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Hackathon

What is a hackathon?

In the context of ImageJ, a hackathon is a coding spree, or if you want, a one or two-week brainstorm session where scientists with programming skills sit together and work in a low-distraction, high-energy environment to advance the software side of their research. Typically, results get accomplished much faster (read: days instead of weeks or months) than without hackathons, because the setting is ideal to discuss advanced ideas with similar-thinking scientists and ideas can sprout much faster. Sometimes, results are achieved that would not have been possible without a hackathon at all.


The "hackathon effect" in effect!

Why?

First and foremost, hackathons are fun. The participants like what they are working on, and rarely have the same opportunities to talk to and inspire each other about their ongoing research.

Also, hackathons are the perfect excuse to concentrate on a particular subject without distractions. A lot gets done at a hackathon (see right!).

Origin of the term hackathon

The term comes from the original meaning of hack, i.e. a clever and unforeseen way to use or improve a technical system.

It is not clear whether Sun's marketing team or OpenBSD were first, combining the words hack and marathon to form hackathon.

Ever since, OpenBSD held annual hackathons during which OpenBSD was improved in leaps and bounds.

In 2007, the first hackathon revolving around neuro-science was taking place at HHMI Janelia Research Campus. In a sense, it can be seen as the first Fiji hackathon, since Fiji was born in the wake of that hackathon, and probably would not have happened without it.

ImageJ hackathons

ImageJ has benefitted from many hackathons over the years:

When Where Who Topic
ImageJ Hackathons
2007 Summer HHMI Janelia
Ashburn, VA, USA 		Albert Cardona, Benjamin Schmid, Gregory Jefferis, Hanchuan Peng, Johannes SchindelinStephan Preibisch, Stephan Saalfeld, Wayne Rasband, Arnim Jenett, Julie Simpson, Torsten Rohlfing, Yuriy Mishchenko Neuroscience
2008 Apr 21 -
2008 Apr 30 		MPI-CBG
Dresden, Germany 		Albert Cardona, Benjamin Schmid, Cornelius Sicker, Daniel James White, Erwin FriseJean-Yves Tinevez, Johannes Schindelin, Mark Hiner, Stephan Preibisch, Stephan Saalfeld, Pavel Tomancak Fiji
2008 Dec 8 -
2008 Dec 13 		INI
Zürich, Switzerland 		? Fiji
2009 Mar 23 -
2009 Apr 03 		MPI-CBG
Dresden, Germany 		Johannes Schindelin, Albert Cardona, Jean-Yves Tinevez, Benjamin Schmid, Ignacio Arganda-CarrerasDaniel James White, Mark Hiner, Pavel Tomancak, Stephan Preibisch, Stephan Saalfeld, Raju Tomer, Misha Kudryashev Segmentation
2010 Mar 14 -
2010 Mar 27 		EMBL
Heidelberg, Germany 		Albert Cardona, Stephan Saalfeld, Benjamin Schmid, Kota Miura, Curtis RuedenJohannes Schindelin, Ignacio Arganda-Carreras, Larry Lindsey, Mark Hiner, Stephan Preibisch, Grant Harris, Verena Kaynig Fiji
2010 Oct 12 -
2010 Oct 23 		LBNL
Berkeley CA, USA 		Erwin Frise, Johannes Schindelin Running Micro-Manager inside Fiji
2011 Jan 27 -
2011 Feb 13 		WID
Madison, WI, USA 		Ignacio Arganda-Carreras, Paul Barber, Albert Cardona, Barry DeZonia, Arthur EdelsteinAdam Fraser, Erwin Frise, Aivar Grislis, Grant Harris, Mark Hiner, Luis Ibanez, Lee Kamentsky, Larry Lindsey, Melissa Linkert, Mark Hiner, Tobias Pietzsch, Stephan Preibisch, Curtis Rueden, Stephan Saalfeld, Johannes Schindelin, Benjamin Schmid, Pavel Tomancak, Kevin Eliceiri, Rick Lentz, Mark Rowley Multidimensional visualization
2011 Dec 9 -
2011 Dec 19 		MPI-CBG
Dresden, Germany 		Jean-Marie Burel, Stephane Dallongeville, Barry DeZonia, Christian Dietz, Michael DoubeFabrice de Chaumont, Erwin Frise, Martin Horn, Daniel James White, Tom Kazimiers, Alexander Krull, Melissa Linkert, Mark Hiner, Josh Moore, Tobias Pietzsch, Stephan Preibisch, Curtis Rueden, Johannes Schindelin, Benjamin Schmid, Pavel Tomancak, Peter Gabriel Pitrone, Kevin Eliceiri, Fernando Carrilo, Jiri Matas, Jurgen Mayer Interoperability
2012 Oct Universität Konstanz
Konstanz, Germany 		Martin Horn, Christian Dietz, Tobias Pietzsch, Johannes Schindelin KNIME+Fiji
2013 Jan 22 -
2013 Jan 25 		LOCI
Madison, WI, USA 		Matt McCormick, Curtis Rueden, Johannes Schindelin, Mark Hiner SCIFIO ImageIO plugin
2013 Apr 14 -
2013 Apr 18 		LOCI
Madison, WI, USA 		Ignacio Arganda-Carreras, Johannes Schindelin, Curtis Rueden Trainable Weka Segmentation
2013 Apr 27 -
2013 May 3 		LOCI
Madison, WI, USA 		Stephan Preibisch, Tobias Pietzsch, Curtis Rueden, Johannes Schindelin, Barry DeZoniaMark Hiner, Aivar Grislis ImgLib2
2013 Sep 9 -
2013 Sep 13 		Institut Pasteur
Paris France 		Tobias Pietzsch, Jean-Yves Tinevez MaMuT, BigDataViewer
2013 Nov 14 -
2013 Nov 27 		LOCI
Madison, WI, USA 		Christian Dietz, Johannes Schindelin, Curtis Rueden KNIME+ImageJ
2014 Mar 4 -
2014 Mar 13 		Universität Konstanz
Konstanz, Germany 		Curtis Rueden, Johannes Schindelin, Christian Dietz, Martin Horn ImageJ Ops
2014 Mar 11 -
2014 Mar 13 		Heimathafen
Wiesbaden, Germany 		Josh Moore, Curtis Rueden ImageJ-OMERO
2014 Mar 20 -
2014 Mar 21 		LOCI
Madison, WI, USA 		Jean-Marie Burel, Peter Walczysko, Curtis Rueden ImageJ-OMERO
2014 Jul 7 -
2014 Jul 10 		LOCI
Madison, WI, USA 		Mark Tsuchida, Chris Weisiger, Johannes Schindelin, Luke Stuyvenberg, Curtis RuedenMark Hiner Micro-Manager and OpenSPIM
2014 Sep 14 -
2014 Sep 18 		LOCI
Madison, WI, USA 		Christian Dietz, Brian Northan, Mark Hiner, Curtis Rueden, Aparna PalYuming Liu, Alison Walter, Ginger Pocock ImageJ Ops + KNIME
2014 Oct 13 -
2014 Oct 17 		LOCI
Madison, WI, USA 		Tobias Pietzsch, Stephan Preibisch, Stephan Saalfeld, Johannes Schindelin, Curtis RuedenMark Hiner ImgLib2
2015 Jan 19 -
2015 Jan 27 		FREIRÄUME
Konstanz, Germany 		Christian Dietz, Curtis Rueden, Mark Hiner, Lee Kamentsky, Tobias PietzschFlorian Jug, Johannes Schindelin, Ignacio Arganda-Carreras, Gabriel Einsdorf, Daniel Seebacher, Kevin Mader, Andreas Graumann, Jonathan Hale, Tim-Oliver Buchholz, Patrick Winter, Andreas Burger, Tobias Kötter ImageJ Ops + KNIME + CellProfiler + more
2015 Apr 12 -
2015 Apr 17 		HHMI Janelia
Ashburn, VA, USA 		Stephan Preibisch, Tobias Pietzsch, Stephan Saalfeld, Pavel Tomancak Multiview-Reconstruction and BigDataViewer
2015 June 29 -
2015 July 3 		BIMSB/MDC
Berlin, Germany 		Stephan Preibisch, Christian Dietz, Mario Emmenlauer, Stephan Janosch Parallelization of Multiview-Reconstruction
and integration with ImageJ Ops & KNIME
2015 Jul 27 -
2015 Jul 31 		HHMI Janelia
Ashburn, VA, USA 		Stephan Saalfeld, Curtis Rueden, Mark Hiner, Tobias Pietzsch, Tom KazimiersBurkhard Höckendorf, Fernando Amat, Phillip Keller SCIFIO performance and generality
2015 Sep 05 -
2015 Sep 15 		WID + LOCI
Madison, WI, USA 		Curtis Rueden, Mark Hiner, Christian Dietz, Tobias Pietzsch, Stephan SaalfeldBrian Northan, Florian Jug, Matt McCormick, Jay Warrick, Tiago Ferreira, Jan Brocher, Ellen Dobson, Alison Walter, Leon Yang, Yuming Liu, Guneet Singh Mehta, Marcel Austenfeld, Karl Bellve, Alex Rigano, Pariksheet Nanda, Mark Tsuchida, Chris Weisiger ImageJ2 Learnathon + ImageJ Ops
2016 Jan 12 -
2016 Jan 22 		KNIME Konstanz Regional Office
Konstanz, Germany 		Christian Dietz, Curtis Rueden, Mark Hiner, Martin Horn, Tobias PietzschFlorian Jug, Loic Royer, Ulrik Günther, Robert Haase, Stefan Helfrich, Kevin Mader, Kyle Harrington, Jan Eglinger, Thomas Re, Tim-Oliver Buchholz, Jonathan Hale, Daniel Seebacher, Patrick Winter, Alexander Fillbrunn, Nico Hoffmann, Timo Sachsenberg, Julianus Pfeuffer, Temesgen H. Dadi KNIME Image Processing
2016 Jun 19 -
2016 Jun 28 		HHMI Janelia
Ashburn, VA, USA 		Stephan Saalfeld, Tobias Pietzsch, Curtis Rueden, Christian Dietz, Kyle Harrington Metadata rich images
2016 Jul 5 -
2016 Jul 14 		KNIME Konstanz Regional Office
Konstanz, Germany 		Christian Dietz, Patrick Winter, Tobias Pietzsch, Ulrik Günther, Curtis RuedenMartin Horn, Stefan Helfrich, Kyle Harrington, Richard Domander, Kevin Mader, Andreas Burger, Marcel Wiedenmann, Simon Schmid, Joshy Cyriac, Jonathan Hale, Alexander Fillbrunn, Jan Eglinger, Tim-Oliver Buchholz, Stefano Woerner, Cyril Mongis, David Hörl, Nico Hoffmann KNIME Image Processing + 3D viz
2016 Dec 6 -
2016 Dec 16 		MPI-CBG
Dresden, Germany 		Florian Jug, Tobias Pietzsch, Pavel Tomancak, Curtis Rueden, Stephan SaalfeldPhilipp Hanslovsky, Kyle Harrington, Richard Domander, Jean-Yves Tinevez, Christian Dietz, Patrick Winter, Ulrik Günther, Loic Royer, Robert Haase, HongKee Moon, Tim-Oliver Buchholz, Marcel Wiedenmann, David Hörl, Klim Kolyvanov, Matthias Arzt, Vladimír Ulman, Carsten Haubold, Jonas Massa Fiji & KNIP
2017 Feb 21 -
2017 Feb 26 		LOCI
Madison, WI, USA 		Tobias Pietzsch, Stephan Saalfeld, Christian Dietz, Curtis Rueden, Alison Walter ImgLib2
2017 Jun 7 -
2017 Jun 14 		LOCI
Madison, WI, USA 		Christian Dietz, Curtis Rueden ImageJ Ops
2017 Sep 20 -
2017 Sep 29 		KNIME Konstanz Regional Office
Konstanz, Germany 		Christian Dietz, Matthias Arzt, Tim-Oliver Buchholz, Jan Eglinger, Gabriel EinsdorfAlexander Fillbrunn, Jon Fuller, Jonathan Hale, Carsten Haubold, Stefan Helfrich, Martin Horn, Florian Jug, David Kolb, Klim Kolyvanov, Kevin Mader, Julianus Pfeuffer, Tobias Pietzsch, Mangal Prakash, Stephan Preibisch, Jonas Probst, René Rahn, Curtis Rueden, Simon Schmid, Deborah Schmidt, Vladimír Ulman, Marcel Wiedenmann, Benjamin Wilhelm, Patrick Winter KNIME Image Processing, ImageJ Ops, Ilastik
2017 Oct 17 -
2017 Oct 18 		UConn Health
Farmington, CT, USA 		Jim Schaff, Curtis Rueden Virtual Cell + ImageJ
2017 Dec 4 -
2017 Dec 15 		MPI-CBG
Dresden, Germany 		Florian Jug, Tobias Pietzsch, Pavel Tomancak, Curtis Rueden, Philipp HanslovskyKyle Harrington, Richard Domander, Jean-Yves Tinevez, Christian Dietz, Ulrik Günther, Loic Royer, Robert Haase, HongKee Moon, Tim-Oliver Buchholz, Marcel Wiedenmann, David Hörl, Klim Kolyvanov, Matthias Arzt, Vladimír Ulman, Carsten Haubold, Petr Bainar, Alison Walter Fiji & KNIP
2018 Apr 22 -
2018 May 2 		University of Idaho
Moscow, ID, USA 		Kyle Harrington, Stephan Saalfeld, Christian Dietz, Curtis Rueden, Matthias ArztTobias Pietzsch, Loic Royer, Brian Northan, Ulrik Günther, Mark Tsuchida, Robert Wiese SciView
2018 May 16 -
2018 May 18 		Galvanize
San Francisco, CA, USA 		Dan Toloudis (AICS), Dyche Mullins (UCSF), Lisa Harrylock (AICS), Tom Goddard (UCSF), Molly Maleckar (AICS)Tom Ferrin (UCSF), Graham Johnson (AICS), Samuel Lord (UCSF/HHMI), Basu Chaudhuri (AICS), Ambrose Carr (CZI), Megan Riel-Megan (AICS), Jeremy Freeman (CZI), Dave Williams (AICS), Nicholas Sofroniew (CZI), Curtis Rueden, Arne Bakker (CZI), Syuan-Ming Guo (CZ Biohub), Andréa Clavijo (CZI), Deep Ganguli (CZI), Shalin Mehta (CZ Biohub), Tony Tung (CZI), Sarah Kefayati (CZ Biohub), Anitha Krishnan (CZ Biohub), Allen Goodman, Norah Klintberg (CZ Biohub), Eric Perlman (Johns Hopkins), Oana Carja (CZ Biohub)

Benny Lin (U Texas Austin), Jeremy Maitlen-Shephard (Google)

Bioimage Analysis in JavaScript, Python + Java
2018 Oct 31 -
2018 Nov 06 		LOCI
Madison, WI, USA 		Christian Dietz, Tobias Pietzsch, Mark Tsuchida, Curtis Rueden ImgLib2, Micro-Manager
2018 Dec 09 -
2018 Dec 14 		MPI-CBG
Dresden, Germany 		Curtis Rueden, Carsten Haubold, Christian Dietz, Gabriel Einsdorf, Benjamin WilhelmMarcel Wiedenmann, Matthias Arzt, Deborah Schmidt, Tobias Pietzsch, Ulrik Günther, Gabriella Turek Hacking
2019 Jan 17 -
2019 Jan 29 		IT4Innovations
Ostrava, Czech Republic 		Florian Jug, Tobias Pietzsch, Pavel Tomancak, Christian Dietz, Tim-Oliver BuchholzMarcel Wiedenmann, Matthias Arzt, Vladimír Ulman, Petr Bainar, Alison Walter, Gabriel Einsdorf, David Kolb, Mangal Prakash, Deborah Schmidt, Benjamin Wilhelm, John Bogovic, Nicolas Chiaruttini, Jana Klímová, Jan Kožusznik, Michal Krumnikl, Manan Lalit, Emil Melnikov, Pavel Moravec, Václav Svatoň, Christian Tischer, Gabriella Turek, Tomas Vicar, Marwan Zouinkhi Parallelization and HPC
2019 Sep 18 -
2019 Sep 24 		KNIME Konstanz Regional Office
Konstanz, Germany 		Michael Crusoe, Stefan Verhoeven, Curtis Rueden, Christian Dietz, Tobias PietzschMarcel Wiedenmann, Daniel Bogenrieder, Deborah Schmidt, Benjamin Wilhelm, Adrian Nembach, Laurent Thomas, Kefang Ding, frankprotopapa, Christian Albrecht, Gabriel Einsdorf, David Kolb KNIME
2019 Dec 9 -
2019 Dec 18 		CSB Dresden
Dresden, Germany 		Philipp Hanslovsky, Curtis Rueden, Tobias Pietzsch, Ulrik Günther, Tim-Oliver BuchholzFlorian Jug, Matt McCormick, Stefan Helfrich, Robert Haase, Marcel Wiedenmann, Emil Nelnikov, Wei Ouyang, Vladimír Ulman, Pavel Tomancak, Uwe Schmidt, Deborah Schmidt, Benjamin Wilhelm, Nicolas Chiaruttini, Mangal Prakash, Maksim Novikov, Christian Tischer, Manan Lalit, Bob Hanson, Adrian Wolny, Gabriella Turek, Tomas Vicar, David Ackerman, Lars Grüter, Mats Moskopp, Arrate Muñoz Barrutia Python+Fiji
2020 Aug 10 -
2020 Aug 21 		IT4Innovations
Ostrava, Czech Republic 		Florian Jug, Pavel Tomancak, Jan Kožusznik, Michal Krumnikl, Pavel MoravecVáclav Svatoň Parallel Macro/Scripts and OpenMPI Plugins
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