Skip to main content

3D Slicer: A Platform for Subject-Specific Image Analysis, Visualization, and Clinical Support

  • Chapter
  • First Online:

Abstract

3D Slicer is an open-source platform for the analysis and display of information derived from medical imaging and similar data sets. Such advanced software environments are in daily use by researchers and clinicians and in many nonmedical applications. 3D Slicer is unique through serving clinical users, multidisciplinary clinical research terms, and software architects within a single technology structure and user community. Functions such as interactive visualization, image registration, and model-based analysis are now being complemented by more advanced capabilities, most notably in neurological imaging and intervention. These functions, originally limited to offline use by technical factors, are integral to large scale, rapidly developing research studies, and they are being increasingly integrated into the management and delivery of care. This activity has been led by a community of basic, applied, and clinical scientists and engineers, from both academic and commercial perspectives. 3D Slicer, a free open-source software package, is based in this community; 3D Slicer provides a set of interactive tools and a stable platform that can quickly incorporate new analysis techniques and evolve to serve more sophisticated real-time applications while remaining compatible with the latest hardware and software generations of host computer systems.

This is a preview of subscription content, log in via an institution.

Buying options

Chapter
USD   29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   169.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   219.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD   219.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Learn about institutional subscriptions

References

  1. GE PET/CT+MR Systems. http://www3.gehealthcare.com/en/Products/Categories/Magnetic_Resonance_Imaging#tabs/tab46496FE3B3FB45898C8D759AA853A8E3. Accessed August 14, 2013.

  2. Siemens Healthcare. http://www.medical.siemens.com/. Accessed August 14, 2013.

  3. Vital Images. http://www.vitalimages.com/home.aspx. Accessed August 14, 2013.

  4. AMIRA 3D Analysis Software for Life Sciences [FEI Website]. http://www.amira.com/. Accessed August 14, 2013.

  5. Mayo Clinic Analyze MD. http://mayoresearch.mayo.edu/mayo/research/robb_lab/analyze-md.cfm. Accessed August 14, 2013.

  6. Osirix Imaging Software. http://www.osirix-viewer.com/. Accessed August 14, 2013.

  7. 3D Slicer. http://www.slicer.org. Accessed August 14, 2013.

  8. Gering D, Nabavi A, Kikinis R, Hata N, O’Donnell LJ, Grimson WEL, Jolesz FA, Wells 3rd WM, Black PM. An integrated visualization system for surgical planning and guidance using image fusion and an open MR. J Mag Res Imaging. 2001;13:967–75.

    Article  CAS  Google Scholar 

  9. The Visualization Toolkit (VTK). http://www.vtk.org. Accessed August 14, 2013.

  10. National Library of Medicine Insight Segmentation and Registration Toolkit (ITK). www.itk.org. Accessed August 14, 2013.

  11. NA-MIC Kit. http://wiki.na-mic.org/Wiki/index.php/NA-MIC-Kit. Accessed August 14, 2013.

  12. Slicer 4 Guided Tour with MRML Tree. http://www.na-mic.org/Wiki/images/4/42/2011_Summer-Slicer4.ppt. Accessed August 14, 2013.

  13. 3D Slicer and Extensible Neuroimaging Archive Toolkit (XNAT). http://wiki.na-mic.org/Wiki/index.php/Projects:ARRA:SlicerWF#Quarterly_Progress. Accessed August 14, 2013.

  14. Git. http://git-scm.com/. Accessed August 14, 2013.

  15. CMake. http://www.cmake.org/Wiki/CMake. Accessed August 14, 2013.

  16. CDash. http://www.cdash.org/cdash/project/about.html. Accessed August 14, 2013.

  17. Gering D. Recognizing deviations from normalcy for brain tumor segmentation. PhD thesis, Massachusetts Institute of Technology; 2003.

    Google Scholar 

  18. DICOM. http://medical.nema.org/. Accessed August 14, 2013.

  19. Simple_Region_Growing-Documentation-3.6 on Slicer. Org. http://www.slicer.org/slicerWiki/index.php/Modules:Simple_Region_Growing-Documentation-3.6. Accessed August 14, 2013.

  20. FastMarchingSegmentation-Documentation-3.6 on Slicer.org. http://www.slicer.org/slicerWiki/index.php/Modules:FastMarchingSegmentation-Documentation-3.6. Accessed August 14, 2013.

  21. EMSegmenter-Tasks on Slicer.org. http://wiki.slicer.org/slicerWiki/index.php/EMSegmenter-Tasks. Accessed August 14, 2013.

  22. VMTKEasyLevelSetSegmentation on Slicer.org. http://www.slicer.org/slicerWiki/index.php/Modules:VMTKEasyLevelSetSegmentation. Accessed August 14, 2013.

  23. Editor-Documentation-3.6 on Slicer.org. http://www.slicer.org/slicerWiki/index.php/Modules:Editor-Documentation-3.6. Accessed August 14, 2013.

  24. GrowCutSegmentation-Documentation-3.6 on Slicer.org. http://www.slicer.org/slicerWiki/index.php/Modules:GrowCutSegmentation-Documentation-3.6. Accessed August 14, 2013.

  25. ModelMaker-Documentation-3.6 on Slicer.org. http://www.slicer.org/slicerWiki/index.php/Modules:ModelMaker-Documentation-3.6. Accessed August 14, 2013.

  26. DiffusionMRIWelcome-Documentation-3.6 on Slicer.org. http://www.slicer.org/slicerWiki/index.php/Modules:DiffusionMRIWelcome-Documentation-3.6. Accessed August 14, 2013.

  27. DicomToNRRD-3.6 on Slicer.org. http://www.slicer.org/slicerWiki/index.php/Modules:DicomToNRRD-3.6. Accessed August 14, 2013.

  28. JointRicianLMMSEImageFilter-Documentation-3.6on Slicer.org. http://www.slicer.org/slicerWiki/index.php/Modules:JointRicianLMMSEImageFilter-Documentation-3.6. Accessed August 14, 2013.

  29. DiffusionTensorEstimation-Documentation-3.6 on Slicer.org. http://www.slicer.org/slicerWiki/index.php/Modules:DiffusionTensorEstimation-Documentation-3.6. Accessed August 14, 2013.

  30. Coordinate Systems on Slicer.org. http://www.slicer.org/slicerWiki/index.php/Coordinate_systems. Accessed August 14, 2013.

  31. Johnson H, Harris G, Williams K. BRAINSFit: mutual information registrations of whole-brain 3D images, using the insight toolkit in Insight Journal-2008. http://www.insight-journal.org/download/viewpdf/180/8169/bitstream. Accessed August 14, 2013.

  32. RegistrationDocumentation:RegLibTable on NA-MIC.org. http://na-mic.org/Wiki/index.php/Projects:RegistrationDocumentation:RegLibTable. Accessed August 14, 2013.

  33. VolumeRendering-Documentation-3.6 on Slicer.org. http://www.slicer.org/slicerWiki/index.php/Modules:VolumeRendering-Documentation-3.6. Accessed August 14, 2013.

  34. OpenIGTLink. http://openigtlink.org/. Accessed August 14, 2013.

  35. Golby AJ, Kindlmann G, Norton I, Yarmarkovich A, Pieper S, Kikinis R. Interactive diffusion tensor tractography visualization for neurosurgical planning. Neurosurgery. 2011;68(2):496–505.

    Article  PubMed Central  PubMed  Google Scholar 

  36. Shenton M, et al. A review of magnetic resonance imaging and diffusion tensor imaging findings in mild traumatic brain injury. Brain Imaging Behav. 2012;6(2):137–92.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  37. Irimia A, Chambers MC, Alger JR, Filippou M, Prastawa MW, Wang B, Hovda D, Gerig G, Toga AW, Kikinis R, Vespa PM, Van Horn JD. Comparison of acute and chronic traumatic brain injury using semi-automatic multimodal segmentation of MR volumes. J Neurotrauma. 2011;28:2287–306.

    Article  PubMed  Google Scholar 

  38. Pilato CM, Collins-Sussman B, Fitzpatrick BW. Version control with submission, 2nd Edn. O’Reilly Media, Inc, Sebastopol, CA. 2008.

    Google Scholar 

  39. http://www.slicer.org/slicerWiki/index.php/Slicer4:Extensions. Accessed November 6, 2013.

  40. http://www.slicer.org/slicerWiki/index.php/Slicer_3.6:Training. Accessed November 6, 2013.

Download references

Acknowledgments

The authors thank the 3D Slicer development community members for their efforts and recognize with gratitude the support of the NIH through NAMIC, NAC, NCIGT, and portions of many other projects. The authors were supported by the Neuroimage Analysis Center (NAC), an NIBIB Resource Center, NIH NIBIB P41 grant EB015902, and the National Alliance for Medical Image Computing (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005419. Information on the National Centers for Biomedical Computing can be obtained from http://nihroadmap.nih.gov/bioinformatics. Drs. Kikinis and Vosburgh were supported in part by the National Center for Image-Guided Therapy, NIH P41 EB015898. Dr. Vosburgh also received support from the Center for Integration of Medicine and Innovative Technology (CIMIT).

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Ron Kikinis MD .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2014 Springer Science+Business Media New York

About this chapter

Cite this chapter

Kikinis, R., Pieper, S.D., Vosburgh, K.G. (2014). 3D Slicer: A Platform for Subject-Specific Image Analysis, Visualization, and Clinical Support. In: Jolesz, F. (eds) Intraoperative Imaging and Image-Guided Therapy. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-7657-3_19

Download citation

  • DOI: https://doi.org/10.1007/978-1-4614-7657-3_19

  • Published:

  • Publisher Name: Springer, New York, NY

  • Print ISBN: 978-1-4614-7656-6

  • Online ISBN: 978-1-4614-7657-3

  • eBook Packages: MedicineMedicine (R0)

Publish with us

Policies and ethics