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caBIG-Related Publications by Imaging Workspace Participants
Recent Abstracts and Papers from TCGA Related Research
Presentations and publications from the TCGA Glioma Phenotype Research Group can be accessed via the Cancer Imaging Archive
Click here for access to Emory University's In Silico papers and Abstracts.
Recent Poster Publications
Implementation of the NINDS Traumatic Brain InjuryAshish Hinger, Dzung L. Pham, Pattanasak Mongkolwat, John A. Butman
Peer-Reviewed Journal Articles
http://www.cancer.gov/clinicaltrials/search/view?cdrid=257938&version=healthprofessional#PublishedResults_CDR0000257938NLST Related Publications
http://stanford.edu/~rubin/pubs/130.pdfRubin, Daniel S. MS,MD, Rodriguez Cesar MD, Shah Priyanka, & Beaulieu Chris, MD, PhD (2008). ipad: semantic annotation and markup of radiological images. AMIA 2008 Symposium Proceedings
Fitzgerald TJ, Bishop-Jodoin M, Cicchetti MG, Hanusik R, Kessel S, Laurie F, McCarten KM, Moni J, Pieters RS, Rosen N, Ulin K, Urie M, Chauvenet AR, Constine LS, Deye J, Vikram B, Friedman D, Marcus RB Jr, Mendenhall NP, Williams JL, Purdy J, Saltz J, Schwartz CL, White KS, Wolden S. Quality of radiotherapy reporting in randomized controlled trials of Hodgkin's lymphoma and non-Hodgkin's lymphoma: in regard to Bekelman and Yahalom (Int J Radiat Oncol Biol Phys 2009;73:492-498). Int J Radiat Oncol Biol Phys.; 77(1):315-6. 2010. http://www.ncbi.nlm.nih.gov/pubmed/20394859 . Accessed 09 August 2010
The Annotation and Image Markup (AIM) Project; Version 2.0 Update: D. S. Channin, P. Mongkolwat, V. Kleper, D. Rubin; Society for Imaging Informatics in Medicine (SIIM), Minneapolis, MN, June 2010.
The caBIG® Annotation and Image Markup Project: D. S. Channin, P. Mongkolwat, V. Kleper, K. Sepukar, D. L. Rubin, Journal of Digital Imaging, Vol 23, No 2 April 2010.
Computing Human Image Annotation: : D. S. Channin, P. Mongkolwat, V. Kleper, D. Rubin; 31st Annual International IEEE Engineering in Medicine and Biology Conference Management System Conference, Minneapolis, MN, September 2009.
The caBIG® Annotation and Image Markup Proposed Standard: D. S. Channin, P. Mongkolwat, V. Kleper, D. Rubin; Society for Imaging Informatics in Medicine (SIIM), Charlotte, NC, June 2009.
Annotation and Image Markup: Accessing and Interoperating with the Semantic Content in Medical Imaging: D. L. Rubin, P. Mongkolwat, V. Kleper, K. Superkar, D. S. Channin, IEEE Intelligent Systems, January 2009.
Joel Saltz, Tahsin Kurc, Shannon Hastings, Stephen Langella, Scott Oster, David Ervin, Ashish Sharma, Tony Pan, Metin Gurcan, Justin Permar, Renato Ferreira, Philip Payne, Umit Catalyurek, Enrico Caserta, Gustavo Leone, Michael C. Ostrowski, Ravi Madduri, Ian Foster, Subhashree Madhavan, Kenneth H. Buetow, Krishnakant Shanbhag, Eliot Siegel, "e-Science, caGrid, and Translational Biomedical Research," Computer, vol. 41, no. 11, pp. 58-66, November, 2008.
Automatic Volumetric Breast Density Assessment in the eXtensible Imaging Platform : C. Sillery, R. Embree, A. Shnayder, P. Mongkolwat, D. S. Channin; Society for Imaging Informatics in Medicine (SIIM), Seattle, WA, May 2008.
Loading DICOM Images and Metadata into the XIP Platform: A. Shnayder, C. Sillery, R. Embree, P. Mongkolwat, D. S. Channin; Society for Imaging Informatics in Medicine (SIIM), Seattle, WA, May 2008.
Rubin DL, Mongkolwat P, Kleper V, Spear K and Channin DS,"Imaging on the Semantic Web: Annotation and Image Markup", In: 2008 AAAI Spring Symposium Series, Semantic Scientific Knowledge Integration, Stanford University, 2008.
Berkant Barla Cambazoglu, Olcay Sertel, Jun Kong, Joel H. Saltz, Metin N. Gurcan, Umit V. Catalyurek, "Efficient Processing of Pathological Images Using the Grid: Computer-Aided Prognosis of Neuroblastoma", Proceedings of the International Workshop on Challenges of Large Applications in Distributed Environments (CLADE 07), 2007.
Erdal S, Catalyurek U, Payne P, Kamal J, Saltz J, Gurcan MN, “A Knowledge-Anchored Integrative Image Search and Retrieval System”, Journal of Digital Imaging, 2007 Nov 27.
S. Erdal, Umit V. Catalyurek, Joel H. Saltz, Jyoti Kamal, Metin N. Gurcan, "Flexible patient information search and retrieval framework: Pilot Implementation", PACS and Imaging Informatics, SPIE Symposium on Medical Imaging, 2007.
Metin N. Gurcan, Tony C. Pan, Ashish Sharma, Tahsin M. Kurc, Scott Oster, Stephen Langella, Shannon L. Hastings, K.M. Siddiqui, Eliot Siegel, Joel H. Saltz, "GridImage: A Novel Use of Grid Computing to Support Interactive Human and Computer-Assisted Detection Decision Support", Journal of Digital Imaging, 2007: pp. 160-171.
Tony C. Pan, Metin N. Gurcan, Stephen Langella, Scott Oster, Shannon L. Hastings, Ashish Sharma, Benjamin Rutt, David W. Ervin, Tahsin M. Kurc, K.M. Siddiqui, Joel H. Saltz, Eliot Siegel, "GridCAD: Grid-based Computer-aided Detection System",RadioGraphics, 2007: pp. 889-897
Fred W. Prior, Bradley J. Erickson, and Lawrence Tarbox, "Open Source Software Projects of the caBIG® In Vivo Imaging Workspace Software Special Interest Group", Journal of Digital Imaging, 2007 Nov 27.
Ashish Sharma, Tony Pan, B. Barla Cambazoglu, Metin Gurcan, Tahsin Kurc and Joel Saltz, "VirtualPACS—A Federating Gateway to Access Remote Image Data Resources over the Grid", Journal of Digital Imaging, 2007 Nov 27.
Virtual Slide image analysis papers:
Gurcan MN, Pan T, Shimada H, Saltz J, “Image analysis for neuroblastoma classification: Segmentation of Cell Nuclei,” 28th Annual International Conference of the IEEE Engineering in Medicine and Biology Society Conference, 30 August – 3 September 2006, New York City, New York.
Kong J, Shimada H, Boyer K, Saltz J, Gurcan MN, “Image analysis for automated assessment of grade of neuroblastic differentiation,” IEEE ISBI2007: International Symposium on Biomedical Imaging: From nano to macro, April 12-15, 2007, Metro Washington, D.C.
Cambazoglu BB, Sertel O, Kong J, Saltz J, Gurcan MN, Catalyurek U, “Efficient processing of pathological images using the grid: Computer-aided prognosis of neuroblastoma,” Challenges of Large Scale Applications in Distributed Environments (CLADE 2007), June 25, 2007, Monterey Bay, CA.
Kong J, Sertel O, Shimada H, Boyer K, Saltz J, Gurcan MN, “Computer-aided grading of neuroblastic differentiation: Multi-resolution and multi-classifier approach,” IEEE ICIP 2007: International Conference on Image Processing, September 16-19, 2007, San Antonio, TX.
Kumar VS, Kurc T, Kong J, Catalyurek U, Gurcan MN, Saltz J, “Performance vs. accuracy tradeoffs for large-scale image analysis applications,” IEEE Cluster 2007, September 17-20, 2007, Austin, TX.
Gurcan MN, Kong J, Sertel O, Cambazoglu BB, Saltz J, Catalyurek U, “Computerized pathological image analysis for neuroblastoma prognosis,” Accepted to AMIA 2007, November 10-14, 2007, Chicago, IL.
Ruiz A, Sertel O, Ujaldon M, Catalyurek U, Saltz J, Gurcan MN, “Pathological Image Analysis Using the GPU: Stroma Classification for Neuroblastoma,” Accepted to IEEE BIBM’07, November 2-4, 2007, Silicon Valley, CA.
Sertel O, Kong J, Lozanski G, Catalyurek U, Saltz J, Gurcan MN, “Computerized microscopic image analysis of follicular lymphoma,” Accepted to SPIE Medical Imaging 2008, 16 - 21 February 2008, San Diego, California.
Sertel O, Kong J, Shimada H, Catalyurek U, Saltz J, Gurcan MN, “Computer-aided prognosis of neuroblastoma: classification of stromal development on whole-slide images,” Accepted to SPIE Medical Imaging 2008, 16 - 21 February 2008, San Diego, California.
Kong J, Sertel O, Shimada H, Boyer K, Saltz J, Gurcan MN, “A multi-resolution image analysis system for computer-assisted grading of neuroblastoma differentiation,” Accepted to SPIE Medical Imaging 2008, 16 - 21 February 2008, San Diego, California.
Abstracts:
Saltz J, Kurc T, Langella S, Hastings S, Oster S, Pan T, Sharma A, Gurcan MN, “gridImage-Grid Computing to Middleware Support Human Markup and Multiple CAD Systems,” 92nd Scientific Assembly and Annual Meeting of Radiological Society of North America (RSNA), November 26-December 1, 2006, Chicago, Illinois.
Saltz J, Kurc T, Langella S, Hastings S, Oster S, Pan T, Sharma A, Gurcan MN, “caGrid (Cancer Grid) Middleware- Connecting Healthcare to the Grid,” 92nd Scientific Assembly and Annual Meeting of Radiological Society of North America (RSNA), November 26-December 1, 2006, Chicago, Illinois.
Erberich S, Gurcan MN, Bhandekar M, Pan T, Sharma A, Nelson M, Shimada H, Saltz J, “Image Quantification for Neuroblastoma Assessment using DCE-MRI: A caBIG® Analytical Service, 92nd Scientific Assembly and Annual Meeting of Radiological Society of North America (RSNA), November 26-December 1, 2006, Chicago, Illinois.
Gurcan MN, Pan T, Shimada H, Saltz J, “Image analysis for neuroblastoma classification: Hysteresis thresholding for nuclei segmentation,” Proceedings of APIII 2006, 15-18 August 2006, Vancouver, British Columbia.
Gurcan MN, Pan T, Rutt B, Sharma A, Saltz J, “gridIMAGE: A Grid computing platform for radiological and pathological image analysis,” SIIM 2007 Annual Meeting, June 7-10, 2007, Providence, Rhode Island.
Hartley, TDR, Sertel O, Khan M, Catalyurek U, Saltz J, Gurcan MN, “Neuroblastoma stroma classification on the Sony Playstation 3,” APIII 2007, September 9-12, 2007, Pittsburgh, PA.
Kong J, Sertel O, Shimada H, Boyer K, Saltz J, Gurcan MN, “Computer-assisted prognosis of neuroblastoma: Grading of differentiation,” APIII 2007, September 9-12, 2007, Pittsburgh, PA.
Kong J, Sertel O, Lozanski G, Boyer K, Saltz J, Gurcan MN, “Automated detection of follicular centers for follicular lymphoma grading,” APIII 2007, September 9-12, 2007, Pittsburgh, PA.
Sertel O, Ruiz A, Catalyurek U, Ujaldon M, Saltz J, Gurcan MN, “Computationally efficient pathological image analysis: Use of GPUs for classification of stromal density,” APIII 2007, September 9-12, 2007, Pittsburgh, PA.
Sertel O, Kong J, Lozanski G, Shimada H, Catalyurek U, Saltz J, Gurcan MN, “Texture characterization for whole-slide histopathological image analysis: Applications to neuroblastoma and follicular lymphoma,” APIII 2007, September 9-12, 2007, Pittsburgh, PA.
Cambazoglu BB, Pan T, Sharma A, Kumar V, Kong J, Sertel O, Gurcan MN, Catalyurek UV, Saltz J, “A grid-enabled image processing infrastructure for large pathology images,” APIII 2007, September 9-12, 2007, Pittsburgh, PA.
Kong J, Sertel O, Gewirtz A, Shana’ah A, Racke F, Zhao J, Boyer K, Catalyurek U, Gurcan MN, Lozanski G, “Development of computer based system to aid pathologists in histological grading of follicular lymphomas,” ASH 2007, December 8-11, 2007, Atlanta, GA.
ANIVATR: caBIG® in Vivo Imaging Workspace's Annotation and Image Markup (AIM) Open Source Tool for Validation and Transcoding between AIM XML, DICOM SR and HL7 CDA; V. Kleper, P. Mongkolwat, K. Superkar, A. Kogan, D. L. Rubin, D. S. Channin; Radiological Society of North America, Chicago, IL, November 2008.
"Saying It in Pictures": Annotation and Image Markup in Radiology (CUM LAUDE); D. L. Rubin, P Mongkolwat, V. Kleper, K. Supekar, D. S. Channin; Radiological Society of North America, Chicago, IL, November 2008
An Open Source, Reference Implementation of caBIG®Annotation and Image Markup (AIM); V Kleper, MS, Chicago, IL; P Mongkolwat, PhD; D L Rubin, MD; A Kogan; D S Channin, MD; Radiological Society of North America, Chicago, IL, November 2009
caBIG® Annotation and Image Markup (AIM) : A Ten Minutes Tutorial; D S Channin, MD, Chicago, IL; D L Rubin, MD; V Kleper, MS; P Mongkolwat, PhD; Radiological Society of North America, Chicago, IL, November 2009
Rubin DL, Rodriguez C, Shah P and Beaulieu C, iPad: Semantic Annotation and Markup of Radiological Images. AMIA Annu Symp Proc: 626-30, 2008.
Hanusik RE, Laurie F, FitzGerald TJ, Kelly S, Bishop-Jodoin M. Extending the Availability of a Large Multi-Institutional Oncology Imaging Archive to Remote Reviewers, Society for Imaging Informatics in Medicine (SIIM) Annual Meeting. Minneapolis, MN. Accepted presentation. Jun 2010. http://www.scarnet.org/WorkArea/showcontent.aspx?id=6924 . Accessed 09 August 2010.
FitzGerald TJ, Hanusik R, Laurie F, McCarten K, Bishop-Jodoin ML, Cicchetti MG. An integrated informatics system for acquiring, managing and reviewing imaging and radiation therapy (RT). Radiological Society of North America (RSNA) Annual Meeting, Chicago, IL. Nov 2009. http://rsna2009.rsna.org/search/search.cfm?page=2 . LL-IN2127-D12. Accessed 09 August 2010.
Additional Materials
FitzGerald TJ, White K, Saltz J, Sharma A, Siegel E, Urie M, Ulin K, Purdy J, Bosch W, Matthews J, Deasy J, Ibbott G, Laurie F, Hanusik R, Yorty J, Bishop-Jodoin M, Kessel S, Cicchetti MG, McCarten K, Rosen N, Pieters R, Voss S, Reaman G, Schnall M, Schilsky R, Knopp M, Schwartz L, Baker L, Comis R, Kun L, Boyett J, Ramamurthy U, Parliament M, Nelson H, Ota D. Development of a Queriable Database for Oncology Outcome Analysis. In: Rubin P, Constine LS, Marks LB, Okunieff P, eds. Cured II - LENT Cancer Survivorship Research And Education. Late Effects on Normal Tissues. New York, NY: Springer; 61-72. 2008. http://www.springer.com/medicine/radiology/book/978-3-540-76270-6 . 9783540762706-t1. Accessed 09 August 2010.
FitzGerald TJ, Bishop-Jodoin M, Ulin K, Urie M, Kessel S, Morano K, Hanusik R, Laurie F. Establishing an integrated database for distributed review of imaging, radiation therapy, and pathology objects. Fourth International Conference on Translational Research and Pre-Clinical Strategies in Radiation Oncology. Geneva, Switzerland. Mar 2009.
Levy ML, Rubin DL."Tool Support for Cancer Lesion Tracking and Quantitative Assessment of Disease Response " Proceedings of the Society of Imaging Informatics and Medicine Annual Meeting, Minneapolis, MN June 2010.
