High-performance systems for in silico microscopy imaging studies

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 6254 LNBI, Issue , 2010, Pages 3-18

  Wang, Fusheng ^a   Kurc, Tahsin ^a   Widener, Patrick ^a   Pan, Tony ^a   Kong, Jun ^a   Cooper, Lee ^a   Gutman, David ^a   Sharma, Ashish ^a   Cholleti, Sharath ^a   Kumar, Vijay ^b   Saltz, Joel ^a  

^a EMORY UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b The Ohio State University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOMEDICAL IMAGES; BUILDING BLOCKES; DATA ACCESS; EXPLORATION SYSTEMS; FUNCTIONAL CHARACTERISTICS; HIGH PERFORMANCE SYSTEMS; HIGH RESOLUTION; IN-SILICO; MEDICAL IMAGES; METADATA MODEL; MICROSCOPY IMAGES; MICROSCOPY IMAGING; SYSTEM SUPPORTS;

DATA HANDLING; METADATA;

MEDICAL IMAGING;

EID: 78049430724     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-642-15120-0_2     Document Type: Conference Paper

References (22)

1. The allen reference atlas, http://www.brain-map.org, http://mouse.brain- map.org/api/
2. Dicom wg-26, http://medical.nema.org/DICOM/minutes/WG-26/
3. The extensible imaging platform project, https://collab01a.scr.siemens. com/xipwiki/
4. The virtual slidebox, http://www.path.uiowa.edu/virtualslidebox/
5. Broekstra, J., Kampman, A., van Harmelen, F.: Sesame: A generic architecture for storing and querying rdf and rdf schema. In: Horrocks, I., Hendler, J. (eds.) ISWC 2002. LNCS, vol. 2342, pp. 54-68. Springer, Heidelberg (2002)
6. Çatalyürek, Ü.V., Beynon, M.D., Chang, C., Kurç, T.M., Sussman, A., Saltz, J.H.: The virtual microscope. IEEE Transactions on Information Technology in Biomedicine 7(4), 230-248 (2003)
7. Channin, D., Mongkolwat, P., Kleper, V., Sepukar, K., Rubin, D.: The caBIG Annotation and Image Markup Project. Journal of Digital Imaging (2009)
8. Gil, Y., Ratnakar, V., Deelman, E., Mehta, G., Kim, J.: Wings for pegasus: Creating large-scale scientific applications using semantic representations of computational workflows. In: AAAI, pp. 1767-1774. AAAI Press, Menlo Park (2007)
9. Goldberg, I., Allan, C., Burel, J.M., Creager, D., Falconi, A., Hochheiser, H., Johnston, J., Mellen, J., Sorger, P., Swedlow, J.: The open microscopy environment (ome) data model and xml file: Open tools for informatics and quantitative analysis in biological imaging. Genome Biol. 6(R47) (2005)
10. Hill, E.F.: Jess in Action: Java Rule-Based Systems. Manning Publications Co, Greenwich (2003)
11. Kiryakov, A., Ognyanov, D., Manov, D.: Owlim - a pragmatic semantic repository for owl. In: WISE Workshops, pp. 182-192 (2005)
12. Kumar, V.S., Rutt, B., Kurç, T.M., Catalyurek, U.V., Pan, T.C., Chow, S., Lamont, S., Martone, M., Saltz, J.H.: Large-scale biomedical image analysis in grid environments. IEEE Transactions on Information Technology in Biomedicine 12(2), 154-161 (2008) (Pubitemid 351460484)
13. Kumar, V.S., Kurç, T.M., Ratnakar, V., Kim, J., Mehta, G., Vahi, K., Nelson, Y., Sadayappan, P., Deelman, E., Gil, Y., Hall, M., Saltz, J.H.: Parameterized specification, configuration and execution of data-intensive scientific workflows. Cluster Computing (April 2010)
14. Kumar, V.S., Narayanan, S., Kurç, T.M., Kong, J., Gurcan, M.N., Saltz, J.H.: Analysis and semantic querying in large biomedical image datasets. IEEE Computer 41(4), 52-59 (2008)
15. Kurç, T.M., Hastings, S., Kumar, V.S., Langella, S., Sharma, A., Pan, T., Oster, S., Ervin, D., Permar, J., Narayanan, S., Gil, Y., Deelman, E., Hall, M.W., Saltz, J.H.: Hpc and grid computing for integrative biomedical research. IJHPCA 23(3), 252-264 (2009)
16. Kvilekval, K., Fedorov, D., Obara, B., Singh, A., Manjunath, B.S.: Bisque: A platform for bioimage analysis and management. Bioinformatics 26(4), 544-552 (2010)
17. Martone, M.E., Tran, J., Wong, W.W., Sargis, J., Fong, L., Larson, S., Lamont, S.P., Gupta, A., Ellisman, M.H.: The cell centered database project: An update on building community resources for managing and sharing 3d imaging data. Journal of Structural Biology 161(3), 220-231 (2008)
18. Martone, M.E., Zhang, S., Gupta, A., Qian, X., He, H., Price, D.L., Wong, M., Santini, S., Ellisman, M.H.: The cell-centered database: a database for multiscale structural and protein localization data from light and electron microscopy. Neuroinformatics 1(4), 379-395 (2003)
19. Narayanan, S.: Efficient Virtualization of Scientific Data. PhD thesis, Ohio State University, Columbus, OH (2008)
20. Oster, S., Langella, S., Hastings, S.L., Ervin, D.W., Madduri, R., Phillips, J., Kurç, T.M., Siebenlist, F., Covitz, P.A., Shanbhag, K., Foster, I., Saltz, J.H.: cagrid 1.0: An enterprise grid infrastructure for biomedical research. Journal of the American Medical Informatics Association, 138-149 (December 2007) (Pubitemid 351288546)
21. Wang, F., Pan, T., Kurç, T., Sharma, A., Saltz, J.H., Chen, W., Chu, V., Hu, J., Yang, L., Foran, a.D.J.: Unified modeling of image annotation and markup. In: APIII: Advancing Practice, Instruction & Innovation Through Informatics, Pittsburgh, PA (September 2009)
22. Zhou, J., Ma, L., Liu, Q., Zhang, L., Yu, Y., Pan, Y.: Minerva: A scalable owl ontology storage and inference system. In: Mizoguchi, R., Shi, Z.-Z., Giunchiglia, F. (eds.) ASWC 2006. LNCS, vol. 4185, pp. 429-443. Springer, Heidelberg (2006)