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2016-07-21 - KNIME Image Processing hackathon

From Tuesday, July 5, 2016 through Thursday, July 14, 2016, Christian Dietz of the University of Konstanz hosted ~20 developers at the KNIME Konstanz Regional Office for a hackathon to develop the KNIME Image Processing extensions along with the underlying ImageJ Ops library, as well as other supporting technologies such as ImgLib2, ClearVolume and the BigDataViewer.


The following chart illustrates when everyone was present:

Preset = TimeHorizontal\_AutoPlaceBars\_UnitYear ImageSize = width:600 Colors = ` id:c01 value:blue` ` id:c02 value:red` ` id:c03 value:green` ` id:c04 value:black` ` id:c05 value:magenta` ` id:c06 value:teal` ` id:c07 value:yelloworange` ` id:c08 value:skyblue` ` id:c09 value:claret` ` id:c10 value:oceanblue` ` id:c11 value:purple` ` id:c12 value:powderblue` ` id:c13 value:coral` ` id:c14 value:redorange` ` id:c15 value:kelleygreen` ` id:c16 value:orange` ` id:c17 value:lightpurple` ` id:c18 value:tan2` ` id:c19 value:gray(0.3)` ` id:c20 value:blue` ` id:c21 value:red` ` id:c22 value:green` ` id:c23 value:black` ` id:c24 value:magenta` ` id:c25 value:teal` ` id:gridLine value:gray(0.5)` ` id:gridCanvas value:gray(0.8)` BackgroundColors = canvas:gridCanvas Period = from:5 till:14 ScaleMajor = unit:year increment:1 start:5 grid:white LineData = ` at:5 color:gridLine layer:back width:0.5` ` at:6 color:gridLine layer:back width:0.5` ` at:7 color:gridLine layer:back width:0.5` ` at:8 color:gridLine layer:back width:0.5` ` at:9 color:gridLine layer:back width:0.5` ` at:10 color:gridLine layer:back width:0.5` ` at:11 color:gridLine layer:back width:0.5` ` at:12 color:gridLine layer:back width:0.5` ` at:13 color:gridLine layer:back width:0.5` ` at:14 color:gridLine layer:back width:0.5` BarData= ` barset:Hackers` PlotData= ` width:15 ` ` fontsize:M` ` textcolor:white` ` align:left ` ` anchor:from ` ` shift:(4,-4) ` ` color:black` ` barSet:Hackers` ` color:c01 from:11 till:14 text:"Tim-Oliver Buchholz (UniKN)"` ` color:c02 from:8 till:9 text:"Joshy Cyriac (USB, 4Quant)"` ` color:c03 from:7 till:13 text:"Richard Domander (RVC)"` ` color:c04 from:7 till:10 text:"Kevin Mader (4Quant, ETHZ)"` ` color:c05 from:7 till:10 text:"Simon Schmid (UniKN)"` ` color:c06 from:7 till:9 text:"Marcel Wiedenmann (UniKN)"` ` color:c07 from:7 till:8 text:"Jan Eglinger (FMI Basel)"` ` color:c08 from:5 till:13 text:"Kyle Harrington (HMS)"` ` color:c09 from:6 till:12 text:"Curtis Rueden (UW-Madison)"` ` color:c10 from:5 till:14 text:"Christian Dietz (UniKN)"` ` color:c11 from:5 till:14 text:"Patrick Winter (UniKN)"` ` color:c12 from:5 till:14 text:"Tobias Pietzsch (MPI-CBG)"` ` color:c13 from:5 till:14 text:"Ulrik Günther (MPI-CBG)"` ` color:c14 from:5 till:14 text:"Martin Horn (UniKN)"` ` color:c15 from:5 till:14 text:"Andreas Burger (UniKN)"` ` color:c16 from:5 till:14 text:"Alexander FIllbrunn (UniKN)"` ` color:c17 from:5 till:14 text:"David Hörl (LMU Munich / MDC Berlin)"` ` color:c18 from:5 till:13 text:"Jonathan Hale (UniKN)"` ` color:c19 from:5 till:12 text:"Nico Hoffmann (TUD)"` ` color:c20 from:5 till:9 text:"Stefan Helfrich (UniKN)"` ` color:c21 from:5 till:8 text:"Cyril Mongis (Uni-Heidelberg)"`

Hackathon progress

Christian Dietz

  • Continued work on KNIME SciJava Nodes and KNIME SciJava Scripting

Richard Domander

Kyle Harrington

Stefan Helfrich

  • Proof-of-principle implementations of MatrixType and VectorType (matrixType )
  • Enable using global thresholds as local thresholds in Ops
  • Improve default OOBF handling for filters

Martin Horn & Alexander Fillbrunn

  • Started JavaScript based Image Viewer with BigDataViewer as tile-server

Curtis Rueden

  • Made major progress on improved op lookups using Nil (a.k.a. “typed null”) objects—work still ongoing on the nil branch of imagej-ops ; prep work already on master ([…226fc2114f0d68786f4a27b8fa498f18681379bf 1], 2 )
  • Cleaned up the dependencies of ImageJ Ops; in particular, use SCIFIO for I/O, not ImageJ 1.x and AWT (imagej-ops#413 )
  • Helped clean up Richard Domander ‘s “Topology namespace and ops” PR (imagej-ops#415 )
  • Created a (not yet functional) Kotlin SciJava script engine (scijava/scripting-kotlin )

Technical discussions

  • The future of ImageJ user interfaces: ImageJFX? KNIME? JavaScript + RESTful image server?
  • Languages on the JVM: using Scala, Kotlin and/or Groovy for future SciJava components