Acknowledgments Slicer 4.0

People And Their Roles

Groups

Funding Sources

ARRA supplement to NAC: Qt port, EM Segmenter, Annotations
Neuroimage Analysis Center
National Alliance for Medical Image Computing
National Center for Image-Guided Therapy
1U01CA151261-01 (PI Fennessy)
1R01CA138419-01 (PI: Wells and Aylward), NCI academia-industry partnership
“Cognitive and Functional Brain Changes in Preclinical Huntington’s Disease (HD)” (HD-fMRI; NS054893)
“Neurobiological Predictors of Huntington's Disease” (PREDICT-HD; NS40068)

Slicer 4.0 home page image acknowledgements

File:Slicer4Announcement-HiRes-Map.png
1 Grow-Cut Algorithm in Slicer's Interactive Editor Module. Image provided by Dr. Steven Pieper, BWH.
2 Volume Rendering Module. Image provided by Dr. Ron Kikinis, BWH.
3 Endoscopy Module: early navigation experiments in bronchoscopy. Image provided by Dr. Jayender Jagadeesan, BWH.
4 Automatic segmentation algorithm result for breast DCE MRI; the tumor is outlined by an expert radiologist. Image provided by Dr. Jayender Jagadeesan, BWH.
5 Prostate multiparametric MRI visualization. Image provided by Dr. Andriy Fedorov, BWH.
6 Using an ROI to crop streamlines from a whole brain tractography. The streamlines display color by orientation, the ellipsoids are displaying fractional anisotropy. Note the deformation of the corpus callosum fibers. Image provided by Dr. Ron Kikinis, BWH.
7 Live Endoscopy Module. Image provided by Dr. Steven Pieper, BWH.
8 Screenshot of the Live Ultrasound Display Module. Image provided by Dr. Andras Lasso, Queens University. Details ...

Acknowledgments Slicer3

Major Sponsors and Contributors

National Institutes of Health National Center for Research Resources National Institute of Biomedical Imaging and Bioengineering National Cancer Institute Telemedicine & Advanced Technology Research Center of the US Army
Neuroimaging Analysis Center National Alliance for Medical Image Computing National Center for Image Guided Therapy Biomedical Informatics Research Network Center for Integration of Medicine and Innovative Technology
Surgical Planning Laboratory Laboratory of Mathematics in Imaging Massachusetts Institute of Technology Johns Hopkins University CISST Georgia Institute of Technology
Harvard NeuroDiscovery Center The Martinos Center
Massachusetts General Hospital 		Kitware, Inc. GE Global Research Isomics, Inc.
Psychiatric Neuroimaging Laboratory Scientific Computing and Imaging Institute Neuroinformatics Tools and Resources Clearinghouse The Harvard Clinical and Translational Science Center Surgical Navigation and Robotics Laboratory
New Energy and Industrial Technology Development Organization, Japan

Slicer3: Individual/Group Contributors

Contribution Developer(s)
Overall concept Steve Pieper, Ron Kikinis, Jim Miller, Michael Halle, Bill Lorensen, Will Schroeder
Major designer and implementer Steve Pieper
MRML, Viewer, and many other things Alex Yarmarkovich
GUI Wendy Plesniak, Sebastien Barre, Yumin Yuan
Command Line Modules Jim Miller, Dan Blezek, Bill Lorensen, Luis Ibanez
Colors, Fiducials, FreeSurfer, QDEC Nicole Aucoin
Testing, Release Engineering Katie Hayes, Andy Cedilnik, Bill Hoffman
Diffusion Support Raul San Jose Estepar, Lauren O'Donnell, Carl-Fredrik Westin
BatchMake Integration Stephen Aylward, Julien Jomier
Image Guided Therapy Noby Hata, Sandy Wells, Haiying Liu
Volume Rendering Andreas Freudling, Lisa Avila, Sebastien Barre


Slicer 3.6 home page image acknowledgements

File:slicer3-6-Acknowledgements-MAPv2.png
A Example endoscopy session for virtual colonoscopy (CT colonography) in Slicer’s Endoscopy Module.
B Volume rendering on multi-channel confocal microscopy image in Slicer’s Volume Rendering Module.
C Example of recovered bias field computed with Slicer’s N4ITKBiasFieldCorrection Module.
D Example PET/CT visualization in 3D Slicer’s PETCT Fusion Module.
E Queens Roadmap Project (Transrectal MRI-guided robotic prostate biopsy)
F O'Donnell L., Westin C-F. High-Dimensional White Matter Atlas Generation and Group Analysis. Int Conf Med Image Comput Comput Assist Interv. 2006;9(Pt 2):243-51. PMID: 17354778.
G Interactive seeding of DTI fiber tracts using vertices of a model in 3D Slicer’s Fiducial Seeding Module.
H Queens Roadmap Project (Transrectal MRI-guided robotic prostate biopsy)
I Margulies R.U., Hsu Y., Kearney R., Stein T., Umek W.H., DeLancey J.O.L. Appearance of the Levator Ani Muscle Subdivisions in Magnetic Resonance Images. Obstet Gynecol. 2006 May;107(5):1064-9. PMID: 16648412. PMCID: PMC1479224.
J An example of fast hardware accelerated volume rendering with VTK version 5.6, available in Slicer 3.6.
K Maddah M., Zollei L., Grimson W.E.L., Westin C-F., Wells III W.M. A Mathematical Framework for Incorporating Anatomical Knowledge in DT-MRI Analysis. Proceedings of the 5th IEEE International Symposium on Biomedical Imaging: From Nano to Macro 2008; 4543943: 105–108. PMID: 19212449. PMCID: PMC2638065.
L Jayender J., Patel R., Michaud G., Hata N. Optimal Transseptal Puncture Location for Robot Assisted Left Atrial Catheter Ablation. Int Conf Med Image Comput Comput Assist Interv. 2009;12(Pt 1):1-8. PMID: 20425964.
M Cardiac segmentation and CT Volume Rendering, February 2008 using data and segmentations from collaboration with Boston Children's Hospital Pediatric Cardiology.
N Limperopoulos C., Soul J.S., Gauvreau K., Huppi P.S., Warfield S.K., Bassan H., Robertson R.L., Volpe J.J., du Plessis A.J. Late Gestation Cerebellar Growth Is Rapid and Impeded by Premature Birth. Pediatrics. 2005 Mar;115(3):688-95. PMID: 15741373.
O Moscufo N., Guttmann C.R.G., Meier D., Csapo I., Hildenbrand P.G., Healy B., Schmidt J., Wolfson L. Brain Regional Lesion Burden and Impaired Mobility in the Elderly. Neurobiol Aging. 2009 May 8. PMID: 19428145.
P NA-MIC NCBC Collaboration: Automated FE Mesh Development
Q Close-up of centerline extraction of coronary arteries computed by Slicer’s VMTKCenterlines module.
R Margulies R.U., Hsu Y., Kearney R., Stein T., Umek W.H., DeLancey J.O.L. Appearance of the Levator Ani Muscle Subdivisions in Magnetic Resonance Images. Obstet Gynecol. 2006 May;107(5):1064-9. PMID: 16648412. PMCID: PMC1479224.
S Tharin S., Golby A.J. Functional Brain Mapping and Its Applications to Neurosurgery. Neurosurgery. 2007 Apr;60(4 Suppl 2):185-201; discussion 201-2. PMID: 17415154.
T Lindig T.M., Kumar V., Kikinis R., Pieper S., Schrödl F., Neuhuber W.L., Brehmer A. Spiny Versus Stubby: 3D Reconstruction of Human Myenteric (type I) Neurons. Histochem Cell Biol. 2009 Jan;131(1):1-12. PMID: 18807064. PMCID: PMC2756529.


Slicer2: Individual/Group Contributors

The main individual contributors to this joint effort are listed below.

Contribution Developer(s)
Overall concept Ron Kikinis, Ferenc Jolesz, Eric Grimson, William Wells III, Michael Halle
Major designer and implementer Dave Gering (1997-1999), Lauren O'Donnell (1999-), Steve Pieper (2001-)
Prototype Noby Hata (1997), Ron Kikinis
OpenMR interface Arya Nabavi (1998-1999), Ferenc Jolesz
Image Guided Therapy Noby Hata, Sandy Wells, Haiying Liu
Diffusion Analysis Carl-Fredrik Westin, Lauren O'Donnell, Raul San-Jose (LMI)
Measurement tools William Lorensen (GE), Peter Everett (SPL), Krishna Yeshwant (SPL)
Robot simulation tools Noby Hata, Oliver Schorr
3D connectivity algorithm Andre Robatino
MI registration William Wells III
Virtual endoscopy tool Delphine Nain (MIT AI lab)
DICOM functionality, robot control, volume rendering Attila Tanacs (Johns Hopkins University)
Cryotherapy planning Torsten Butz (EPFL)
Architecture Michael Halle (SPL)
EMSegmenter Kilian Pohl (MIT AI lab)
Tetramesh, volumeMath, developer.tcl Samson Timoner (MIT AI lab)
Print header Mark Anderson (SPL)
Training and Download requests Marianna Jakab (SPL)
Model Hierarchies Arne Hans (SPL)
Application development Steven Haker (SPL)
Craniofacial Krishna Yeshwant (SPL)
FreeSurfer Volume Readers Kevin Teich (MGH), Nicole Aucoin (BWH)
Nightly Builds, Testing, QA Kathryn Hayes (BWH)
Training Materials Sonia Pujol (BWH)
Feedback/Recommendations on Tool Development Martha Shenton and Members of the Psychiatric Neuroimaging Laboratory

We are sincerely thankful for the grants and fellowships supporting this project, and we wish to acknowledge them here.

Individual Support
David Gering GE Medical Systems
Lauren O'Donnell National Science Foundation Graduate Research Fellowship
Ron Kikinis NIH grants P41 RR13218, P01 CA67165, R01 RR11747 and ERC 9731748
Ferenc Jolesz NIH grants P41 RR13218 and P01 CA67165
William Wells III Whitaker Foundation Biomedical Engineering Research Grant
W. Eric L. Grimson NSF grant IIS-9610249, ERC 9731748
Attila Tanacs ERC 9731748
Kevin Teich NIH-NCRR grant 3 P41 RR14075-03S1

Slicer Programming

Slicer is built on an open source software infrastructure based on the NA-MIC Kit and consisting of the following elements:

Toolkits

Software Tools to Support Software Engineering Methodology

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