Bisque: A platform for bioimage analysis and management

Bioinformatics

Volumn 26, Issue 4, 2009, Pages 544-552

  Kvilekval, Kristian ^a   Fedorov, Dmitry ^a   Obara, Boguslaw ^a,b   Singh, Ambuj ^a   Manjunath, B S ^a  

^a University of California   (United States)

^b UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 77949523520     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btp699     Document Type: Article

References (38)

1. Altinok, A. et al. (2007a) Model based dynamics analysis in live cell microtubule images. BMC Cell Biology, 8(Suppl. 1), S4.
2. Altinok, A. et al. (2007b) Segmenting filamentous biological structures by automated tracing. In Society for Neuroscience Annual Meeting, San Diego, CA, USA.
3. Andrews, P.D. et al. (2002) To 5D and beyond: quantitative fluorescence microscopy in the postgenomic era. Traffic, 3, 29-36.
4. Belleau, F. et al. (2008) Bio2rdf: towards a mashup to build bioinformatics knowledge systems. J. Biomed. Inform. 41, 706-716.
5. Bertelli, L. et al. (2007) A variational approach to exploit prior information in objectbackground segregation: application to retinal images. In IEEE International Conference on Image Processing, Vol. 6, pp. 61-64, San Antonio, TX, USA.
6. Bisque (2009) Bisque: Bio-Image Semantic Query User Environment. Center for Bio-Image Informatics, University of California, Santa Barbara, CA, USA. Available at http://bioimage.ucsb.edu/bisque/ (last accessed date January 11, 2010).
7. Brent, R. (2004) A partnership between biology and engineering. Nat. Biotechnol.. 22, 1211-1214.
8. Byun, J. et al. (2006a) Automated tool for the detection of cell nuclei in digital microscopic images: application to retinal images. Mol. Vision, 12, 949-960.
9. Byun, J. et al. (2006b) Quantifying structural distortions in retinal tissue before and after injury. InWorkshop on Multiscale Biological Imaging, Data Mining & Informatics, Santa Barbara, CA, USA.
10. Carpenter, A.E. (2007) Software opens the door to quantitative imaging. Nat. Methods. 4, 120-121.
11. CellProfiler (2009) Cell image analysis software. Broad Institute of MIT and Harvard, Cambridge, MA, USA. Available at http://www.cellprofiler .org/ (last accessed date January 11, 2010).
12. Damme, C.V. et al. (2007) Folksontology: an integrated approach for turning folksonomies into ontologies. In Bridging the gap between semantic Web and Web 2.0 (ESWC 2007), pp. 57-70, Innsbruck, Austria.
13. Feinstein, S.C. and Wilson, L. (2005) Inability of tau to properly regulate neuronal microtubule dynamics: a loss-of-function mechanism by which tau might mediate neuronal cell death. Biochim. Biophys. Acta., 1739, 268-279.
14. Fielding, R.T. and Taylor, R.N. (2002) Principled design of the modern web architecture. ACM Trans. Internet Technol.. 2, 115-150.
15. Fisher, S.K. et al. (2006) Image informatics tools for the analysis of retinal images. In Invest Ophthalmol Vision Science. Association for Research in Vision and Ophthalmology (ARVO 2006), pp. 4225, Fort Lauderdale, FL, USA.
16. Goldberg, I. et al. (2005) The Open Microscopy Environment (OME) Data Model and XMLfile: open tools for informatics and quantitative analysis in biological imaging. Genome Biol.. 6, R47.
17. Gordon, S.P. et al. (2007) Pattern formation during de novo assembly of theArabidopsis shoot meristem. Development. 134, 3539-3548.
18. Heisler, M.G. and Jönsson, H. (2007) Modeling meristem development in plants. Curr. Opin. Plant Biol.. 10, 92-97.
19. Hunter, J. et al. (2008) Harvana: harvesting community tags to enrich collection metadata. In 8th ACM/IEEE-CS joint conference on Digital libraries, pp. 147-156, Pittsburgh, PA, USA.
20. Image, J. (2009) ImageJ. National Institute of Mental Health, Bethesda, MA, USA. Available at http://rsbweb.nih.gov/ij/ (last accessed date January 11, 2010).
21. Jönsson, H. et al. (2005) Modeling the organization of the WUSCHEL expression domain in the shoot apical meristem. Bioinformatics. 21, 232-240.
22. Jordan, M.A. and Wilson, L. (2004) Microtubules as a target for anticancer drugs. Nat. Rev. Cancer. 4, 253-265.
23. Marcus, D.S. et al. (2005) The Extensible Neuroimaging Archive Toolkit (XNAT): an informatics platform for managing, exploring, and sharing neuroimaging data. Neuroinformatics. 5, 11-34.
24. MicroApps (2009) MicroApps. Available at http://microapps.org/ (last accessed date January 11, 2010).
25. Murphy, R.F. (2005) Location proteomics: a systems approach to subcellular location. Biochemical Soc. Trans.. 33, 535-538.
26. NIH (2009) NIH data sharing policy. National Institute of Health. Available at http:// grants1.nih.gov/grants/policy/data_sharing/ (last accessed date January 11, 2010).
27. Obara, B. et al. (2008) Automatic nuclei detection and dataflow in Bisquik system. In Workshop on Bio-Image Informatics: Biological Imaging, Computer Vision and Data Mining, Santa Barbara, CA, USA.
28. Pautasso, C. et al. (2008) Restful web services vs. "big" web services: making the right architectural decision. In 17th International World Wide Web Conference (WWW2008), pp. 805-814, Beijing, China.
29. Peng, H. (2008) Bioimage informatics: a new area of engineering biology. Bioinformatics. 24, 1827-1836.
30. Reid, R. and Edwards, P. (2009) Ourspaces - a social semantic web environment for eScience. In Spring Symposium on Social SemanticWeb: WhereWeb 2.0 meetsWeb 3.0 (AAAI 2009), Stanford, CA, USA.
31. Sargin, M.E. et al. (2007) Tracing curvilinear structures in live cell images. In IEEE International Conference on Image Processing, Vol. 6, pp. 285-288, San Antonio, TX, USA.
32. Schilling, M. et al. (2008) Sharing images. Standardizing Exp. Protocols. 19, 354-359.
33. Sigmoid (2009) Sigmoid: a database of cellular signaling pathways and their models. Bioinformatics and Genomics at the University of California Irvine, Beckman Institute of the California Institute of Technology, Bioengineering Department at Johns Hopkins University, USA. Available at http://www.iplantcollaborative.org/grand-challenges/about-grand-challenges/past-projects (last accessed date January 13, 2010).
34. Swedlow, J.R. et al. (2003) Informatics and quantitative analysis in biological imaging. Science. 300, 100-102.
35. Swedlow,J.R. et al. (2006) Modelling data across labs, genomes, space and time. Nat. Cell Biol.. 8, 1190-1194.
36. Tuan, R. and Lo, C. (eds) (2000) Developmental Biology Protocols, Volume 137 of Methods in Molecular Biology. Humana Press, Totowa, NJ, USA.
37. Vannier, M.W. and Summers, R.M. (2003) Sharing images. Radiology. 228, 23-25.
38. Vu, N. et al. (2007) Retina layer segmentation and spatial alignment of antibody expression levels. In IEEE International Conference on Image Processing, Vol. 2, pp. 421-424, San Antonio, TX, USA.