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The Open Microscopy Environment (OME) Data Model and XML file: open tools for informatics and quantitative analysis in biological imaging
Ilya G Goldberg, Chris Allan, Jean-Marie Burel, Doug Creager, Andrea Falconi, Harry Hochheiser, Josiah Johnston, Jeff Mellen, Peter K Sorger, Jason R Swedlow
Genome Biol. 2005; 6(5): R47. Published online 2005 May 3. doi: 10.1186/gb-2005-6-5-r47
PMCID:
PMC1175959
Abstract Full Text PDF–2.3M
 Is Cited by the Following 28 Articles in this Archive:
Data Ontology and an Information System Realization for Web-Based Management of Image Measurements
Dimiter Prodanov
Front Neuroinform. 2011; 5: 25. Published online 2011 November 25. doi: 10.3389/fninf.2011.00025
PMCID:
PMC3254173
Abstract Full Text PDF–2.0M
A data model and database for high-resolution pathology analytical image informatics
Fusheng Wang, Jun Kong, Lee Cooper, Tony Pan, Tahsin Kurc, Wenjin Chen, Ashish Sharma, Cristobal Niedermayr, Tae W Oh, Daniel Brat, Alton B Farris, David J Foran, Joel Saltz
J Pathol Inform. 2011; 2: 32. Published online 2011 July 26. doi: 10.4103/2153-3539.83192
PMCID:
PMC3153692
Abstract Full Text
BioIMAX: A Web 2.0 approach for easy exploratory and collaborative access to multivariate bioimage data
Christian Loyek, Nasir M Rajpoot, Michael Khan, Tim W Nattkemper
BMC Bioinformatics. 2011; 12: 297. Published online 2011 July 21. doi: 10.1186/1471-2105-12-297
PMCID:
PMC3161928
Abstract Full Text PDF–2.1M Supplementary Material
Adaptive informatics for multi-factorial and high content biological data
Bjorn L Millard, Mario Niepel, Michael P Menden, Jeremy L Muhlich, Peter K Sorger
Nat Methods. Author manuscript; available in PMC 2011 December 1.
Published in final edited form as: Nat Methods. 2011 June; 8(6): 487–492. Published online 2011 April 24. doi: 10.1038/nmeth.1600
PMCID:
PMC3105758
Abstract Full Text PDF–1.1M Supplementary Material
Pattern Recognition Software and Techniques for Biological Image Analysis
Lior Shamir, John D. Delaney, Nikita Orlov, D. Mark Eckley, Ilya G. Goldberg
PLoS Comput Biol. 2010 November; 6(11): e1000974. Published online 2010 November 24. doi: 10.1371/journal.pcbi.1000974
PMCID:
PMC2991255
Abstract Full Text PDF–184K
Metadata matters: access to image data in the real world
Melissa Linkert, Curtis T. Rueden, Chris Allan, Jean-Marie Burel, Will Moore, Andrew Patterson, Brian Loranger, Josh Moore, Carlos Neves, Donald MacDonald, Aleksandra Tarkowska, Caitlin Sticco, Emma Hill, Mike Rossner, Kevin W. Eliceiri, Jason R. Swedlow
J Cell Biol. 2010 May 31; 189(5): 777–782. doi: 10.1083/jcb.201004104
PMCID:
PMC2878938
Abstract Full Text PDF–2.6M
The Yeast Resource Center Public Image Repository: A large database of fluorescence microscopy images
Michael Riffle, Trisha N Davis
BMC Bioinformatics. 2010; 11: 263. Published online 2010 May 19. doi: 10.1186/1471-2105-11-263
PMCID:
PMC2882934
Abstract Full Text PDF–1.3M
Automated microscopy for high-content RNAi screening
Christian Conrad, Daniel W. Gerlich
J Cell Biol. 2010 February 22; 188(4): 453–461. doi: 10.1083/jcb.200910105
PMCID:
PMC2828931
Abstract Full Text PDF–3.0M
Replication factory activation can be decoupled from the replication timing program by modulating Cdk levels
Alexander M. Thomson, Peter J. Gillespie, J. Julian Blow
J Cell Biol. 2010 January 25; 188(2): 209–221. doi: 10.1083/jcb.200911037
PMCID:
PMC2812520
Abstract Full Text PDF–6.1M Supplementary Material
Introduction to the Quantitative Analysis of Two-Dimensional Fluorescence Microscopy Images for Cell-Based Screening
Vebjorn Ljosa, Anne E. Carpenter
PLoS Comput Biol. 2009 December; 5(12): e1000603. Published online 2009 December 24. doi: 10.1371/journal.pcbi.1000603
PMCID:
PMC2791844
Full Text PDF–801K
Exploration of Chromatic Aberration for Multiplanar Imaging: Proof of Concept with Implications for Fast, Efficient Autofocus
Martin Weinigel, Albert L. Kellner, Jeffrey H. Price
Cytometry A. Author manuscript; available in PMC 2010 December 1.
Published in final edited form as: Cytometry A. 2009 December; 75(12): 999–1006. doi: 10.1002/cyto.a.20788
PMCID:
PMC2838728
Abstract Full Text PDF–1.4M
Open source bioimage informatics for cell biology
Jason R. Swedlow, Kevin W. Eliceiri
Trends Cell Biol. 2009 November; 19(11-3): 656–660. doi: 10.1016/j.tcb.2009.08.007
PMCID:
PMC2789254
Abstract Full Text PDF–42K
Generating ‘Omic Knowledge’: The Role of Informatics in High Content Screening
Mark A Collins
Comb Chem High Throughput Screen. 2009 November; 12(9): 917–925. doi: 10.2174/138620709789383259
PMCID:
PMC2885606
Abstract Full Text PDF–446K
Information management for high content live cell imaging
Daniel Jameson, David A Turner, John Ankers, Stephnie Kennedy, Sheila Ryan, Neil Swainston, Tony Griffiths, David G Spiller, Stephen G Oliver, Michael RH White, Douglas B Kell, Norman W Paton
BMC Bioinformatics. 2009; 10: 226. Published online 2009 July 21. doi: 10.1186/1471-2105-10-226
PMCID:
PMC2723092
Abstract Full Text PDF–1.0M Supplementary Material
Adaptable data management for systems biology investigations
John Boyle, Hector Rovira, Chris Cavnor, David Burdick, Sarah Killcoyne, Ilya Shmulevich
BMC Bioinformatics. 2009; 10: 79. Published online 2009 March 6. doi: 10.1186/1471-2105-10-79
PMCID:
PMC2670281
Abstract Full Text PDF–1.0M
A Semantic Image Annotation Model to Enable Integrative Translational Research
Daniel L. Rubin, Pattanasak Mongkolwat, David S. Channin
Summit on Translat Bioinforma. 2009; 2009: 106–110. Published online 2009 March 1.
PMCID:
PMC3041574
Abstract Full Text PDF–101K
Knee X-ray image analysis method for automated detection of Osteoarthritis
Lior Shamir, Shari M. Ling, William W. Scott, Angelo Bos, Nikita Orlov, Tomasz Macura, D. Mark Eckley, Luigi Ferrucci, Ilya G. Goldberg
IEEE Trans Biomed Eng. Author manuscript; available in PMC 2010 February 1.
Published in final edited form as: IEEE Trans Biomed Eng. 2009 February; 56(2): 407–415. doi: 10.1109/TBME.2008.2006025
PMCID:
PMC2665928
Abstract Full Text PDF–1.0M
Cell-ID Software for Microscope-Based Cytometry
Ariel Chernomoretz, Alan Bush, Richard Yu, Andrew Gordon, Alejandro Colman-Lerner
Curr Protoc Mol Biol. Author manuscript; available in PMC 2009 November 27.
Published in final edited form as: Curr Protoc Mol Biol. 2008 October; CHAPTER: Unit–14.18. doi: 10.1002/0471142727.mb1418s84
PMCID:
PMC2784696
Abstract Full Text PDF–1.8M
IICBU 2008 - A Proposed Benchmark Suite for Biological Image Analysis
Lior Shamir, Nikita Orlov, D. Mark Eckley, Tomasz J. Macura, Ilya G. Goldberg
Med Biol Eng Comput. Author manuscript; available in PMC 2009 May 1.
Published in final edited form as: Med Biol Eng Comput. 2008 September; 46(9): 943–947. Published online 2008 July 31. doi: 10.1007/s11517-008-0380-5
PMCID:
PMC2562655
Abstract Full Text PDF–351K
Wndchrm – an open source utility for biological image analysis
Lior Shamir, Nikita Orlov, D Mark Eckley, Tomasz Macura, Josiah Johnston, Ilya G Goldberg
Source Code Biol Med. 2008; 3: 13. Published online 2008 July 8. doi: 10.1186/1751-0473-3-13
PMCID:
PMC2478650
Abstract Full Text PDF–261K
Systems biology driven software design for the research enterprise
John Boyle, Christopher Cavnor, Sarah Killcoyne, Ilya Shmulevich
BMC Bioinformatics. 2008; 9: 295. Published online 2008 June 25. doi: 10.1186/1471-2105-9-295
PMCID:
PMC2478690
Abstract Full Text PDF–532K
Evaluation of Face Datasets as Tools for Assessing the Performance of Face Recognition Methods
Lior Shamir
Int J Comput Vis. Author manuscript; available in PMC 2008 September 5.
Published in final edited form as: Int J Comput Vis. 2008; 79(3): 225–230. doi: 10.1007/s11263-008-0143-7
PMCID:
PMC2529479
Abstract Full Text PDF–485K
Intelligent Interfaces for Mining Large-Scale RNAi-HCS Image Databases
Chen Lin, Wayne Mak, Pengyu Hong, Katharine Sepp, Norbert Perrimon
Proc IEEE Int Symp Bioinformatics Bioeng. Author manuscript; available in PMC 2011 January 27.
Published in final edited form as: Proc IEEE Int Symp Bioinformatics Bioeng. 2007 November 5; 2007: 1333–1337. doi: 10.1109/BIBE.2007.4375742
PMCID:
PMC3028207
Abstract Full Text PDF–1.3M
An in situ hybridization-based screen for heterogeneously expressed genes in mouse ES cells
Mark G. Carter, Carole A. Stagg, Geppino Falco, Toshiyuki Yoshikawa, Uwem C. Bassey, Kazuhiro Aiba, Lioudmila V. Sharova, Nabeebi Shaik, Minoru S.H. Ko
Gene Expr Patterns. Author manuscript; available in PMC 2009 February 1.
Published in final edited form as: Gene Expr Patterns. 2008 February; 8(3): 181–198. Published online 2007 November 4. doi: 10.1016/j.gep.2007.10.009
PMCID:
PMC2238805
Abstract Full Text PDF–4.3M Supplementary Material
THE CELL CENTERED DATABASE PROJECT: AN UPDATE ON BUILDING COMMUNITY RESOURCES FOR MANAGING AND SHARING 3D IMAGING DATA
Maryann E. Martone, Joshua Tran, Willy W. Wong, Joy Sargis, Lisa Fong, Stephen Larson, Stephan P. Lamont, Amarnath Gupta, Mark H. Ellisman
J Struct Biol. Author manuscript; available in PMC 2009 March 1.
Published in final edited form as: J Struct Biol. 2008 March; 161(3): 220–231. Published online 2007 October 16. doi: 10.1016/j.jsb.2007.10.003
PMCID:
PMC2367257
Abstract Full Text PDF–2.2M
Loss of APC induces polyploidy as a result of a combination of defects in mitosis and apoptosis
Dina Dikovskaya, David Schiffmann, Ian P. Newton, Abigail Oakley, Karin Kroboth, Owen Sansom, Thomas J. Jamieson, Valerie Meniel, Alan Clarke, Inke S. Näthke
J Cell Biol. 2007 January 15; 176(2): 183–195. doi: 10.1083/jcb.200610099
Correction in:
J Cell Biol. 2007 January 29; 176(3): 369.
PMCID:
PMC2063938
Abstract Full Text PDF–5.2M Correction
Imaging of cell migration
Dirk Dormann, Cornelis J Weijer
EMBO J. 2006 August 9; 25(15): 3480–3493. doi: 10.1038/sj.emboj.7601227
PMCID:
PMC1538568
Abstract Full Text PDF–577K Supplementary Material
Automated tracking of gene expression in individual cells and cell compartments
Hailin Shen, Glyn Nelson, David E Nelson, Stephnie Kennedy, David G Spiller, Tony Griffiths, Norman Paton, Stephen G Oliver, Michael R.H White, Douglas B Kell
J R Soc Interface. 2006 December 22; 3(11): 787–794. Published online 2006 June 14. doi: 10.1098/rsif.2006.0137
PMCID:
PMC1885368
Abstract Full Text PDF–363K Supplementary Material
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