Abstract
High-resolution medical images from advanced instruments provide rich information about morphological and functional characteristics of biological systems. However, most of the information available in biomedical images remains underutilized in research projects. In this paper, we discuss the requirements and design of system support for composing, executing, and exploring in silico experiments involving microscopy images. This framework aims to provide building blocks for large scale, high-performance analytical image exploration systems, through rich metadata models, comprehensive query and data access capabilities, and efficient database and HPC support.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
The allen reference atlas, http://www.brain-map.org , http://mouse.brain-map.org/api/
Dicom wg-26, http://medical.nema.org/DICOM/minutes/WG-26/
The extensible imaging platform project, https://collab01a.scr.siemens.com/xipwiki/
The virtual slidebox, http://www.path.uiowa.edu/virtualslidebox/
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)
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)
Channin, D., Mongkolwat, P., Kleper, V., Sepukar, K., Rubin, D.: The caBIG Annotation and Image Markup Project. Journal of Digital Imaging (2009)
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)
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)
Hill, E.F.: Jess in Action: Java Rule-Based Systems. Manning Publications Co, Greenwich (2003)
Kiryakov, A., Ognyanov, D., Manov, D.: Owlim - a pragmatic semantic repository for owl. In: WISE Workshops, pp. 182–192 (2005)
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)
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)
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)
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)
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)
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)
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)
Narayanan, S.: Efficient Virtualization of Scientific Data. PhD thesis, Ohio State University, Columbus, OH (2008)
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)
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)
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)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2010 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Wang, F. et al. (2010). High-Performance Systems for in Silico Microscopy Imaging Studies. In: Lambrix, P., Kemp, G. (eds) Data Integration in the Life Sciences. DILS 2010. Lecture Notes in Computer Science(), vol 6254. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-15120-0_2
Download citation
DOI: https://doi.org/10.1007/978-3-642-15120-0_2
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-15119-4
Online ISBN: 978-3-642-15120-0
eBook Packages: Computer ScienceComputer Science (R0)