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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

    TODO personlist: {"content"=>"Albertcardona|bene51|jefferis|hanchuan|Schindelin|StephanP|Saalfeld|rasband|Arnim Jenett|Julie Simpson|Torsten Rohlfing|Yuriy Mishchenko"}

    Neuroscience

    2008 Apr 21 -
    2008 Apr 30

    MPI-CBG
    Dresden, Germany

    TODO personlist: {"content"=>"Albertcardona|bene51|ysis|White|frederikfly|JeanYvesTinevez|Schindelin|Hinerm|StephanP|Saalfeld|Tomancak"}

    Fiji

    2008 Dec 8 -
    2008 Dec 13

    INI
    Zürich, Switzerland

    ?

    Fiji

    2009 Mar 23 -
    2009 Apr 03

    MPI-CBG
    Dresden, Germany

    TODO personlist: {"content"=>"Schindelin|Albertcardona|JeanYvesTinevez|bene51|Iarganda|White|Hinerm|Tomancak|StephanP|Saalfeld|Raju Tomer|Misha Kudryashev"}

    Segmentation

    2010 Mar 14 -
    2010 Mar 27

    EMBL
    Heidelberg, Germany

    TODO personlist: {"content"=>"Albertcardona|Saalfeld|bene51|cmci|Rueden|Schindelin|Iarganda|Lindsey|Hinerm|StephanP|Harris|vkaynig"}

    Fiji

    2010 Oct 12 -
    2010 Oct 23

    LBNL
    Berkeley CA, USA

    TODO personlist: {"content"=>"frederikfly|Schindelin"}

    Running Micro-Manager inside Fiji

    2011 Jan 27 -
    2011 Feb 13

    WID
    Madison, WI, USA

    TODO personlist: {"content"=>"Iarganda|paulbarber|Albertcardona|Bdezonia|arthuredelstein|afraser|frederikfly|Grislis|Harris|hinerm|luisibanez|LeeKamentsky|Lindsey|Linkert|Hinerm|Pietzsch|StephanP|Rueden|Saalfeld|Schindelin|bene51|Tomancak|Eliceiri|Lentz|Mark Rowley"}

    Multidimensional visualization

    2011 Dec 9 -
    2011 Dec 19

    MPI-CBG
    Dresden, Germany

    TODO personlist: {"content"=>"jburel|Stephane-D|Bdezonia|Dietzc|Michaeldoube|Fab14|frederikfly|hornm|White|tomka|alex-krull|Linkert|Hinerm|Moore|Pietzsch|StephanP|Rueden|Schindelin|bene51|Tomancak|Peter-Gabriel-Pitrone|Eliceiri|Fernando Carrilo, Jiri Matas, Jurgen Mayer"}

    Interoperability

    2012 Oct

    Universität Konstanz
    Konstanz, Germany

    TODO personlist: {"content"=>"hornm|Dietzc|Pietzsch|Schindelin"}

    KNIME+Fiji

    2013 Jan 22 -
    2013 Jan 25

    LOCI
    Madison, WI, USA

    TODO personlist: {"content"=>"thewtex|Rueden|Schindelin|hinerm"}

    SCIFIO ImageIO plugin

    2013 Apr 14 -
    2013 Apr 18

    LOCI
    Madison, WI, USA

    TODO personlist: {"content"=>"Iarganda|Schindelin|Rueden"}

    Trainable Weka Segmentation

    2013 Apr 27 -
    2013 May 3

    LOCI
    Madison, WI, USA

    TODO personlist: {"content"=>"StephanP|Pietzsch|Rueden|Schindelin|Bdezonia|hinerm|Grislis"}

    ImgLib2

    2013 Sep 9 -
    2013 Sep 13

    Institut Pasteur
    Paris France

    TODO personlist: {"content"=>"Pietzsch|JeanYvesTinevez"}

    MaMuT, BigDataViewer

    2013 Nov 14 -
    2013 Nov 27

    LOCI
    Madison, WI, USA

    TODO personlist: {"content"=>"Dietzc|Schindelin|Rueden"}

    KNIME+ImageJ

    2014 Mar 4 -
    2014 Mar 13

    Universität Konstanz
    Konstanz, Germany

    TODO personlist: {"content"=>"Rueden|Schindelin|Dietzc|hornm"}

    ImageJ Ops |- valign="top" |

    2014 Mar 20 -
    2014 Mar 21

    LOCI
    Madison, WI, USA

    TODO personlist: {"content"=>"jburel|pwalczysko|Rueden"}

    ImageJ-OMERO

    2014 Jul 7 -
    2014 Jul 10

    LOCI
    Madison, WI, USA

    TODO personlist: {"content"=>"marktsuchida|ChrisWeisiger|Schindelin|stuyvenberg|Rueden|hinerm"}

    Micro-Manager and OpenSPIM

    2014 Sep 14 -
    2014 Sep 18

    LOCI
    Madison, WI, USA

    TODO personlist: {"content"=>"Dietzc|bnorthan|hinerm|Rueden|apal4|yuminguw|Awalter2|Ginger Pocock"}

    ImageJ Ops + KNIME

    2014 Oct 13 -
    2014 Oct 17

    LOCI
    Madison, WI, USA

    TODO personlist: {"content"=>"Pietzsch|StephanP|Saalfeld|Schindelin|Rueden|hinerm"}

    ImgLib2

    2015 Jan 19 -
    2015 Jan 27

    FREIRÄUME
    Konstanz, Germany

    TODO personlist: {"content"=>"Dietzc|Rueden|hinerm|LeeKamentsky|Pietzsch|Jug|Schindelin|Iarganda|gab1one|seebacherd|kmader|angrauma|Squareys|tibuch|patrick-winter-knime|AndreasBurger|Tobias Kötter"}

    ImageJ Ops + KNIME + CellProfiler + more

    2015 Apr 12 -
    2015 Apr 17

    HHMI Janelia
    Ashburn, VA, USA

    TODO personlist: {"content"=>"StephanP|Pietzsch|Saalfeld|Tomancak"}

    Multiview-Reconstruction and BigDataViewer

    2015 June 29 -
    2015 July 3

    BIMSB/MDC
    Berlin, Germany

    TODO personlist: {"content"=>"StephanP|Dietzc|emmenlau|StephanJanosch"}

    Parallelization of Multiview-Reconstruction
    and integration with ImageJ Ops & KNIME

    2015 Jul 27 -
    2015 Jul 31

    HHMI Janelia
    Ashburn, VA, USA

    TODO personlist: {"content"=>"Saalfeld|Rueden|hinerm|Pietzsch|tomka|bhoeckendorf|fernandoamat|Phillip Keller"}

    SCIFIO performance and generality

    2015 Sep 05 -
    2015 Sep 15

    WID + LOCI
    Madison, WI, USA

    TODO personlist: {"content"=>"Rueden|hinerm|Dietzc|Pietzsch|Saalfeld|bnorthan|Jug|thewtex|jaywarrick|Tiago|biovoxxel|etarena|Awalter2|LeonYang5114|yuminguw|guneetsinghmehta|Bio7|kbellve|Akramhar|Omsai|marktsuchida|ChrisWeisiger"}

    ImageJ2 Learnathon + ImageJ Ops

    2016 Jan 12 -
    2016 Jan 22

    KNIME Konstanz Regional Office
    Konstanz, Germany

    TODO personlist: {"content"=>"Dietzc|Rueden|Hinerm|hornm|Pietzsch|Jug|royerloic|skalarproduktraum|Haesleinhuepf|Stelfrich|kmader|Kharrington|Eglinger|drtjre|tibuch|Squareys|seebacherd|patrick-winter-knime|AlexanderFillbrunn|Nico Hoffmann|Timo Sachsenberg|Julianus Pfeuffer|Temesgen H. Dadi"}

    KNIME Image Processing

    2016 Jun 19 -
    2016 Jun 28

    HHMI Janelia
    Ashburn, VA, USA

    TODO personlist: {"content"=>"Saalfeld|Pietzsch|Rueden|Dietzc|Kharrington"}

    Metadata rich images

    2016 Jul 5 -
    2016 Jul 14

    KNIME Konstanz Regional Office
    Konstanz, Germany

    TODO personlist: {"content"=>"Dietzc|patrick-winter-knime|Pietzsch|skalarproduktraum|Rueden|hornm|Stelfrich|Kharrington|Rdom|kmader|AndreasBurger|MarcelWiedenmann|SimonSchmid|irrwitz|Squareys|AlexanderFillbrunn|Eglinger|tibuch|StefanoWoerner|cmongis|hoerldavid|Nico Hoffmann"}

    KNIME Image Processing + 3D viz

    2016 Dec 6 -
    2016 Dec 16

    MPI-CBG
    Dresden, Germany

    TODO personlist: {"content"=>"Jug|Pietzsch|Tomancak|Rueden|Saalfeld|hanslovsky|kephale|rimadoma|tinevez|dietzc|patrick-winter-knime|skalarproduktraum|royerloic|Haesleinhuepf|hkmoon|tibuch|MarcelWiedenmann|hoerldavid|milkyklim|maarzt|xulman|Chaubold|Jonas Massa"}

    Fiji & KNIP

    2017 Feb 21 -
    2017 Feb 26

    LOCI
    Madison, WI, USA

    TODO personlist: {"content"=>"Pietzsch|Saalfeld|Dietzc|Rueden|Awalter2"}

    ImgLib2

    2017 Jun 7 -
    2017 Jun 14

    LOCI
    Madison, WI, USA

    TODO personlist: {"content"=>"dietzc|Rueden"}

    ImageJ Ops

    2017 Sep 20 -
    2017 Sep 29

    KNIME Konstanz Regional Office
    Konstanz, Germany

    TODO personlist: {"content"=>"dietzc|maarzt|tibuch|imagejan|gab1one|AlexanderFillbrunn|Jon Fuller|Squareys|Chaubold|stelfrich|hornm|fjug|Treiblesschorle|milkyklim|kmader|Julianus Pfeuffer|tpietzsch|mp007|StephanPreibisch|Jonas Probst|René Rahn|ctrueden|SimonSchmid|frauzufall|xulman|MarcelWiedenmann|HedgehogCode|patrick-winter-knime"}

    KNIME Image Processing, ImageJ Ops, Ilastik

    2017 Oct 17 -
    2017 Oct 18

    UConn Health
    Farmington, CT, USA

    TODO personlist: {"content"=>"jcschaff|Rueden"}

    Virtual Cell + ImageJ

    2017 Dec 4 -
    2017 Dec 15

    MPI-CBG
    Dresden, Germany

    TODO personlist: {"content"=>"Jug|Pietzsch|Tomancak|Rueden|hanslovsky|kephale|rimadoma|tinevez|dietzc|skalarproduktraum|royerloic|Haesleinhuepf|hkmoon|tibuch|MarcelWiedenmann|hoerldavid|milkyklim|maarzt|xulman|Chaubold|Pbainar|Awalter2"}

    Fiji & KNIP

    2018 Apr 22 -
    2018 May 2

    University of Idaho
    Moscow, ID, USA

    TODO personlist: {"content"=>"Kharrington|Saalfeld|Dietzc|Rueden|Maarzt|Pietzsch|royerloic|Bnorthan|skalarproduktraum|marktsuchida|Robert Wiese"}

    SciView

    2018 May 16 -
    2018 May 18

    Galvanize
    San Francisco, CA, USA

    TODO personlist: {"content"=>"\nDan 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=\"User_Rueden\">Curtis Rueden</a>\n|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/0x00b1\">Allen Goodman</a>\n|Norah Klintberg (CZ Biohub)|Eric Perlman (Johns Hopkins)|Oana Carja (CZ Biohub) Benny Lin (U Texas Austin)|Jeremy Maitlen-Shephard (Google)\n"}

    Bioimage Analysis in JavaScript, Python + Java

    2018 Oct 31 -
    2018 Nov 06

    LOCI
    Madison, WI, USA

    TODO personlist: {"content"=>"Dietzc|Pietzsch|marktsuchida|Rueden"}

    ImgLib2, Micro-Manager

    2018 Dec 09 -
    2018 Dec 14

    MPI-CBG
    Dresden, Germany

    TODO personlist: {"content"=>"Rueden|Chaubold|Dietzc|gab1one|HedgehogCode|MarcelWiedenmann|maarzt|frauzufall|Pietzsch|skalarproduktraum|turekg"}

    Hacking

    2019 Jan 17 -
    2019 Jan 29

    IT4Innovations
    Ostrava, Czech Republic

    TODO personlist: {"content"=>"Jug|Pietzsch|Tomancak|dietzc|tibuch|MarcelWiedenmann|maarzt|xulman|Pbainar|Awalter2|gab1one|Treiblesschorle|mp007|frauzufall|HedgehogCode| 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

    TODO personlist: {"content"=>"mr-c|sverhoeven|ctrueden|dietzc|tpietzsch|MarcelWiedenmann|DanielBogenrieder|frauzufall|HedgehogCode|AtR1an|LauLauThom|KFDing|frankprotopapa|ChristianAlbrecht|gab1one|Treiblesschorle"}

    KNIME

    2019 Dec 9 -
    2019 Dec 18

    CSB Dresden
    Dresden, Germany

    TODO personlist: {"content"=>"hanslovsky|ctrueden|tpietzsch|skalarproduktraum|tibuch|fjug|thewtex|stelfrich|haesleinhuepf|MarcelWiedenmann|emilmelnikov|oeway|xulman|tomancak|uschmidt83|frauzufall|HedgehogCode|NicoKiaru|mangalp|m-novikov|tischi|MLbyML|BobHanson|wolny|turekg|tomasvicar|davidackerman|lagru|axon900|arrmunoz"}

    Python+Fiji

    2020 Aug 10 -
    2020 Aug 21

    IT4Innovations
    Ostrava, Czech Republic

    TODO personlist: {"content"=>"Jug|Tomancak| Jan Kožusznik| Michal Krumnikl| Pavel Moravec| Václav Svatoň"}

    Parallel Macro/Scripts and OpenMPI Plugins