Curtis Rueden

Software architect, martial artist, gamer.

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My name is Curtis Rueden, and I am a software developer from Madison, WI, USA. I have been programming since 1988, a Java developer since 1997, and a Linux geek since 2003.

Professionally, I oversee the software development efforts of the Laboratory for Optical and Computational Instrumentation at the University of Wisconsin-Madison. Projects in which I am involved are many, and include ImageJ, Bio-Formats, the Open Microscopy Environment, VisBio and VisAD.

Technologies I know and love: Java, Perl, Flex, PHP, Drupal, zsh, bash, GNU/Linux, OS X, XML, HTML, CSS, Eclipse, vim, Maven, Git
Technologies I know less well but want to learn more about: HTML5, Node.js, Julia, Docker, Python, Jupyter, Android
Technologies I use and often tolerate: C/C++, MATLAB, Ant, Subversion
Obsolete technologies of which I am fond: QBasic, Pascal, Mac OS Classic, MS-DOS and Windows ;-).

CONTACT

Curtis Rueden
Laboratory for Optical and Computational Instrumentation
Rm 271 Animal Sciences
1675 Observatory Drive
Madison, WI 53706
Email: ctrueden@wisc.edu

EDUCATION

M.S. December 2001 Computer Sciences, University of Wisconsin-Madison
B.S. June 2000 Computer Sciences, with Honors in the Liberal Arts,
University of Wisconsin-Madison

EXPERIENCE

2002- Software Architect, Laboratory for Optical and Computational Instrumentation, Department of Molecular Biology, University of Wisconsin-Madison
2007-2008 Programmer, Eclipse Academic Systems, Madison, WI
2000-2001 Programmer (graduate), SSEC Visualization Project, Space Science and Engineering Center, University of Wisconsin-Madison
1997-2000 Programmer (undergraduate), SSEC Visualization Project, Space Science and Engineering Center, University of Wisconsin-Madison

INVITED PRESENTATIONS

"Open Source Tool Blending: Image Analysis in KNIME." KNIME Fall Summit 2016 - San Francisco, Mission Bay Conference Center, 1675 Owens St #251, San Francisco, CA (16 Sep. 2016).

"ImageJ2 scripts: Parameters + ImageJ Ops." ImageJ User & Developer Conference 2015, Wisconsin Institutes for Discovery, 330 N. Orchard St., Madison, WI (4 Sep. 2015).

"ImageJ2 and Fiji: The ImageJ2 platform, and the Fiji distribution of ImageJ." ImageJ User & Developer Conference 2015, Wisconsin Institutes for Discovery, 330 N. Orchard St., Madison, WI (3 Sep. 2015).

"Open Imaging Platforms Laboratory" and "Object Identification Laboratory." Analytical and Quantitative Light Microscopy 2015, Marine Biological Laboratory, Woods Hole, MA (6 May 2015).

"ImageJ2: Current Status and Future Directions." ImageJ User & Developer Conference 2012, L-5601 Mondorf-les-Bains, Luxembourg (24 Oct. 2012).

"ImageJ2 – ImageJ for the Next Generation of Biological Image Data." "Bioimage analysis software: Is there a future beyond ImageJ?" ISBI 2012. Barcelona (30 Apr. - 1 May 2012). [web site]

"OME + ImageJ2." OME Users Meeting, Institut Pasteur, Paris, France (16 Jun. 2011).

"Open Imaging Platforms Laboratory" and "Object Identification Laboratory." Analytical and Quantitative Light Microscopy 2011, Marine Biological Laboratory, Woods Hole, MA (20 May 2011).

"ImageJDev: Next Generation ImageJ." ImageJ User & Developer Conference 2010, L-5601 Mondorf-les-Bains, Luxembourg (27 Oct. 2010).

"OME-XML." Workshop on Raw Image Formats in Structural Biology, Brookhaven National Laboratory, National Center for Macromolecular Imaging, Upton, NY (22 May 2008).

"OME-TIFF and Bio-Formats." OME European Users Meeting, Institut Pasteur, Paris, France (29 Apr. 2008).

"OME at LOCI." Image Database Meeting, Janelia Farm Research Campus, Loudoun County, Virginia (26 Aug. 2007).

"OME-XML and Bio-Formats." Data and Image Analysis Special Interest Group, 13th Annual SBS Conference, Montreal, Canada (16 Apr. 2007).

"Bio-Formats." OME European Users Meeting, Institut Pasteur, Paris, France (29 Mar. 2007).

"LOCI OME Progress Report." OME Users Meeting, 46th Annual ASCB Conference, San Diego, CA (11 Dec. 2006).

"OME-XML." BIRN Ontology Terminology Workshop, University of California, San Diego (7 Dec. 2006).

PUBLICATIONS

See Google Scholar for an up-to-date list.

Rueden, C. T., J. Schindelin, M. C. Hiner, B. E. DeZonia, A. E. Walter, E. T. Arena, K. W. Eliceiri. "ImageJ2: ImageJ for the next generation of scientific image data." BMC Bioinformatics 18:529 (29 November 2017). [full text]

Harrington, K. I. S., C. T. Rueden, & K. W. Eliceiri. "FunImageJ: a Lisp framework for scientific image processing." Bioinformatics btx710 (2017). [full text]

Arganda-Carreras, I., V. Kaynig, C. Rueden, K. W. Eliceiri, J. Schindelin, A. Cardona, H. S. Seung. "Trainable Weka Segmentation: a machine learning tool for microscopy pixel classification." Bioinformatics 33, no. 15 (1 August 2017): 2424-2426. [full text]

Hiner, M. C., C. T. Rueden, & K. W. Eliceiri. "SCIFIO: an extensible framework to support scientific image formats." BMC Bioinformatics 17, no. 1 (2016): 521. [full text]

Arena, E. T., C. T. Rueden, M. C. Hiner, S. Wang, M. Yuan, & K. W. Eliceiri. "Quantitating the cell: turning images into numbers with ImageJ." Wiley Interdisciplinary Reviews: Developmental Biology (2016). [full text]

Hiner, M. C., C. T. Rueden, & K. W. Eliceiri. "ImageJ-MATLAB: a bidirectional framework for scientific image analysis interoperability." Bioinformatics btw681 (2016). [abstract]

Rueden, C. T., M. C. Hiner, & K. W. Eliceiri. "ImageJ: Image Analysis Interoperability for the Next Generation of Biological Image Data." Microscopy and Microanalysis. 22 no. S3 (2016): 2066-2067. [full text]

Schindelin, J., C. T. Rueden, M. C. Hiner, & K. W. Eliceiri. "The ImageJ ecosystem: An open platform for biomedical image analysis." Molecular Reproduction and Development 82, no. 7-8 (2015): 518-529. [full text]

Buschke, D. G., J. M. Squirrell, A. Vivekanandan, C. T. Rueden, K. W. Eliceiri, and B. M. Ogle. "Noninvasive sorting of stem cell aggregates based on intrinsic markers." Cytometry Part A 85, no. 4 (2014): 353-358. [full text]

Rueden, Curtis T., Johannes Schindelin, Barry E. Dezonia, Aivar R. Grislis, Mark C. Hiner, and Kevin W. Eliceiri. "Open Source BioImage Informatics: Tools for Interoperability." Microscopy and Microanalysis 19, no. S2 (2013): 754-755. [abstract, full text]

Buschke, D., A. Vivekanandan, J. M. Squirrell, C. T. Rueden, K. W. Eliceiri and B. Ogle. "Large particle multiphoton flow cytometry to purify intact embryoid bodies exhibiting enhanced potential for cardiomyocyte differentiation." Integr. Biol. (2013). [full text]

Schindelin, J., I. Arganda-Carreras, E. Frise, V. Kaynig, M. Longair, T. Pietzsch, S. Preibisch, C. Rueden, S. Saalfeld, B. Schmid, J. Y. Tinevez, D. J. White, V. Hartenstein, K. Eliceiri, P. Tomancak and A. Cardona. "Fiji: an open-source platform for biological-image analysis." Nature Methods 9.7 (July 2012): 676-682. [abstract, full text]

Kamentsky, L., T. Jones, A. Fraser, M. Bray, D. J. Logan, K. Madden, V. Ljosa, C. Rueden, K. Eliceiri and A. Carpenter. "Improved structure, function, and compatibility for CellProfiler: modular high-throughput image analysis software." Bioinformatics 27.8 (15 Apr. 2011):1179-80. [abstract]

Buschke, D., J. Squirrell, H. Ansari, M. Smith, C. Rueden, J. Williams, G. Lyons, T. Kamp, K. Eliceiri and B. Ogle. "Multiphoton Flow Cytometry to Assess Intrinsic and Extrinsic Fluorescence in Cellular Aggregates: Applications to Stem Cells." Microscopy and Microanalysis CJO (5 Aug. 2010): 1-16. [abstract]

Linkert, M., C. T. Rueden, C. Allan, J. Burel, W. Moore, A. Patterson, B. Loranger, J. Moore, C. Neves, D. MacDonald, A. Tarkowska, C. Sticco, E. Hill, M. Rossner, K. W. Eliceiri and J. R. Swedlow. "Metadata matters: access to image data in the real world." The Journal of Cell Biology 189.5 (May 2010): 777-782. [full text]

Swedlow, J. R., I. G. Goldberg, K. W. Eliceiri and the OME Consortium. "Bioimage Informatics for Experimental Biology." Annual Review of Biophysics 38 (June 2009): 327-346. [full text]

Swedlow, J. R., C. T. Rueden, J. Burel, M. Linkert, B. Loranger, C. Allan and K. W. Eliceiri. "Open File Formats for High Content Analysis." High Content Screening: Science, Techniques, and Applications. Ed. Steven A. Haney. Hoboken, NJ: John Wiley & Sons, Inc., 2008. 319-328. [table of contents]

Provenzano, P. P., C. T. Rueden, S. M. Trier, L. Yan, S. M. Ponik, D. R. Inman, P. J. Keely and K. W. Eliceiri. "Nonlinear optical imaging and spectral-lifetime computational analysis of endogenous and exogenous fluorophores in breast cancer." J Biomed Opt 13.3 (May-June 2008): 031220. [abstract]

Provenzano, P. P., D. R. Inman, K. W. Eliceiri, J. G. Knittel, L. Yan, C. T. Rueden, J. G. White and P. J. Keely. "Collagen density promotes mammary tumor initiation and progression." BMC Medicine 6.11 (Apr. 2008). [abstract, full text]

Rueden, C. T. and K. W. Eliceiri. "Visualization approaches for multidimensional biological image data." BioTechniques 43 (July 2007): S31-S36. [full text]

Long Yan, C. T. Rueden, J. G. White, and K. W. Eliceiri. "Applications of Combined Spectral Lifetime Microscopy for Biology." BioTechniques 41.3 (Sep. 2006): 249-257. [full text]

Rueden, C. T. and K. W. Eliceiri. "VisBio: a Flexible Open-Source Visualization Package for Multidimensional Image Data." Microscopy Today 14.3 (May 2006): 6-10. [journal]

Eliceiri, K. W. and C. Rueden. "Tools for Visualizing Multidimensional Images from Living Specimens." Photochemistry and Photobiology 81.5 (Apr. 2005): 1116-1122. [abstract]

Hibbard, W., C. Rueden, S. Emmerson, T. Rink, D. Glowacki, T. Whittaker, D. Murray, D. Fulker and J. Anderson. "Java distributed components for numerical visualization in VisAD." Communications of the ACM 48.3 (Mar. 2005): 98-104. [abstract, full text]

Rueden, C., K. W. Eliceiri and J. G. White. "VisBio: A Computational Tool for Visualization of Multidimensional Biological Image Data." Traffic 5.6 (June 2004): 411-417. [abstract, full text]

Rueden, C., K. W. Eliceiri and J. G. White. "VisBio: a Biological Tool for Visualization and Analysis." Computer Graphics 37.2 (May 2003): 5-7. [abstract]

Eliceiri, K. W., C. Rueden, W. A. Mohler, W. L. Hibbard and J. G. White. "Analysis of Multidimensional Biological Image Data." BioTechniques 33.6 (Dec. 2002): 1268-1273. [full text]

Hibbard, W., C. Rueden, S. Emmerson, T. Rink, D. Glowacki, T. Whittaker, D. Fulker and J. Anderson. "Java distributed objects for numerical visualization in VisAD." Communications of the ACM 45.4 (Apr. 2002): 160-170. [abstract]

Hibbard, W., S. Emmerson, C. Rueden, T. Rink, D. Glowacki, N. Rasmussen, D. Fulker and J. Anderson. "Collaborative visualization and computation in the earth sciences using VisAD." Preprints, Conf. Interactive Information and Processing Systems for Meteorology, Oceanography, and Hydrology. Dallas, Amer. Meteor. Soc. (1999): 478-480.

Hibbard, W., C. Rueden, T. Rink, S. Emmerson, D. Fulker and J. Anderson. "The VisAD Java Class Library for Scientific Data and Visualization." Scientific Visualization Conference (dagstuhl '97) (1997): 115-123. [abstract, abstract, abstract]

RELATED ARTICLES

Schneider, C. A., W. S. Rasband, & K. W. Eliceiri. "NIH Image to ImageJ: 25 years of image analysis." Nat methods 9, no. 7 (2012): 671-675. [full text]

Marx, V. "OME's Commercial Arm Glencoe to Sell Licenses for Open-Source Bio-Formats Library." BioInform 12.47 (5 Dec. 2008). [full text]

Collins, T. J. "ImageJ for microscopy." BioTechniques 43 (Jul. 2007): S25-S30. [full text]

Eisenstein, M. "Microscopy: Something to see." Nature 443 (26 Oct. 2006): 1017-1021. [full text]

Eisenstein, M. "Microscopy: Tower of Babel." Nature 443 (26 Oct. 2006): 1021. [full text]