-nc-nd/4.0/This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License. http://creativecommons.org/licenses/by-nc-nd/4.0/ (https://creativecommons.org/licenses/by-nc-nd/4.0/)
spellingShingle Article
SAUNDERS, SARA L.
LENG, ETHAN
SPILSETH, BENJAMIN
WASSERMAN, NEIL
METZGER, GREGORY J.
BOLAN, PATRICK J.
Training Convolutional Networks for Prostate Segmentation With Limited Data
title Training Convolutional Networks for Prostate Segmentation With Limited Data
title_full Training Convolutional Networks for Prostate Segmentation With Limited Data
title_fullStr Training Convolutional Networks for Prostate Segmentation With Limited Data
title_full_unstemmed Training Convolutional Networks for Prostate Segmentation With Limited Data
title_short Training Convolutional Networks for Prostate Segmentation With Limited Data
title_sort training convolutional networks for prostate segmentation with limited data
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8438764/
https://www.ncbi.nlm.nih.gov/pubmed/34527506
http://dx.doi.org/10.1109/access.2021.3100585
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