NDLI: Deep learning tools for the cancer clinic: an open-source framework with head and neck contour validation

Content Provider	Springer Nature : BioMed Central
Author	Asbach, John C. Singh, Anurag K. Matott, L. Shawn Le, Anh H.
Abstract	Background With the rapid growth of deep learning research for medical applications comes the need for clinical personnel to be comfortable and familiar with these techniques. Taking a proven approach, we developed a straightforward open-source framework for producing automatic contours for head and neck planning computed tomography studies using a convolutional neural network (CNN). Methods Anonymized studies of 229 patients treated at our clinic for head and neck cancer from 2014 to 2018 were used to train and validate the network. We trained a separate CNN iteration for each of 11 common organs at risk, and then used data from 19 patients previously set aside as test cases for evaluation. We used a commercial atlas-based automatic contouring tool as a comparative benchmark on these test cases to ensure acceptable CNN performance. For the CNN contours and the atlas-based contours, performance was measured using three quantitative metrics and physician reviews using survey and quantifiable correction time for each contour. Results The CNN achieved statistically better scores than the atlas-based workflow on the quantitative metrics for 7 of the 11 organs at risk. In the physician review, the CNN contours were more likely to need minor corrections but less likely to need substantial corrections, and the cumulative correction time required was less than for the atlas-based contours for all but two test cases. Conclusions With this validation, we packaged the code framework and trained CNN parameters and a no-code, browser-based interface to facilitate reproducibility and expansion of the work. All scripts and files are available in a public GitHub repository and are ready for immediate use under the MIT license. Our work introduces a deep learning tool for automatic contouring that is easy for novice personnel to use.
Related Links	https://ro-journal.biomedcentral.com/counter/pdf/10.1186/s13014-022-01982-y.pdf
Ending Page	13
Page Count	13
Starting Page	1
File Format	HTM / HTML
DOI	10.1186/s13014-022-01982-y
Journal	Radiation Oncology
Issue Number	1
Volume Number	17
Language	English
Publisher	BioMed Central
Publisher Date	2022-02-08
Access Restriction	Open
Subject Keyword	Cancer Research Oncology Radiotherapy Imaging Radiology Deep learning Software Contouring Head and neck Open-source
Content Type	Text
Resource Type	Article
Subject	Radiology, Nuclear Medicine and Imaging Oncology
Journal Impact Factor	3.3/2023
5-Year Journal Impact Factor	3.6/2023

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1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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