Curtis Rueden

Software architect, gamer, martial artist, dad.

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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.

CONTACT

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, LOCI/Eliceiri Lab, 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

"ImageJ and Friends: Retrospective, Current Status and Future." From Images to Knowledge with ImageJ & Friends (I2K), EMBL Heidelberg, Germany (6 Dec. 2018).

"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 CT, Hiner MC, Evans III EL, Pinkert MA, Lucas AM, Carpenter AE, Cimini BA, Eliceiri KW. "PyImageJ: A library for integrating ImageJ and Python." Nature Methods. 2022 Oct 17. [doi:10.1038/s41592-022-01655-4]

Gahm NA, Rueden CT, Evans III EL, Selzer G, Hiner MC, Chacko JV, Gao D, Sherer NM, Eliceiri KW. "New Extensibility and Scripting Tools in the ImageJ Ecosystem." Current protocols. 2021 Aug;1(8):e204. [doi:10.1002/cpz1.204]

Schroeder AB, Dobson ET, Rueden CT, Tomancak P, Jug F, Eliceiri KW. "The ImageJ ecosystem: Open‐source software for image visualization, processing, and analysis." Protein Science. 2021 Jan;30(1):234-49. [doi:10.1002/pro.3993]

Gao D, Barber PR, Chacko JV, Kader Sagar MA, Rueden CT, Grislis AR, Hiner MC, Eliceiri KW. "FLIMJ: an open-source ImageJ toolkit for fluorescence lifetime image data analysis." PloS one. 2020 Dec 30;15(12):e0238327. [doi:10.1371/journal.pone.0238327]

Dietz C, Rueden CT, Helfrich S, Dobson ET, Horn M, Eglinger J, Evans III EL, McLean DT, Novitskaya T, Ricke WA, Sherer NM. "Integration of the ImageJ Ecosystem in KNIME Analytics Platform." Frontiers in computer science. 2020 Mar 17;2:8. [doi:10.3389/fcomp.2020.00008]

Rueden CT, Eliceiri KW. "ImageJ for the next generation of scientific image data." Microscopy and microanalysis. 2019 Aug;25(S2):142-3. [doi:10.1017/S1431927619001442]

Rueden CT, Ackerman J, Arena ET, Eglinger J, Cimini BA, Goodman A, Carpenter AE, Eliceiri KW. "Scientific Community Image Forum: A discussion forum for scientific image software." PLOS Biology. 19 June 2019. [doi:10.1371/journal.pbio.3000340]

Yang SJ, Berndl M, Ando DM, Barch M, Narayanaswamy A, Christiansen E, Hoyer S, Roat C, Hung J, Rueden CT, Shankar, A. "Assessing microscope image focus quality with deep learning." BMC Bioinformatics. 19:1 (15 March 2018). [doi:10.1017/S1431927610000280]

Rueden CT, Schindelin J, Hiner MC, DeZonia BE, Walter AE, Arena ET, Eliceiri KW. "ImageJ2: ImageJ for the next generation of scientific image data." BMC Bioinformatics 18:529 (29 November 2017). [doi:10.1186/s12859-017-1934-z]

Harrington KIS, Rueden CT, Eliceiri KW. "FunImageJ: a Lisp framework for scientific image processing." Bioinformatics btx710 (2017). [doi:10.1093/bioinformatics/btx710]

Arganda-Carreras, I., Kaynig V, Rueden C, Eliceiri KW, Schindelin J, Cardona A, Seung HS. "Trainable Weka Segmentation: a machine learning tool for microscopy pixel classification." Bioinformatics 33, no. 15 (1 August 2017): 2424-2426. [doi:10.1093/bioinformatics/btx180]

Hiner MC, Rueden CT, Eliceiri KW. "SCIFIO: an extensible framework to support scientific image formats." BMC Bioinformatics 17, no. 1 (2016): 521. [doi:10.1186/s12859-016-1383-0]

Arena ET, Rueden CT, Hiner MC, Wang S, Yuan M, Eliceiri KW. "Quantitating the cell: turning images into numbers with ImageJ." Wiley Interdisciplinary Reviews: Developmental Biology (2016). [doi:10.1002/wdev.260]

Hiner MC, Rueden CT, Eliceiri KW. "ImageJ-MATLAB: a bidirectional framework for scientific image analysis interoperability." Bioinformatics btw681 (2016). [doi:10.1093/bioinformatics/btw681]

Rueden CT, Hiner MC, Eliceiri KW. "ImageJ: Image Analysis Interoperability for the Next Generation of Biological Image Data." Microscopy and Microanalysis. 22 no. S3 (2016): 2066-2067. [doi:10.1017/S143192761601117X]

Schindelin, J., Rueden CT, Hiner MC, Eliceiri KW. "The ImageJ ecosystem: An open platform for biomedical image analysis." Molecular Reproduction and Development 82, no. 7-8 (2015): 518-529. [doi:10.1002/mrd.22489]

Buschke DG, Squirrell JM, Vivekanandan A, Rueden CT, Eliceiri KW, Ogle BM. "Noninvasive sorting of stem cell aggregates based on intrinsic markers." Cytometry Part A 85, no. 4 (2014): 353-358. [doi:10.1002/cyto.a.22436]

Rueden CT, Schindelin J, DeZonia BE, Grislis AR, Hiner MC, Eliceiri KW. "Open Source BioImage Informatics: Tools for Interoperability." Microscopy and Microanalysis 19, no. S2 (2013): 754-755. [doi:10.1017/S143192761300576X]

Buschke, D., Vivekanandan A, Squirrell JM, Rueden CT, Eliceiri KW, Ogle B. "Large particle multiphoton flow cytometry to purify intact embryoid bodies exhibiting enhanced potential for cardiomyocyte differentiation." Integr. Biol. (2013). [doi:10.1039/C3IB20286K]

Schindelin, J., Arganda I-Carreras, Frise E, Kaynig V, Longair M, Pietzsch T, Preibisch S, Rueden C, Saalfeld S, Schmid B, Tinevez JY, White DJ, Hartenstein V, Eliceiri K, Tomancak P, Cardona A. "Fiji: an open-source platform for biological-image analysis." Nature Methods 9.7 (July 2012): 676-682. [doi:10.1038/nmeth.2019]

Kamentsky, L., Jones T, Fraser A, Bray M, Logan DJ, Madden K, Ljosa V, Rueden C, Eliceiri K, Carpenter A. "Improved structure, function, and compatibility for CellProfiler: modular high-throughput image analysis software." Bioinformatics 27.8 (15 Apr. 2011):1179-80. [doi:10.1093/bioinformatics/btr095]

Buschke, D., Squirrell J, Ansari H, Smith M, Rueden C, Williams J, Lyons G, Kamp T, Eliceiri K, Ogle B. "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. [doi:10.1017/S1431927610000280]

Linkert, M., Rueden CT, Allan C, Burel J, Moore W, Patterson A, Loranger B, Moore J, Neves C, MacDonald D, Tarkowska A, Sticco C, Hill E, Rossner M, Eliceiri KW, Swedlow JR. "Metadata matters: access to image data in the real world." The Journal of Cell Biology 189.5 (May 2010): 777-782. [doi:10.1083/jcb.201004104]

Swedlow JR, Goldberg IG, Eliceiri KW, the OME Consortium. "Bioimage Informatics for Experimental Biology." Annual Review of Biophysics 38 (June 2009): 327-346. [doi:10.1146/annurev.biophys.050708.133641]

Swedlow JR, Rueden CT, Burel J, Linkert M, Loranger B, Allan C, Eliceiri KW. "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 PP, Rueden CT, Trier SM, Yan L, Ponik SM, Inman DR, Keely PJ, Eliceiri KW. "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. [doi:10.1117/1.2940365]

Provenzano PP, Inman DR, Eliceiri KW, Knittel JG, Yan L, Rueden CT, White JG, Keely PJ. "Collagen density promotes mammary tumor initiation and progression." BMC Medicine 6.11 (Apr. 2008). [doi:10.1186/1741-7015-6-11]

Rueden CT, Eliceiri KW. "Visualization approaches for multidimensional biological image data." BioTechniques 43 (July 2007): S31-S36. [doi:10.2144/000112511]

Long Yan, Rueden CT, White JG, Eliceiri KW. "Applications of Combined Spectral Lifetime Microscopy for Biology." BioTechniques 41.3 (Sep. 2006): 249-257. [doi:10.2144/000112251]

Rueden CT, Eliceiri KW. "VisBio: a Flexible Open-Source Visualization Package for Multidimensional Image Data." Microscopy Today 14.3 (May 2006): 6-10. [doi:10.1017/S155192950005759X]

Eliceiri KW, Rueden C. "Tools for Visualizing Multidimensional Images from Living Specimens." Photochemistry and Photobiology 81.5 (Apr. 2005): 1116-1122. [doi:10.1562/2004-11-22-ir-377]

Hibbard, W., Rueden C, Emmerson S, Rink T, Glowacki D, Whittaker T, Murray D, Fulker D, Anderson J. "Java distributed components for numerical visualization in VisAD." Communications of the ACM 48.3 (Mar. 2005): 98-104. [doi:10.1145/1047671.1047676]

Rueden, C., Eliceiri KW, White JG. "VisBio: A Computational Tool for Visualization of Multidimensional Biological Image Data." Traffic 5.6 (June 2004): 411-417. [doi:10.1111/j.1600-0854.2004.00189.x]

Rueden, C., Eliceiri KW, White JG. "VisBio: a Biological Tool for Visualization and Analysis." Computer Graphics 37.2 (May 2003): 5-7. [doi:10.1145/941552.941556]

Eliceiri KW, Rueden C, Mohler WA, Hibbard WL, White JG. "Analysis of Multidimensional Biological Image Data." BioTechniques 33.6 (Dec. 2002): 1268-1273. [doi:10.2144/02336bt01]

Hibbard, W., Rueden C, Emmerson S, Rink T, Glowacki D, Whittaker T, Fulker D, Anderson J. "Java distributed objects for numerical visualization in VisAD." Communications of the ACM 45.4 (Apr. 2002): 160-170. [doi:10.1145/505248.506005]

Hibbard, W., Emmerson S, Rueden C, Rink T, Glowacki D, Rasmussen N, Fulker D, Anderson J. "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., Rueden C, Rink T, Emmerson S, Fulker D, Anderson J. "The VisAD Java Class Library for Scientific Data and Visualization." Scientific Visualization Conference (dagstuhl '97) (1997): 115-123. [doi:10.5555/789080.789118] https://10.1109/dagstuhl.1997.10025

RELATED ARTICLES

Schneider CA, Rasband WS, Eliceiri KW. "NIH Image to ImageJ: 25 years of image analysis." Nat methods 9, no. 7 (2012): 671-675. [doi:10.1038/nmeth.2089]

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 TJ "ImageJ for microscopy." BioTechniques 43 (Jul. 2007): S25-S30. [doi:10.2144/000112517]

Eisenstein, M. "Microscopy: Something to see." Nature 443 (26 Oct. 2006): 1017-1021. [doi:10.1038/4431017a]

Eisenstein, M. "Microscopy: Tower of Babel." Nature 443 (26 Oct. 2006): 1021. [doi:10.1038/4431021a]