publication . Article . Other literature type . 2019

Using the CustusX toolkit to create an image guided bronchoscopy application: Fraxinus.

Ole Vegard Solberg; Ingerid Reinertsen; Erlend Fagertun Hofstad; Jon Wostryck Eiesland; Håkon Olav Leira; Janne Beate Lervik Bakeng; Tormod Selbekk; Geir Arne Tangen; Tore Amundsen; Thomas Langø;
Open Access English
  • Published: 08 Feb 2019 Journal: PLoS ONE (issn: 1932-6203, Copyright policy)
  • Publisher: Public Library of Science (PLoS)
  • Country: Norway
Abstract
Purpose The aim of this paper is to show how a specialized planning and guidance application called Fraxinus, can be built on top of the CustusX platform (www.custusx.org), which is an open source image-guided intervention software platform. Fraxinus has been customized to meet the clinical needs in navigated bronchoscopy. Methods The application requirements for Fraxinus were defined in close collaboration between research scientists, software developers and clinicians (pulmonologists), and built on top of CustusX. Its superbuild system downloads specific versions of the required libraries and builds them for the application in question, including the selected ...
Subjects
free text keywords: Medicine, R, Science, Q, Research Article, Computer and Information Sciences, Computer Software, Open Source Software, Science Policy, Open Science, Research and Analysis Methods, Imaging Techniques, Neuroimaging, Computed Axial Tomography, Biology and Life Sciences, Neuroscience, Medicine and Health Sciences, Diagnostic Medicine, Diagnostic Radiology, Tomography, Radiology and Imaging, Computer Architecture, User Interfaces, Engineering and Technology, Human Factors Engineering, Man-Computer Interface, Graphical User Interfaces, Software Engineering, Software Development, Computer Hardware, Navigation, General Biochemistry, Genetics and Molecular Biology, General Agricultural and Biological Sciences, General Medicine, Quality assurance, business.industry, business, Computer science, Workflow, Plug-in, computer.software_genre, computer, Graphical user interface, User interface, Personalization, Iterative and incremental development, Software
Communities
Science and Innovation Policy Studies
Neuroinformatics
20 references, page 1 of 2

1 Baaklini WA, Reinoso MA, Gorin AB, Sharafkaneh A, Manian P. Diagnostic yield of fiberoptic bronchoscopy in evaluating solitary pulmonary nodules. CHEST Journal. 2000;117(4):1049–1054. 10.1378/chest.117.4.1049 [OpenAIRE] [DOI]

2 Schreiber G, McCrory DC. Performance characteristics of different modalities for diagnosis of suspected lung cancer: summary of published evidence. Chest journal. 2003;123(1_suppl):115S–128S. 10.1378/chest.123.1_suppl.115S [DOI]

3 Yung R. Tissue diagnosis of suspected lung cancer: selecting between bronchoscopy, transthoracic needle aspiration, and resectional biopsy. Respiratory care clinics of North America. 2003;9(1):51–76. 12820712 [PubMed]

4 Reynisson PJ, Leira HO, Hernes TN, Hofstad EF, Scali M, Sorger H, et al Navigated bronchoscopy: a technical review. J Bronchology Interv Pulmonol. 2014;21(3):242–64. 10.1097/LBR.0000000000000064 24992135 [OpenAIRE] [PubMed] [DOI]

5 Ince DC, Hatton L, Graham-Cumming J. The case for open computer programs. Nature. 2012;482(7386):485–488. 10.1038/nature10836 22358837 [OpenAIRE] [PubMed] [DOI]

6 Askeland C, Solberg O, Bakeng J, Reinertsen I, Tangen G, Hofstad E, et al CustusX: an open-source research platform for image-guided therapy. International Journal of Computer Assisted Radiology and Surgery. 2015; p. 1–15. 10.1007/s11548-015-1292-0 [OpenAIRE] [DOI]

7 Leira HO, Amundsen T, Tangen GA, BøLE, Manstad-Hulaas F, LangøT. A novel research platform for electromagnetic navigated bronchoscopy using cone beam CT imaging and an animal model. Minimally Invasive Therapy & Allied Technologies. 2011;20(1):30–41. 10.3109/13645706.2010.518747 20874055 [OpenAIRE] [PubMed] [DOI]

8 Sorger H, Hofstad EF, Amundsen T, LangøT, Leira HO. A novel platform for electromagnetic navigated ultrasound bronchoscopy (EBUS). International Journal of Computer Assisted Radiology and Surgery. 2015;Accepted for publication, In print. [OpenAIRE]

9 Smistad E, Elster AC, Lindseth F. GPU accelerated segmentation and centerline extraction of tubular structures from medical images. Int J Comput Assist Radiol Surg. 2014;9(4):561–75. 10.1007/s11548-013-0956-x 24177985 [OpenAIRE] [PubMed] [DOI]

10 Smistad E, Elster AC, Lindseth F. GPU-based airway segmentation and centerline extraction for image guided bronchoscopy. Norsk informatikkonferanse. 2012;2012. [OpenAIRE]

11 Nolden M, Zelzer S, Seitel A, Wald D, Muller M, Franz AM, et al The Medical Imaging Interaction Toolkit: challenges and advances: 10 years of open-source development. Int J Comput Assist Radiol Surg. 2013;8(4):607–20. 10.1007/s11548-013-0840-8 23588509 [OpenAIRE] [PubMed] [DOI]

12 OSGI Alliance. OSGi Service Platform, Core Specification, Release 4, Version 4.2; 2009. Available from: http://www.osgi.org/Download/Release4V42.

13 Dingsøyr T, Nerur S, Balijepally V, Moe NB. A decade of agile methodologies: Towards explaining agile software development. Journal of Systems and Software. 2012;85(6):1213–1221. 10.1016/j.jss.2012.02.033 [OpenAIRE] [DOI]

14 Martin K, Hoffman B. Mastering CMake: a cross-platform build system: version 3.1 New York, NY: Kitware; 2015.

15 Tokuda J, Fischer GS, Papademetris X, Yaniv Z, Ibanez L, Cheng P, et al OpenIGTLink: an open network protocol for image-guided therapy environment. The International Journal of Medical Robotics and Computer Assisted Surgery. 2009;5(4):423–434. 10.1002/rcs.274 19621334 [OpenAIRE] [PubMed] [DOI]

20 references, page 1 of 2
Abstract
Purpose The aim of this paper is to show how a specialized planning and guidance application called Fraxinus, can be built on top of the CustusX platform (www.custusx.org), which is an open source image-guided intervention software platform. Fraxinus has been customized to meet the clinical needs in navigated bronchoscopy. Methods The application requirements for Fraxinus were defined in close collaboration between research scientists, software developers and clinicians (pulmonologists), and built on top of CustusX. Its superbuild system downloads specific versions of the required libraries and builds them for the application in question, including the selected ...
Subjects
free text keywords: Medicine, R, Science, Q, Research Article, Computer and Information Sciences, Computer Software, Open Source Software, Science Policy, Open Science, Research and Analysis Methods, Imaging Techniques, Neuroimaging, Computed Axial Tomography, Biology and Life Sciences, Neuroscience, Medicine and Health Sciences, Diagnostic Medicine, Diagnostic Radiology, Tomography, Radiology and Imaging, Computer Architecture, User Interfaces, Engineering and Technology, Human Factors Engineering, Man-Computer Interface, Graphical User Interfaces, Software Engineering, Software Development, Computer Hardware, Navigation, General Biochemistry, Genetics and Molecular Biology, General Agricultural and Biological Sciences, General Medicine, Quality assurance, business.industry, business, Computer science, Workflow, Plug-in, computer.software_genre, computer, Graphical user interface, User interface, Personalization, Iterative and incremental development, Software
Communities
Science and Innovation Policy Studies
Neuroinformatics
20 references, page 1 of 2

1 Baaklini WA, Reinoso MA, Gorin AB, Sharafkaneh A, Manian P. Diagnostic yield of fiberoptic bronchoscopy in evaluating solitary pulmonary nodules. CHEST Journal. 2000;117(4):1049–1054. 10.1378/chest.117.4.1049 [OpenAIRE] [DOI]

2 Schreiber G, McCrory DC. Performance characteristics of different modalities for diagnosis of suspected lung cancer: summary of published evidence. Chest journal. 2003;123(1_suppl):115S–128S. 10.1378/chest.123.1_suppl.115S [DOI]

3 Yung R. Tissue diagnosis of suspected lung cancer: selecting between bronchoscopy, transthoracic needle aspiration, and resectional biopsy. Respiratory care clinics of North America. 2003;9(1):51–76. 12820712 [PubMed]

4 Reynisson PJ, Leira HO, Hernes TN, Hofstad EF, Scali M, Sorger H, et al Navigated bronchoscopy: a technical review. J Bronchology Interv Pulmonol. 2014;21(3):242–64. 10.1097/LBR.0000000000000064 24992135 [OpenAIRE] [PubMed] [DOI]

5 Ince DC, Hatton L, Graham-Cumming J. The case for open computer programs. Nature. 2012;482(7386):485–488. 10.1038/nature10836 22358837 [OpenAIRE] [PubMed] [DOI]

6 Askeland C, Solberg O, Bakeng J, Reinertsen I, Tangen G, Hofstad E, et al CustusX: an open-source research platform for image-guided therapy. International Journal of Computer Assisted Radiology and Surgery. 2015; p. 1–15. 10.1007/s11548-015-1292-0 [OpenAIRE] [DOI]

7 Leira HO, Amundsen T, Tangen GA, BøLE, Manstad-Hulaas F, LangøT. A novel research platform for electromagnetic navigated bronchoscopy using cone beam CT imaging and an animal model. Minimally Invasive Therapy & Allied Technologies. 2011;20(1):30–41. 10.3109/13645706.2010.518747 20874055 [OpenAIRE] [PubMed] [DOI]

8 Sorger H, Hofstad EF, Amundsen T, LangøT, Leira HO. A novel platform for electromagnetic navigated ultrasound bronchoscopy (EBUS). International Journal of Computer Assisted Radiology and Surgery. 2015;Accepted for publication, In print. [OpenAIRE]

9 Smistad E, Elster AC, Lindseth F. GPU accelerated segmentation and centerline extraction of tubular structures from medical images. Int J Comput Assist Radiol Surg. 2014;9(4):561–75. 10.1007/s11548-013-0956-x 24177985 [OpenAIRE] [PubMed] [DOI]

10 Smistad E, Elster AC, Lindseth F. GPU-based airway segmentation and centerline extraction for image guided bronchoscopy. Norsk informatikkonferanse. 2012;2012. [OpenAIRE]

11 Nolden M, Zelzer S, Seitel A, Wald D, Muller M, Franz AM, et al The Medical Imaging Interaction Toolkit: challenges and advances: 10 years of open-source development. Int J Comput Assist Radiol Surg. 2013;8(4):607–20. 10.1007/s11548-013-0840-8 23588509 [OpenAIRE] [PubMed] [DOI]

12 OSGI Alliance. OSGi Service Platform, Core Specification, Release 4, Version 4.2; 2009. Available from: http://www.osgi.org/Download/Release4V42.

13 Dingsøyr T, Nerur S, Balijepally V, Moe NB. A decade of agile methodologies: Towards explaining agile software development. Journal of Systems and Software. 2012;85(6):1213–1221. 10.1016/j.jss.2012.02.033 [OpenAIRE] [DOI]

14 Martin K, Hoffman B. Mastering CMake: a cross-platform build system: version 3.1 New York, NY: Kitware; 2015.

15 Tokuda J, Fischer GS, Papademetris X, Yaniv Z, Ibanez L, Cheng P, et al OpenIGTLink: an open network protocol for image-guided therapy environment. The International Journal of Medical Robotics and Computer Assisted Surgery. 2009;5(4):423–434. 10.1002/rcs.274 19621334 [OpenAIRE] [PubMed] [DOI]

20 references, page 1 of 2
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