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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 bene51 jefferis Hanchuan Peng Johannes Schindelin Stephan Preibisch Stephan Saalfeld rasband Arnim Jenett Julie Simpson Torsten Rohlfing Yuriy Mishchenko

Neuroscience

2008 Apr 21 -
2008 Apr 30

MPI-CBG
Dresden, Germany

Albert Cardona bene51 Cornelius Sicker Daniel James White frederikfly Jean-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 bene51 Ignacio Arganda-Carreras Daniel 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 bene51 cmci Curtis Rueden Johannes Schindelin Ignacio Arganda-Carreras Larry Lindsey Mark Hiner Stephan Preibisch Grant Harris vkaynig

Fiji

2010 Oct 12 -
2010 Oct 23

LBNL
Berkeley CA, USA

frederikfly 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 Edelstein Adam Fraser frederikfly Aivar Grislis Grant Harris hinerm Luis Ibanez LeeKamentsky Larry Lindsey Melissa Linkert Mark Hiner Tobias Pietzsch Stephan Preibisch Curtis Rueden Stephan Saalfeld Johannes Schindelin bene51 Pavel Tomancak Kevin Eliceiri Rick Lentz Mark Rowley

Multidimensional visualization

2011 Dec 9 -
2011 Dec 19

MPI-CBG
Dresden, Germany

jburel Stephane Dallongeville Barry DeZonia Christian Dietz Michael Doube Fabrice de Chaumont frederikfly Martin Horn Daniel James White tomka alex-krull Melissa Linkert Mark Hiner Moore Tobias Pietzsch Stephan Preibisch Curtis Rueden Johannes Schindelin bene51 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

thewtex Curtis Rueden Johannes Schindelin hinerm

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 DeZonia hinerm 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 |- valign="top" |

2014 Mar 20 -
2014 Mar 21

LOCI
Madison, WI, USA

jburel Peter Walczysko Curtis Rueden

ImageJ-OMERO

2014 Jul 7 -
2014 Jul 10

LOCI
Madison, WI, USA

Mark Tsuchida Chris Weisiger Johannes Schindelin stuyvenberg Curtis Rueden hinerm

Micro-Manager and OpenSPIM

2014 Sep 14 -
2014 Sep 18

LOCI
Madison, WI, USA

Christian Dietz bnorthan hinerm Curtis Rueden apal4 Yuming 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 Rueden hinerm

ImgLib2

2015 Jan 19 -
2015 Jan 27

FREIRÄUME
Konstanz, Germany

Christian Dietz Curtis Rueden hinerm LeeKamentsky Tobias Pietzsch Florian Jug Johannes Schindelin Ignacio Arganda-Carreras gab1one Daniel Seebacher kmader Andreas Graumann Jonathan Hale tibuch 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 hinerm Tobias Pietzsch tomka Burkhard Höckendorf Fernando Amat Phillip Keller

SCIFIO performance and generality

2015 Sep 05 -
2015 Sep 15

WID + LOCI
Madison, WI, USA

Curtis Rueden hinerm Christian Dietz Tobias Pietzsch Stephan Saalfeld bnorthan Florian Jug thewtex Jay Warrick Tiago Ferreira biovoxxel etarena Alison Walter LeonYang5114 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 Pietzsch Florian Jug Loic Royer skalarproduktraum Robert Haase Stefan Helfrich kmader Kyle Harrington Jan Eglinger Thomas Re tibuch 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 skalarproduktraum Curtis Rueden Martin Horn Stefan Helfrich Kyle Harrington Richard Domander kmader Andreas Burger Marcel Wiedenmann Simon Schmid Joshy Cyriac Jonathan Hale Alexander Fillbrunn Jan Eglinger tibuch Stefano Woerner Cyril Mongis hoerldavid 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 Saalfeld hanslovsky kephale rimadoma tinevez dietzc Patrick Winter skalarproduktraum Loic Royer Robert Haase hkmoon tibuch Marcel Wiedenmann hoerldavid milkyklim maarzt 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

dietzc Curtis Rueden

ImageJ Ops

2017 Sep 20 -
2017 Sep 29

KNIME Konstanz Regional Office
Konstanz, Germany

dietzc maarzt tibuch imagejan gab1one Alexander Fillbrunn Jon Fuller Jonathan Hale Carsten Haubold stelfrich Martin Horn fjug David Kolb milkyklim kmader Julianus Pfeuffer tpietzsch Mangal Prakash StephanPreibisch Jonas Probst René Rahn ctrueden 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

jcschaff Curtis Rueden

Virtual Cell + ImageJ

2017 Dec 4 -
2017 Dec 15

MPI-CBG
Dresden, Germany

Florian Jug Tobias Pietzsch Pavel Tomancak Curtis Rueden hanslovsky kephale rimadoma tinevez dietzc skalarproduktraum Loic Royer Robert Haase hkmoon tibuch Marcel Wiedenmann hoerldavid milkyklim maarzt Vladimír Ulman Carsten Haubold Pbainar 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 Arzt Tobias Pietzsch Loic Royer Brian Northan skalarproduktraum 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) <a class="person" href="https://github.com/Curtis Rueden ">Curtis Rueden </a> 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) <a class="person" href="https://github.com/Allen Goodman ">Allen Goodman </a> 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 gab1one Benjamin Wilhelm Marcel Wiedenmann maarzt Deborah Schmidt Tobias Pietzsch skalarproduktraum Gabriella Turek

Hacking

2019 Jan 17 -
2019 Jan 29

IT4Innovations
Ostrava, Czech Republic

Florian Jug Tobias Pietzsch Pavel Tomancak dietzc tibuch Marcel Wiedenmann maarzt Vladimír Ulman Pbainar Alison Walter gab1one 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 ctrueden dietzc tpietzsch Marcel Wiedenmann Daniel Bogenrieder Deborah Schmidt Benjamin Wilhelm Adrian Nembach Laurent Thomas Kefang Ding frankprotopapa Christian Albrecht gab1one David Kolb

KNIME

2019 Dec 9 -
2019 Dec 18

CSB Dresden
Dresden, Germany

hanslovsky ctrueden tpietzsch skalarproduktraum tibuch fjug thewtex stelfrich haesleinhuepf Marcel Wiedenmann Emil Nelnikov Wei Ouyang Vladimír Ulman 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 Moravec Václav Svatoň

Parallel Macro/Scripts and OpenMPI Plugins